Cadmium in PDB 1np8: 18-K C-Terminally Trunucated Small Subunit of Calpain
Protein crystallography data
The structure of 18-K C-Terminally Trunucated Small Subunit of Calpain, PDB code: 1np8
was solved by
E.K.Leinala,
J.S.Arthur,
P.Grochulski,
P.L.Davies,
J.S.Elce,
Z.Jia,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
50.00 /
2.00
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
58.040,
67.570,
75.070,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19.6 /
23.9
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the 18-K C-Terminally Trunucated Small Subunit of Calpain
(pdb code 1np8). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the
18-K C-Terminally Trunucated Small Subunit of Calpain, PDB code: 1np8:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
11;
12;
13;
Cadmium binding site 1 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 1 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd700
b:18.3
occ:1.00
|
OE1
|
A:GLU79
|
2.1
|
20.0
|
1.0
|
|
O
|
A:LYS74
|
2.3
|
21.2
|
1.0
|
|
OD1
|
A:ASP68
|
2.3
|
17.7
|
1.0
|
|
OD1
|
A:ASP70
|
2.3
|
27.6
|
1.0
|
|
O
|
A:HOH778
|
2.4
|
17.2
|
1.0
|
|
OG1
|
A:THR72
|
2.5
|
25.5
|
1.0
|
|
CD
|
A:GLU79
|
2.8
|
20.7
|
1.0
|
|
OE2
|
A:GLU79
|
2.9
|
22.5
|
1.0
|
|
CG
|
A:ASP70
|
3.2
|
26.1
|
1.0
|
|
CG
|
A:ASP68
|
3.4
|
21.6
|
1.0
|
|
OD2
|
A:ASP70
|
3.4
|
26.9
|
1.0
|
|
C
|
A:LYS74
|
3.5
|
19.9
|
1.0
|
|
CB
|
A:THR72
|
3.7
|
23.8
|
1.0
|
|
N
|
A:THR72
|
3.8
|
24.0
|
1.0
|
|
CG2
|
A:THR72
|
3.9
|
24.4
|
1.0
|
|
N
|
A:GLY76
|
4.1
|
18.9
|
1.0
|
|
CA
|
A:ASP68
|
4.2
|
20.6
|
1.0
|
|
CA
|
A:LEU75
|
4.2
|
19.6
|
1.0
|
|
CB
|
A:ASP68
|
4.2
|
19.5
|
1.0
|
|
N
|
A:LEU75
|
4.2
|
19.2
|
1.0
|
|
OE2
|
A:GLU30
|
4.3
|
27.4
|
1.0
|
|
OE1
|
A:GLU30
|
4.3
|
22.5
|
1.0
|
|
CG
|
A:GLU79
|
4.3
|
21.1
|
1.0
|
|
CA
|
A:THR72
|
4.3
|
24.1
|
1.0
|
|
OD2
|
A:ASP68
|
4.3
|
24.8
|
1.0
|
|
N
|
A:LYS74
|
4.3
|
18.8
|
1.0
|
|
N
|
A:ASP70
|
4.4
|
24.9
|
1.0
|
|
C
|
A:ASP68
|
4.5
|
22.2
|
1.0
|
|
CB
|
A:ASP70
|
4.5
|
25.6
|
1.0
|
|
CA
|
A:LYS74
|
4.5
|
19.7
|
1.0
|
|
N
|
A:THR71
|
4.6
|
23.8
|
1.0
|
|
C
|
A:LEU75
|
4.6
|
19.0
|
1.0
|
|
CD
|
A:GLU30
|
4.6
|
22.9
|
1.0
|
|
N
|
A:GLY73
|
4.6
|
22.8
|
1.0
|
|
C
|
A:ASP70
|
4.7
|
24.9
|
1.0
|
|
CA
|
A:ASP70
|
4.7
|
24.7
|
1.0
|
|
O
|
A:ASP68
|
4.8
|
22.6
|
1.0
|
|
C
|
A:THR72
|
4.8
|
23.4
|
1.0
|
|
N
|
A:SER69
|
4.9
|
22.6
|
1.0
|
|
C
|
A:THR71
|
5.0
|
25.5
|
1.0
|
|
CB
|
A:GLU79
|
5.0
|
19.0
|
1.0
|
|
CD1
|
A:LEU75
|
5.0
|
20.3
|
1.0
|
|
Cadmium binding site 2 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 2 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd701
b:18.2
occ:1.00
|
OD2
|
A:ASP100
|
2.3
|
17.1
|
1.0
|
|
O
|
A:HOH774
|
2.4
|
14.1
|
1.0
|
|
O
|
A:HOH771
|
2.4
|
18.0
|
1.0
|
|
O
|
A:HOH769
|
2.4
|
1.0
|
1.0
|
|
CG
|
A:ASP100
|
3.2
|
18.8
|
1.0
|
|
CB
|
A:ASP100
|
3.6
|
16.7
|
1.0
|
|
OE2
|
A:GLU109
|
4.1
|
11.7
|
1.0
|
|
OD1
|
A:ASP100
|
4.2
|
14.0
|
1.0
|
|
O
|
A:HOH805
|
4.3
|
19.1
|
1.0
|
|
O
|
A:HOH720
|
4.3
|
12.8
|
1.0
|
|
CD
|
A:GLU109
|
4.4
|
10.7
|
1.0
|
|
ND2
|
A:ASN108
|
4.5
|
18.9
|
1.0
|
|
CG
|
A:GLU109
|
4.6
|
13.7
|
1.0
|
|
O
|
A:HOH723
|
4.6
|
16.3
|
1.0
|
|
CB
|
A:ASN108
|
4.7
|
18.3
|
1.0
|
|
CA
|
A:ASP100
|
5.0
|
18.0
|
1.0
|
|
OE1
|
A:GLU109
|
5.0
|
13.9
|
1.0
|
|
Cadmium binding site 3 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 3 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd702
b:15.9
occ:1.00
|
OD1
|
A:ASP98
|
2.1
|
14.5
|
1.0
|
|
OD1
|
A:ASP100
|
2.2
|
14.0
|
1.0
|
|
O
|
A:HOH720
|
2.2
|
12.8
|
1.0
|
|
OE1
|
A:GLU109
|
2.3
|
13.9
|
1.0
|
|
OG
|
A:SER102
|
2.3
|
15.7
|
1.0
|
|
O
|
A:THR104
|
2.4
|
13.8
|
1.0
|
|
OE2
|
A:GLU109
|
2.7
|
11.7
|
1.0
|
|
CD
|
A:GLU109
|
2.8
|
10.7
|
1.0
|
|
CG
|
A:ASP100
|
3.2
|
18.8
|
1.0
|
|
CG
|
A:ASP98
|
3.2
|
17.2
|
1.0
|
|
OD2
|
A:ASP100
|
3.5
|
17.1
|
1.0
|
|
CB
|
A:SER102
|
3.5
|
19.4
|
1.0
|
|
C
|
A:THR104
|
3.5
|
14.7
|
1.0
|
|
CA
|
A:ASP98
|
3.8
|
17.0
|
1.0
|
|
CB
|
A:ASP98
|
3.9
|
17.0
|
1.0
|
|
N
|
A:SER102
|
3.9
|
18.8
|
1.0
|
|
OG1
|
A:THR104
|
4.1
|
14.2
|
1.0
|
|
N
|
A:GLY106
|
4.2
|
13.1
|
1.0
|
|
OD2
|
A:ASP98
|
4.2
|
17.7
|
1.0
|
|
CA
|
A:ILE105
|
4.3
|
15.5
|
1.0
|
|
C
|
A:ASP98
|
4.3
|
17.4
|
1.0
|
|
CA
|
A:SER102
|
4.3
|
18.2
|
1.0
|
|
N
|
A:ILE105
|
4.3
|
12.2
|
1.0
|
|
N
|
A:THR104
|
4.3
|
15.0
|
1.0
|
|
CG
|
A:GLU109
|
4.3
|
13.7
|
1.0
|
|
N
|
A:ASP100
|
4.4
|
18.0
|
1.0
|
|
CA
|
A:THR104
|
4.5
|
13.3
|
1.0
|
|
OD1
|
A:ASN139
|
4.5
|
24.5
|
1.0
|
|
CB
|
A:ASP100
|
4.5
|
16.7
|
1.0
|
|
N
|
A:ARG101
|
4.6
|
19.1
|
1.0
|
|
C
|
A:ILE105
|
4.7
|
13.7
|
1.0
|
|
N
|
A:THR99
|
4.7
|
18.3
|
1.0
|
|
C
|
A:ASP100
|
4.7
|
19.4
|
1.0
|
|
N
|
A:GLY103
|
4.8
|
17.7
|
1.0
|
|
CA
|
A:ASP100
|
4.8
|
18.0
|
1.0
|
|
O
|
A:ASP98
|
4.8
|
17.9
|
1.0
|
|
C
|
A:SER102
|
4.9
|
17.9
|
1.0
|
|
CB
|
A:THR104
|
4.9
|
15.6
|
1.0
|
|
O
|
A:HOH774
|
4.9
|
14.1
|
1.0
|
|
Cadmium binding site 4 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 4 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd703
b:17.6
occ:1.00
|
O
|
A:ALA25
|
2.2
|
18.3
|
1.0
|
|
OD1
|
A:ASP28
|
2.2
|
22.5
|
1.0
|
|
O
|
A:HOH772
|
2.2
|
16.3
|
1.0
|
|
OE2
|
A:GLU35
|
2.4
|
17.2
|
1.0
|
|
O
|
A:GLU30
|
2.4
|
16.1
|
1.0
|
|
OE1
|
A:GLU35
|
2.4
|
15.4
|
1.0
|
|
O
|
A:HOH726
|
2.5
|
19.3
|
1.0
|
|
CD
|
A:GLU35
|
2.7
|
16.7
|
1.0
|
|
CG
|
A:ASP28
|
3.1
|
25.9
|
1.0
|
|
C
|
A:ALA25
|
3.2
|
19.6
|
1.0
|
|
OD2
|
A:ASP28
|
3.3
|
26.9
|
1.0
|
|
C
|
A:GLU30
|
3.6
|
16.3
|
1.0
|
|
CA
|
A:ALA25
|
3.8
|
18.1
|
1.0
|
|
CG
|
A:GLU35
|
4.2
|
16.3
|
1.0
|
|
N
|
A:GLU30
|
4.3
|
19.2
|
1.0
|
|
N
|
A:GLY26
|
4.3
|
21.1
|
1.0
|
|
N
|
A:SER32
|
4.3
|
16.0
|
1.0
|
|
O
|
A:HOH732
|
4.4
|
26.3
|
1.0
|
|
CA
|
A:VAL31
|
4.5
|
14.5
|
1.0
|
|
CB
|
A:ALA25
|
4.5
|
19.3
|
1.0
|
|
N
|
A:VAL31
|
4.5
|
16.4
|
1.0
|
|
CB
|
A:ASP28
|
4.5
|
24.4
|
1.0
|
|
O
|
A:LEU24
|
4.5
|
18.2
|
1.0
|
|
N
|
A:ASP28
|
4.6
|
25.6
|
1.0
|
|
O
|
A:HOH817
|
4.6
|
36.2
|
1.0
|
|
CA
|
A:GLY26
|
4.6
|
22.1
|
1.0
|
|
CA
|
A:GLU30
|
4.6
|
18.5
|
1.0
|
|
O
|
A:HOH810
|
4.7
|
24.4
|
1.0
|
|
N
|
A:MET29
|
4.8
|
23.2
|
1.0
|
|
OG
|
A:SER32
|
4.8
|
14.2
|
1.0
|
|
C
|
A:GLY26
|
4.8
|
23.1
|
1.0
|
|
CB
|
A:SER32
|
4.8
|
16.3
|
1.0
|
|
C
|
A:VAL31
|
4.8
|
15.8
|
1.0
|
|
CA
|
A:ASP28
|
4.9
|
23.9
|
1.0
|
|
Cadmium binding site 5 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 5 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd704
b:14.9
occ:1.00
|
OD2
|
A:ASP143
|
2.1
|
10.4
|
1.0
|
|
OD1
|
A:ASP53
|
2.1
|
15.7
|
1.0
|
|
OD1
|
A:ASP141
|
2.2
|
19.0
|
1.0
|
|
O
|
A:HOH729
|
2.3
|
16.0
|
1.0
|
|
O
|
A:HOH773
|
2.3
|
17.1
|
1.0
|
|
OD1
|
A:ASN144
|
2.5
|
15.3
|
1.0
|
|
OD2
|
A:ASP141
|
2.5
|
12.7
|
1.0
|
|
CG
|
A:ASP141
|
2.7
|
15.0
|
1.0
|
|
CG
|
A:ASP143
|
2.9
|
14.0
|
1.0
|
|
OD1
|
A:ASP143
|
3.1
|
15.5
|
1.0
|
|
CG
|
A:ASP53
|
3.2
|
16.8
|
1.0
|
|
O
|
A:HOH725
|
3.3
|
19.3
|
1.0
|
|
CG
|
A:ASN144
|
3.3
|
13.2
|
1.0
|
|
OD2
|
A:ASP53
|
3.5
|
23.7
|
1.0
|
|
O
|
A:HOH717
|
3.7
|
12.9
|
1.0
|
|
ND2
|
A:ASN144
|
4.0
|
13.1
|
1.0
|
|
N
|
A:ASN144
|
4.1
|
11.9
|
1.0
|
|
CB
|
A:ASP141
|
4.2
|
15.4
|
1.0
|
|
N
|
A:ASP53
|
4.3
|
13.4
|
1.0
|
|
CB
|
A:ASP143
|
4.3
|
13.9
|
1.0
|
|
CB
|
A:ASN144
|
4.3
|
11.5
|
1.0
|
|
O
|
A:HOH757
|
4.4
|
23.4
|
1.0
|
|
O
|
B:HOH239
|
4.5
|
35.6
|
1.0
|
|
CB
|
A:ASP53
|
4.5
|
15.8
|
1.0
|
|
O
|
A:HOH755
|
4.5
|
29.7
|
1.0
|
|
O
|
A:HOH713
|
4.5
|
52.1
|
1.0
|
|
CA
|
A:ASN144
|
4.7
|
11.9
|
1.0
|
|
C
|
A:ASP143
|
4.8
|
13.7
|
1.0
|
|
CA
|
A:ASP53
|
4.9
|
14.4
|
1.0
|
|
CA
|
A:ASP143
|
4.9
|
12.8
|
1.0
|
|
O
|
A:GLY54
|
4.9
|
15.0
|
1.0
|
|
N
|
A:ASP143
|
4.9
|
12.9
|
1.0
|
|
O
|
A:HOH765
|
5.0
|
34.9
|
1.0
|
|
Cadmium binding site 6 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 6 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd705
b:16.8
occ:1.00
|
O
|
A:HOH776
|
2.2
|
16.8
|
1.0
|
|
OD1
|
A:ASP27
|
2.3
|
27.2
|
1.0
|
|
O
|
A:HOH768
|
2.4
|
1.0
|
1.0
|
|
CG
|
A:ASP27
|
3.0
|
28.7
|
1.0
|
|
OD2
|
A:ASP27
|
3.1
|
29.3
|
1.0
|
|
O
|
A:HOH791
|
4.3
|
36.4
|
1.0
|
|
CB
|
A:ASP27
|
4.5
|
27.6
|
1.0
|
|
Cadmium binding site 7 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 7 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd711
b:29.6
occ:1.00
|
OD2
|
A:ASP49
|
2.2
|
22.1
|
1.0
|
|
ND1
|
A:HIS47
|
2.3
|
19.3
|
1.0
|
|
OD1
|
A:ASP49
|
2.5
|
21.4
|
1.0
|
|
O
|
A:HOH777
|
2.7
|
10.0
|
1.0
|
|
CG
|
A:ASP49
|
2.7
|
22.6
|
1.0
|
|
O
|
B:HOH140
|
3.2
|
20.0
|
1.0
|
|
CG
|
A:HIS47
|
3.2
|
19.2
|
1.0
|
|
CB
|
A:HIS47
|
3.3
|
18.2
|
1.0
|
|
CE1
|
A:HIS47
|
3.4
|
21.2
|
1.0
|
|
CA
|
A:HIS47
|
4.1
|
17.5
|
1.0
|
|
CB
|
A:ASP49
|
4.2
|
19.4
|
1.0
|
|
NZ
|
A:LYS95
|
4.2
|
36.3
|
1.0
|
|
NE2
|
B:HIS624
|
4.3
|
42.3
|
1.0
|
|
CD2
|
A:HIS47
|
4.4
|
18.0
|
1.0
|
|
NE2
|
A:HIS47
|
4.4
|
19.9
|
1.0
|
|
CE
|
A:LYS95
|
4.6
|
35.5
|
1.0
|
|
CE1
|
B:HIS624
|
4.6
|
43.2
|
1.0
|
|
CD
|
A:LYS95
|
4.7
|
33.0
|
1.0
|
|
C
|
A:HIS47
|
4.7
|
17.3
|
1.0
|
|
NE2
|
A:GLN91
|
4.8
|
18.7
|
1.0
|
|
N
|
A:ASP49
|
4.9
|
18.1
|
1.0
|
|
Cadmium binding site 8 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 8 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd707
b:17.6
occ:1.00
|
OG1
|
B:THR572
|
2.1
|
20.1
|
1.0
|
|
OE1
|
B:GLU579
|
2.2
|
22.0
|
1.0
|
|
OD1
|
B:ASP570
|
2.2
|
21.0
|
1.0
|
|
O
|
B:HOH112
|
2.2
|
15.8
|
1.0
|
|
OD1
|
B:ASP568
|
2.3
|
13.9
|
1.0
|
|
O
|
B:LYS574
|
2.4
|
15.2
|
1.0
|
|
CD
|
B:GLU579
|
3.0
|
20.9
|
1.0
|
|
OE2
|
B:GLU579
|
3.1
|
20.5
|
1.0
|
|
CG
|
B:ASP570
|
3.1
|
21.3
|
1.0
|
|
CG
|
B:ASP568
|
3.4
|
18.5
|
1.0
|
|
OD2
|
B:ASP570
|
3.4
|
19.4
|
1.0
|
|
CB
|
B:THR572
|
3.4
|
19.9
|
1.0
|
|
C
|
B:LYS574
|
3.6
|
16.9
|
1.0
|
|
N
|
B:THR572
|
3.7
|
19.9
|
1.0
|
|
CG2
|
B:THR572
|
3.8
|
20.9
|
1.0
|
|
N
|
B:GLY576
|
4.0
|
18.6
|
1.0
|
|
OE1
|
B:GLU530
|
4.1
|
22.9
|
1.0
|
|
CB
|
B:ASP568
|
4.1
|
16.5
|
1.0
|
|
CA
|
B:ASP568
|
4.1
|
18.0
|
1.0
|
|
CA
|
B:THR572
|
4.1
|
20.3
|
1.0
|
|
CA
|
B:LEU575
|
4.2
|
16.4
|
1.0
|
|
OD2
|
B:ASP568
|
4.2
|
16.8
|
1.0
|
|
OE2
|
B:GLU530
|
4.3
|
24.8
|
1.0
|
|
N
|
B:LYS574
|
4.3
|
17.7
|
1.0
|
|
N
|
B:LEU575
|
4.4
|
15.5
|
1.0
|
|
CG
|
B:GLU579
|
4.4
|
17.9
|
1.0
|
|
CB
|
B:ASP570
|
4.4
|
20.1
|
1.0
|
|
N
|
B:ASP570
|
4.5
|
22.3
|
1.0
|
|
N
|
B:THR571
|
4.5
|
20.7
|
1.0
|
|
N
|
B:GLY573
|
4.5
|
17.6
|
1.0
|
|
C
|
B:ASP568
|
4.5
|
19.6
|
1.0
|
|
CD
|
B:GLU530
|
4.6
|
24.4
|
1.0
|
|
C
|
B:LEU575
|
4.6
|
17.8
|
1.0
|
|
CA
|
B:LYS574
|
4.6
|
17.6
|
1.0
|
|
C
|
B:ASP570
|
4.7
|
21.0
|
1.0
|
|
C
|
B:THR572
|
4.7
|
18.5
|
1.0
|
|
CA
|
B:ASP570
|
4.8
|
21.0
|
1.0
|
|
C
|
B:THR571
|
4.8
|
22.2
|
1.0
|
|
O
|
B:ASP568
|
4.9
|
19.2
|
1.0
|
|
N
|
B:SER569
|
5.0
|
20.2
|
1.0
|
|
CA
|
B:GLY576
|
5.0
|
19.1
|
1.0
|
|
CB
|
B:GLU579
|
5.0
|
19.3
|
1.0
|
|
Cadmium binding site 9 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 9 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd708
b:16.4
occ:1.00
|
OD1
|
B:ASP598
|
2.0
|
13.2
|
1.0
|
|
O
|
B:HOH138
|
2.1
|
12.4
|
1.0
|
|
OE1
|
B:GLU609
|
2.1
|
15.7
|
1.0
|
|
OD1
|
B:ASP600
|
2.2
|
16.6
|
1.0
|
|
OG
|
B:SER602
|
2.3
|
18.5
|
1.0
|
|
O
|
B:THR604
|
2.4
|
15.9
|
1.0
|
|
OE2
|
B:GLU609
|
2.6
|
10.1
|
1.0
|
|
CD
|
B:GLU609
|
2.7
|
14.0
|
1.0
|
|
CG
|
B:ASP598
|
3.1
|
17.5
|
1.0
|
|
CG
|
B:ASP600
|
3.1
|
20.4
|
1.0
|
|
OD2
|
B:ASP600
|
3.4
|
20.1
|
1.0
|
|
C
|
B:THR604
|
3.4
|
17.1
|
1.0
|
|
CB
|
B:SER602
|
3.5
|
18.7
|
1.0
|
|
CA
|
B:ASP598
|
3.9
|
16.1
|
1.0
|
|
CB
|
B:ASP598
|
3.9
|
16.3
|
1.0
|
|
N
|
B:SER602
|
4.0
|
20.0
|
1.0
|
|
OD2
|
B:ASP598
|
4.0
|
18.6
|
1.0
|
|
N
|
B:GLY606
|
4.1
|
15.3
|
1.0
|
|
CA
|
B:ILE605
|
4.2
|
14.3
|
1.0
|
|
CG
|
B:GLU609
|
4.2
|
15.3
|
1.0
|
|
OG1
|
B:THR604
|
4.2
|
18.1
|
1.0
|
|
N
|
B:ILE605
|
4.2
|
15.5
|
1.0
|
|
CA
|
B:SER602
|
4.3
|
19.8
|
1.0
|
|
N
|
B:THR604
|
4.3
|
18.5
|
1.0
|
|
C
|
B:ASP598
|
4.3
|
18.3
|
1.0
|
|
OD1
|
B:ASN639
|
4.4
|
21.3
|
1.0
|
|
N
|
B:ASP600
|
4.4
|
19.0
|
1.0
|
|
CA
|
B:THR604
|
4.4
|
17.9
|
1.0
|
|
CB
|
B:ASP600
|
4.5
|
18.4
|
1.0
|
|
C
|
B:ILE605
|
4.6
|
15.4
|
1.0
|
|
N
|
B:THR599
|
4.7
|
18.2
|
1.0
|
|
N
|
B:ARG601
|
4.7
|
19.5
|
1.0
|
|
CA
|
B:ASP600
|
4.8
|
19.0
|
1.0
|
|
N
|
B:GLY603
|
4.8
|
19.1
|
1.0
|
|
C
|
B:ASP600
|
4.8
|
19.5
|
1.0
|
|
C
|
B:SER602
|
4.8
|
19.1
|
1.0
|
|
O
|
B:ASP598
|
4.9
|
17.4
|
1.0
|
|
CB
|
B:THR604
|
5.0
|
17.8
|
1.0
|
|
Cadmium binding site 10 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 10 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd709
b:19.8
occ:1.00
|
O
|
B:HOH142
|
2.2
|
17.4
|
1.0
|
|
O
|
B:ALA525
|
2.2
|
20.9
|
1.0
|
|
OE2
|
B:GLU535
|
2.3
|
18.0
|
1.0
|
|
OD1
|
B:ASP528
|
2.3
|
27.6
|
1.0
|
|
O
|
B:GLU530
|
2.4
|
18.4
|
1.0
|
|
O
|
B:HOH186
|
2.5
|
22.5
|
1.0
|
|
OE1
|
B:GLU535
|
2.5
|
12.2
|
1.0
|
|
CD
|
B:GLU535
|
2.7
|
16.3
|
1.0
|
|
CG
|
B:ASP528
|
3.1
|
29.9
|
1.0
|
|
OD2
|
B:ASP528
|
3.2
|
32.5
|
1.0
|
|
C
|
B:ALA525
|
3.3
|
20.7
|
1.0
|
|
C
|
B:GLU530
|
3.6
|
19.9
|
1.0
|
|
CA
|
B:ALA525
|
3.8
|
20.5
|
1.0
|
|
CG
|
B:GLU535
|
4.2
|
16.7
|
1.0
|
|
N
|
B:GLU530
|
4.2
|
21.7
|
1.0
|
|
N
|
B:SER532
|
4.3
|
15.0
|
1.0
|
|
N
|
B:GLY526
|
4.4
|
22.4
|
1.0
|
|
CB
|
B:ASP528
|
4.5
|
30.1
|
1.0
|
|
CA
|
B:VAL531
|
4.5
|
16.6
|
1.0
|
|
O
|
B:HOH61
|
4.5
|
28.4
|
1.0
|
|
N
|
B:VAL531
|
4.5
|
19.7
|
1.0
|
|
N
|
B:ASP528
|
4.5
|
30.3
|
1.0
|
|
CA
|
B:GLU530
|
4.5
|
21.9
|
1.0
|
|
CB
|
B:ALA525
|
4.5
|
20.6
|
1.0
|
|
O
|
B:HOH184
|
4.6
|
39.7
|
1.0
|
|
CD
|
B:LYS574
|
4.7
|
24.6
|
1.0
|
|
CA
|
B:GLY526
|
4.7
|
22.9
|
1.0
|
|
O
|
B:LEU524
|
4.7
|
19.8
|
1.0
|
|
OG
|
B:SER532
|
4.7
|
15.2
|
1.0
|
|
N
|
B:MET529
|
4.7
|
26.1
|
1.0
|
|
C
|
B:GLY526
|
4.8
|
23.6
|
1.0
|
|
CB
|
B:SER532
|
4.8
|
15.2
|
1.0
|
|
C
|
B:VAL531
|
4.8
|
17.4
|
1.0
|
|
CA
|
B:ASP528
|
4.8
|
29.4
|
1.0
|
|
O
|
B:HOH187
|
5.0
|
42.5
|
1.0
|
|
Cadmium binding site 11 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 11 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 11 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd710
b:18.1
occ:1.00
|
OD2
|
B:ASP643
|
2.1
|
14.7
|
1.0
|
|
O
|
B:HOH119
|
2.2
|
30.0
|
1.0
|
|
OD1
|
B:ASP553
|
2.3
|
20.9
|
1.0
|
|
OD1
|
B:ASP641
|
2.3
|
15.0
|
1.0
|
|
OD1
|
B:ASN644
|
2.5
|
19.6
|
1.0
|
|
OD2
|
B:ASP641
|
2.7
|
13.8
|
1.0
|
|
CG
|
B:ASP643
|
2.7
|
14.9
|
1.0
|
|
OD1
|
B:ASP643
|
2.8
|
12.7
|
1.0
|
|
CG
|
B:ASP641
|
2.8
|
15.5
|
1.0
|
|
O
|
B:HOH209
|
3.2
|
33.1
|
1.0
|
|
CG
|
B:ASP553
|
3.2
|
22.1
|
1.0
|
|
CG
|
B:ASN644
|
3.3
|
19.5
|
1.0
|
|
OD2
|
B:ASP553
|
3.4
|
26.1
|
1.0
|
|
ND2
|
B:ASN644
|
3.8
|
18.9
|
1.0
|
|
O
|
B:HOH38
|
3.9
|
21.2
|
1.0
|
|
N
|
B:ASN644
|
4.1
|
14.4
|
1.0
|
|
CB
|
B:ASP643
|
4.2
|
14.3
|
1.0
|
|
N
|
B:ASP553
|
4.3
|
17.8
|
1.0
|
|
CB
|
B:ASN644
|
4.3
|
17.3
|
1.0
|
|
CB
|
B:ASP641
|
4.3
|
18.2
|
1.0
|
|
O
|
B:HOH118
|
4.4
|
28.9
|
1.0
|
|
CB
|
B:ASP553
|
4.5
|
19.7
|
1.0
|
|
CA
|
B:ASN644
|
4.7
|
14.7
|
1.0
|
|
C
|
B:ASP643
|
4.7
|
14.7
|
1.0
|
|
CA
|
B:ASP643
|
4.8
|
13.2
|
1.0
|
|
N
|
B:ASP643
|
4.9
|
13.7
|
1.0
|
|
O
|
B:HOH42
|
4.9
|
24.3
|
1.0
|
|
CA
|
B:ASP553
|
4.9
|
19.3
|
1.0
|
|
Cadmium binding site 12 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 12 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 12 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd712
b:58.0
occ:1.00
|
ND1
|
B:HIS547
|
2.3
|
32.4
|
1.0
|
|
OD1
|
B:ASP549
|
2.3
|
39.5
|
1.0
|
|
NZ
|
B:LYS595
|
2.7
|
30.5
|
1.0
|
|
OD2
|
B:ASP549
|
2.7
|
39.1
|
1.0
|
|
CG
|
B:ASP549
|
2.9
|
37.2
|
1.0
|
|
CE
|
B:LYS595
|
3.0
|
29.1
|
1.0
|
|
CG
|
B:HIS547
|
3.2
|
31.7
|
1.0
|
|
CE1
|
B:HIS547
|
3.2
|
31.8
|
1.0
|
|
CB
|
B:HIS547
|
3.5
|
30.7
|
1.0
|
|
CD
|
B:LYS595
|
3.5
|
30.6
|
1.0
|
|
CA
|
B:HIS547
|
4.3
|
30.9
|
1.0
|
|
CD2
|
B:HIS547
|
4.3
|
30.6
|
1.0
|
|
NE2
|
B:HIS547
|
4.3
|
29.2
|
1.0
|
|
CB
|
B:ASP549
|
4.3
|
35.0
|
1.0
|
|
CG
|
B:LYS595
|
4.7
|
28.3
|
1.0
|
|
CG
|
B:LEU550
|
4.8
|
33.7
|
1.0
|
|
C
|
B:HIS547
|
4.9
|
32.0
|
1.0
|
|
NE2
|
B:GLN591
|
4.9
|
25.5
|
1.0
|
|
Cadmium binding site 13 out
of 13 in 1np8
Go back to
Cadmium Binding Sites List in 1np8
Cadmium binding site 13 out
of 13 in the 18-K C-Terminally Trunucated Small Subunit of Calpain
 Mono view
 Stereo pair view
|
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 13 of 18-K C-Terminally Trunucated Small Subunit of Calpain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd713
b:40.7
occ:1.00
|
O
|
B:HOH198
|
2.3
|
23.4
|
1.0
|
|
ND1
|
B:HIS624
|
2.4
|
42.7
|
1.0
|
|
O
|
B:HOH148
|
2.6
|
18.8
|
1.0
|
|
CG
|
B:HIS624
|
3.4
|
43.5
|
1.0
|
|
CE1
|
B:HIS624
|
3.4
|
43.2
|
1.0
|
|
SD
|
B:MET628
|
3.5
|
56.4
|
1.0
|
|
CB
|
B:HIS624
|
3.6
|
43.6
|
1.0
|
|
CA
|
B:HIS624
|
3.8
|
43.5
|
1.0
|
|
NE2
|
B:HIS624
|
4.5
|
42.3
|
1.0
|
|
CD2
|
B:HIS624
|
4.5
|
42.9
|
1.0
|
|
CG
|
B:MET628
|
4.6
|
53.4
|
1.0
|
|
OE1
|
B:GLN623
|
4.6
|
47.3
|
1.0
|
|
N
|
B:HIS624
|
4.7
|
42.9
|
1.0
|
|
CE
|
A:LYS95
|
4.8
|
35.5
|
1.0
|
|
NZ
|
A:LYS95
|
4.9
|
36.3
|
1.0
|
|
C
|
B:HIS624
|
5.0
|
43.0
|
1.0
|
|
Reference:
E.K.Leinala,
J.S.Arthur,
P.Grochulski,
P.L.Davies,
J.S.Elce,
Z.Jia.
A Second Binding Site Revealed By C-Terminal Truncation of Calpain Small Subunit, A Penta-Ef-Hand Protein Proteins: V. 53 649 2003STRUCT.,Funct.,Genet..
ISSN: ISSN 0887-3585
PubMed: 14579356
DOI: 10.1002/PROT.10453
Page generated: Wed Oct 28 09:55:09 2020
|
