Cadmium in PDB 5b42: Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
Protein crystallography data
The structure of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl., PDB code: 5b42
was solved by
K.Fukui,
S.Baba,
T.Kumasaka,
T.Yano,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.70 /
1.35
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.349,
35.349,
161.560,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14 /
18.3
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
(pdb code 5b42). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the
Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl., PDB code: 5b42:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
Cadmium binding site 1 out
of 6 in 5b42
Go back to
Cadmium Binding Sites List in 5b42
Cadmium binding site 1 out
of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd201
b:13.9
occ:0.89
|
NE2
|
A:HIS30
|
2.3
|
14.7
|
1.0
|
OE2
|
A:GLU34
|
2.3
|
16.6
|
1.0
|
O
|
A:HOH373
|
2.4
|
16.5
|
1.0
|
O
|
A:HOH369
|
2.4
|
22.4
|
1.0
|
SG
|
A:CYS48
|
2.6
|
18.2
|
1.0
|
O
|
A:HOH381
|
2.7
|
18.4
|
1.0
|
CE1
|
A:HIS30
|
3.3
|
13.3
|
1.0
|
CD2
|
A:HIS30
|
3.3
|
12.3
|
1.0
|
CD
|
A:GLU34
|
3.4
|
13.8
|
1.0
|
CB
|
A:CYS48
|
3.5
|
13.8
|
1.0
|
CD
|
A:CD205
|
3.7
|
25.1
|
0.8
|
OE1
|
A:GLU34
|
3.9
|
17.1
|
1.0
|
CD
|
A:CD202
|
3.9
|
14.3
|
0.8
|
O
|
A:HOH345
|
4.2
|
21.4
|
1.0
|
CA
|
A:CYS48
|
4.3
|
14.7
|
1.0
|
CE1
|
A:HIS81
|
4.4
|
21.5
|
1.0
|
ND1
|
A:HIS30
|
4.4
|
12.8
|
1.0
|
CG
|
A:GLU34
|
4.4
|
14.6
|
1.0
|
CG
|
A:HIS30
|
4.4
|
11.4
|
1.0
|
O
|
A:HOH394
|
4.6
|
29.6
|
1.0
|
ND1
|
A:HIS81
|
4.6
|
21.6
|
1.0
|
CB
|
A:GLU34
|
4.9
|
11.6
|
1.0
|
|
Cadmium binding site 2 out
of 6 in 5b42
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Cadmium Binding Sites List in 5b42
Cadmium binding site 2 out
of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd202
b:14.3
occ:0.85
|
OE1
|
A:GLU34
|
2.3
|
17.1
|
1.0
|
ND1
|
A:HIS81
|
2.4
|
21.6
|
1.0
|
O
|
A:HOH373
|
2.4
|
16.5
|
1.0
|
SG
|
A:CYS79
|
2.5
|
15.4
|
1.0
|
O
|
A:HOH345
|
2.5
|
21.4
|
1.0
|
CD
|
A:GLU34
|
3.1
|
13.8
|
1.0
|
OE2
|
A:GLU34
|
3.2
|
16.6
|
1.0
|
CE1
|
A:HIS81
|
3.3
|
21.5
|
1.0
|
CG
|
A:HIS81
|
3.3
|
20.1
|
1.0
|
CB
|
A:CYS79
|
3.4
|
14.9
|
1.0
|
CB
|
A:HIS81
|
3.6
|
17.7
|
1.0
|
CD2
|
A:LEU31
|
3.8
|
14.7
|
1.0
|
CD
|
A:CD201
|
3.9
|
13.9
|
0.9
|
N
|
A:HIS81
|
4.0
|
16.9
|
1.0
|
O
|
A:HOH381
|
4.2
|
18.4
|
1.0
|
CD
|
A:PRO80
|
4.2
|
18.2
|
1.0
|
CA
|
A:HIS81
|
4.4
|
16.9
|
1.0
|
NE2
|
A:HIS81
|
4.4
|
24.6
|
1.0
|
CG
|
A:GLU34
|
4.5
|
14.6
|
1.0
|
N
|
A:PRO80
|
4.5
|
17.0
|
1.0
|
CD2
|
A:HIS81
|
4.5
|
26.5
|
1.0
|
CG
|
A:PRO80
|
4.5
|
22.8
|
1.0
|
CA
|
A:CYS79
|
4.6
|
14.5
|
1.0
|
C
|
A:CYS79
|
4.7
|
16.6
|
1.0
|
|
Cadmium binding site 3 out
of 6 in 5b42
Go back to
Cadmium Binding Sites List in 5b42
Cadmium binding site 3 out
of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd203
b:17.3
occ:0.94
|
OE2
|
A:GLU61
|
2.4
|
17.1
|
1.0
|
OE1
|
A:GLU61
|
2.5
|
18.5
|
1.0
|
O
|
A:HOH380
|
2.5
|
10.9
|
1.0
|
O
|
A:HOH376
|
2.5
|
11.2
|
1.0
|
CD
|
A:GLU61
|
2.8
|
16.9
|
1.0
|
NE
|
A:ARG64
|
4.1
|
20.3
|
1.0
|
CG
|
A:GLU61
|
4.3
|
15.7
|
1.0
|
O
|
A:HOH382
|
4.4
|
28.9
|
1.0
|
CG
|
A:GLU65
|
4.5
|
21.9
|
1.0
|
CB
|
A:ARG64
|
4.6
|
15.6
|
1.0
|
O
|
A:GLU61
|
4.7
|
17.4
|
1.0
|
CD
|
A:ARG64
|
4.8
|
18.9
|
1.0
|
OE2
|
A:GLU65
|
4.9
|
34.1
|
1.0
|
NH2
|
A:ARG64
|
5.0
|
21.6
|
1.0
|
|
Cadmium binding site 4 out
of 6 in 5b42
Go back to
Cadmium Binding Sites List in 5b42
Cadmium binding site 4 out
of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd204
b:24.5
occ:0.52
|
OD2
|
A:ASP43
|
2.5
|
29.8
|
1.0
|
O
|
A:HOH383
|
2.5
|
28.6
|
1.0
|
O
|
A:HOH374
|
2.6
|
17.1
|
1.0
|
OD1
|
A:ASP43
|
2.7
|
27.6
|
1.0
|
CG
|
A:ASP43
|
2.9
|
28.6
|
1.0
|
O
|
A:HOH393
|
3.8
|
36.5
|
1.0
|
CB
|
A:ASN45
|
4.2
|
24.2
|
1.0
|
O
|
A:HOH359
|
4.3
|
29.4
|
1.0
|
N
|
A:LEU46
|
4.4
|
19.1
|
1.0
|
CB
|
A:ASP43
|
4.4
|
24.8
|
1.0
|
CB
|
A:LEU46
|
4.7
|
19.1
|
1.0
|
OD1
|
A:ASN45
|
4.8
|
43.3
|
1.0
|
|
Cadmium binding site 5 out
of 6 in 5b42
Go back to
Cadmium Binding Sites List in 5b42
Cadmium binding site 5 out
of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd205
b:25.1
occ:0.78
|
O
|
A:HOH301
|
2.4
|
29.0
|
1.0
|
O
|
A:HOH381
|
2.5
|
18.4
|
1.0
|
O
|
A:HOH394
|
2.5
|
29.6
|
1.0
|
SG
|
A:CYS48
|
2.6
|
18.2
|
1.0
|
O
|
A:HOH370
|
2.7
|
24.8
|
1.0
|
CB
|
A:CYS48
|
3.5
|
13.8
|
1.0
|
CD
|
A:CD201
|
3.7
|
13.9
|
0.9
|
O
|
A:HOH369
|
3.9
|
22.4
|
1.0
|
CE1
|
A:HIS81
|
4.5
|
21.5
|
1.0
|
ND2
|
A:ASN45
|
4.7
|
40.5
|
1.0
|
OE2
|
A:GLU34
|
4.7
|
16.6
|
1.0
|
NE2
|
A:HIS81
|
4.9
|
24.6
|
1.0
|
CA
|
A:CYS48
|
4.9
|
14.7
|
1.0
|
|
Cadmium binding site 6 out
of 6 in 5b42
Go back to
Cadmium Binding Sites List in 5b42
Cadmium binding site 6 out
of 6 in the Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl.
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Crystal Structure of the C-Terminal Endonuclease Domain of Aquifex Aeolicus Mutl. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd208
b:26.4
occ:0.51
|
OE1
|
A:GLU96
|
2.4
|
43.7
|
1.0
|
OE2
|
A:GLU96
|
2.6
|
34.9
|
1.0
|
O
|
A:HOH371
|
2.7
|
36.9
|
1.0
|
OE1
|
A:GLU93
|
2.7
|
49.5
|
1.0
|
O
|
A:HOH307
|
2.7
|
40.9
|
1.0
|
OE2
|
A:GLU93
|
2.8
|
44.3
|
1.0
|
CD
|
A:GLU96
|
2.8
|
38.8
|
1.0
|
O
|
A:HOH352
|
2.8
|
45.4
|
1.0
|
CD
|
A:GLU93
|
3.1
|
44.3
|
1.0
|
CG
|
A:GLU96
|
4.2
|
24.4
|
1.0
|
NE
|
A:ARG92
|
4.5
|
31.1
|
1.0
|
CG
|
A:GLU93
|
4.5
|
33.3
|
1.0
|
O
|
A:HOH323
|
4.6
|
28.9
|
1.0
|
CA
|
A:GLU93
|
4.7
|
15.1
|
1.0
|
NH2
|
A:ARG92
|
4.8
|
34.5
|
1.0
|
|
Reference:
K.Fukui,
S.Baba,
T.Kumasaka,
T.Yano.
Structural Features and Functional Dependency on Beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease Mutl J.Biol.Chem. V. 291 16990 2016.
ISSN: ESSN 1083-351X
PubMed: 27369079
DOI: 10.1074/JBC.M116.739664
Page generated: Fri Jul 19 18:12:12 2024
|