Cadmium in PDB 4utp: Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
Protein crystallography data
The structure of Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State, PDB code: 4utp
was solved by
Z.Luo,
R.M.Counago,
M.Maher,
B.Kobe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.97 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.239,
47.911,
101.524,
90.00,
106.96,
90.00
|
R / Rfree (%)
|
22.052 /
26.028
|
Cadmium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
25;
Binding sites:
The binding sites of Cadmium atom in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
(pdb code 4utp). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 25 binding sites of Cadmium where determined in the
Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State, PDB code: 4utp:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Cadmium binding site 1 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 1 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
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 Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1315
b:26.2
occ:1.00
|
OD2
|
A:ASP280
|
2.1
|
36.6
|
1.0
|
NE2
|
A:HIS139
|
2.3
|
32.3
|
1.0
|
NE2
|
A:HIS67
|
2.3
|
27.2
|
1.0
|
OE1
|
A:GLU205
|
2.4
|
19.7
|
1.0
|
OE2
|
A:GLU205
|
2.5
|
22.9
|
1.0
|
OD1
|
A:ASP280
|
2.7
|
37.3
|
1.0
|
CG
|
A:ASP280
|
2.7
|
36.6
|
1.0
|
CD
|
A:GLU205
|
2.7
|
22.3
|
1.0
|
CE1
|
A:HIS67
|
3.2
|
26.7
|
1.0
|
CE1
|
A:HIS139
|
3.2
|
30.5
|
1.0
|
CD2
|
A:HIS139
|
3.3
|
31.7
|
1.0
|
CD2
|
A:HIS67
|
3.3
|
26.7
|
1.0
|
ND2
|
A:ASN226
|
3.9
|
27.9
|
1.0
|
O
|
A:HOH2062
|
4.2
|
28.2
|
1.0
|
CG
|
A:ASN226
|
4.2
|
30.1
|
1.0
|
CB
|
A:ASP280
|
4.2
|
34.6
|
1.0
|
CG
|
A:GLU205
|
4.2
|
24.1
|
1.0
|
ND1
|
A:HIS67
|
4.3
|
26.3
|
1.0
|
O
|
A:HOH2056
|
4.4
|
27.7
|
0.9
|
CG
|
A:HIS67
|
4.4
|
27.6
|
1.0
|
ND1
|
A:HIS139
|
4.4
|
31.5
|
1.0
|
CG
|
A:HIS139
|
4.4
|
30.6
|
1.0
|
CB
|
A:ALA207
|
4.6
|
30.6
|
1.0
|
OD1
|
A:ASN226
|
4.6
|
30.1
|
1.0
|
CD1
|
A:LEU92
|
4.7
|
29.4
|
1.0
|
CB
|
A:ASN226
|
4.8
|
31.2
|
1.0
|
|
Cadmium binding site 2 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 2 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
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 Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1316
b:34.2
occ:0.66
|
ND1
|
A:HIS57
|
2.4
|
34.5
|
1.0
|
O
|
A:HOH2009
|
2.5
|
18.9
|
1.0
|
O
|
A:HOH2075
|
2.6
|
30.4
|
1.0
|
CE1
|
A:HIS57
|
3.2
|
34.0
|
1.0
|
CD
|
A:CD1326
|
3.3
|
51.4
|
0.6
|
CG
|
A:HIS57
|
3.5
|
34.0
|
1.0
|
CB
|
A:HIS57
|
3.9
|
33.8
|
1.0
|
CA
|
A:HIS57
|
4.0
|
33.3
|
1.0
|
NE2
|
A:HIS57
|
4.4
|
35.4
|
1.0
|
O
|
A:LEU56
|
4.5
|
30.9
|
1.0
|
CD2
|
A:HIS57
|
4.5
|
35.0
|
1.0
|
N
|
A:SER58
|
4.6
|
32.8
|
1.0
|
C
|
A:HIS57
|
4.9
|
33.0
|
1.0
|
|
Cadmium binding site 3 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 3 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
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 Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1317
b:52.3
occ:0.78
|
O
|
A:HOH2064
|
2.2
|
33.7
|
1.0
|
O
|
A:HOH2012
|
2.5
|
39.2
|
1.0
|
OE2
|
A:GLU230
|
2.6
|
50.0
|
1.0
|
OE1
|
A:GLU230
|
2.8
|
47.1
|
1.0
|
O
|
A:HOH2076
|
2.9
|
42.3
|
1.0
|
CD
|
A:GLU230
|
3.1
|
48.0
|
1.0
|
O
|
A:HOH2013
|
3.1
|
44.4
|
1.0
|
O
|
A:ASN226
|
4.1
|
37.0
|
1.0
|
OD2
|
A:ASP65
|
4.3
|
40.9
|
1.0
|
CD
|
A:CD1318
|
4.3
|
37.4
|
0.6
|
OE2
|
A:GLU68
|
4.4
|
40.1
|
1.0
|
CG
|
A:GLU230
|
4.5
|
46.5
|
1.0
|
CG
|
A:ASP65
|
4.7
|
38.0
|
1.0
|
|
Cadmium binding site 4 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 4 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
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 Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1318
b:37.4
occ:0.55
|
O
|
A:HOH2076
|
2.4
|
42.3
|
1.0
|
OE2
|
A:GLU68
|
2.4
|
40.1
|
1.0
|
OE1
|
A:GLU68
|
2.7
|
40.1
|
1.0
|
CD
|
A:GLU68
|
2.9
|
40.3
|
1.0
|
O
|
A:HOH2012
|
4.2
|
39.2
|
1.0
|
O
|
A:THR227
|
4.2
|
43.6
|
1.0
|
CD
|
A:CD1317
|
4.3
|
52.3
|
0.8
|
CG
|
A:GLU68
|
4.4
|
39.2
|
1.0
|
O
|
A:ASN226
|
4.8
|
37.0
|
1.0
|
C
|
A:THR227
|
4.8
|
44.3
|
1.0
|
CA
|
A:THR227
|
4.9
|
42.5
|
1.0
|
|
Cadmium binding site 5 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 5 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
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 Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1319
b:50.6
occ:0.67
|
OE2
|
A:GLU305
|
2.1
|
50.0
|
1.0
|
CD
|
A:CD1322
|
2.2
|
58.1
|
0.7
|
OD2
|
A:ASP301
|
2.3
|
43.9
|
1.0
|
OD1
|
A:ASP301
|
2.8
|
42.4
|
1.0
|
CG
|
A:ASP301
|
2.9
|
40.8
|
1.0
|
CD
|
A:GLU305
|
3.1
|
45.7
|
1.0
|
CG
|
A:GLU305
|
3.8
|
43.6
|
1.0
|
OE1
|
A:GLU305
|
4.1
|
46.8
|
1.0
|
CB
|
A:ASP301
|
4.4
|
38.1
|
1.0
|
NZ
|
A:LYS302
|
4.8
|
43.4
|
1.0
|
O
|
A:ASP301
|
4.9
|
32.7
|
1.0
|
O
|
A:HOH2052
|
4.9
|
63.1
|
1.0
|
C
|
A:ASP301
|
5.0
|
34.3
|
1.0
|
|
Cadmium binding site 6 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 6 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
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 Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1320
b:52.4
occ:0.66
|
O
|
A:HOH2072
|
2.0
|
39.2
|
1.0
|
O
|
A:HOH2073
|
2.5
|
42.4
|
1.0
|
OD2
|
A:ASP290
|
2.6
|
35.9
|
1.0
|
OD1
|
A:ASP290
|
2.7
|
33.8
|
1.0
|
CG
|
A:ASP290
|
3.0
|
33.1
|
1.0
|
O
|
A:LYS287
|
4.1
|
39.5
|
1.0
|
NE2
|
A:GLN285
|
4.2
|
54.6
|
1.0
|
N
|
A:GLY286
|
4.4
|
42.6
|
1.0
|
CB
|
A:ASP290
|
4.5
|
32.7
|
1.0
|
CA
|
A:GLY286
|
4.5
|
43.6
|
1.0
|
C
|
A:GLY286
|
4.8
|
43.9
|
1.0
|
|
Cadmium binding site 7 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 7 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1321
b:84.8
occ:0.88
|
O
|
A:GLU186
|
2.3
|
45.3
|
1.0
|
O
|
A:HOH2051
|
2.7
|
50.4
|
1.0
|
OD1
|
A:ASP189
|
2.8
|
48.4
|
1.0
|
C
|
A:GLU186
|
3.5
|
43.8
|
1.0
|
CG
|
A:ASP189
|
3.7
|
47.6
|
1.0
|
OD2
|
A:ASP189
|
3.9
|
50.5
|
1.0
|
NZ
|
B:LYS133
|
4.1
|
57.9
|
1.0
|
CA
|
A:GLU186
|
4.2
|
44.3
|
1.0
|
N
|
A:SER187
|
4.5
|
41.3
|
1.0
|
CB
|
A:GLU186
|
4.5
|
45.6
|
1.0
|
CA
|
A:SER187
|
4.7
|
40.0
|
1.0
|
N
|
A:LYS190
|
4.9
|
41.0
|
1.0
|
|
Cadmium binding site 8 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 8 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1322
b:58.1
occ:0.71
|
CD
|
A:CD1319
|
2.2
|
50.6
|
0.7
|
OD1
|
A:ASP301
|
2.3
|
42.4
|
1.0
|
O
|
A:HOH2052
|
3.2
|
63.1
|
1.0
|
CG
|
A:ASP301
|
3.2
|
40.8
|
1.0
|
OE2
|
A:GLU305
|
3.3
|
50.0
|
1.0
|
OD2
|
A:ASP301
|
3.5
|
43.9
|
1.0
|
CG
|
A:GLU305
|
3.6
|
43.6
|
1.0
|
CD
|
A:GLU305
|
3.8
|
45.7
|
1.0
|
O
|
A:ASP301
|
4.4
|
32.7
|
1.0
|
CB
|
A:ASP301
|
4.6
|
38.1
|
1.0
|
CA
|
A:ASP301
|
4.8
|
35.4
|
1.0
|
C
|
A:ASP301
|
4.8
|
34.3
|
1.0
|
|
Cadmium binding site 9 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 9 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 9 of Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1323
b:66.5
occ:0.59
|
OE2
|
A:GLU186
|
2.0
|
55.3
|
1.0
|
O
|
A:HOH2049
|
2.2
|
40.8
|
1.0
|
CD
|
A:GLU186
|
3.0
|
52.5
|
1.0
|
OE1
|
A:GLU186
|
3.4
|
55.8
|
1.0
|
CG
|
A:GLU186
|
4.3
|
50.0
|
1.0
|
CE
|
A:LYS182
|
4.5
|
50.4
|
1.0
|
NZ
|
A:LYS182
|
4.6
|
52.8
|
1.0
|
|
Cadmium binding site 10 out
of 25 in 4utp
Go back to
Cadmium Binding Sites List in 4utp
Cadmium binding site 10 out
of 25 in the Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 10 of Crystal Structure of Pneumococcal Surface Antigen Psaa in the Cd-Bound, Closed State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1324
b:57.4
occ:0.57
|
OE2
|
A:GLU70
|
2.3
|
46.5
|
1.0
|
OE1
|
A:GLU70
|
2.7
|
44.2
|
1.0
|
CD
|
A:GLU70
|
2.8
|
44.0
|
1.0
|
CG
|
A:GLU70
|
4.3
|
41.0
|
1.0
|
|
Reference:
S.L.Begg,
B.A.Eijkelkamp,
Z.Luo,
R.M.Counago,
J.R.Morey,
M.J.Maher,
B.Kobe,
M.L.Omara,
J.C.Paton,
C.A.Mcdevitt.
Crystal Structure of Pneumococcal Surface Antigen Psaa To Be Published.
Page generated: Fri Jul 19 17:59:14 2024
|