Zinc in PDB 5wms: Phosphotriesterase Variant S7
Protein crystallography data
The structure of Phosphotriesterase Variant S7, PDB code: 5wms
was solved by
C.M.Miton,
E.C.Campbell,
C.J.Jackson,
N.Tokuriki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
43.06 /
1.60
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.658,
86.125,
176.870,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
26.4 /
29.3
|
Other elements in 5wms:
The structure of Phosphotriesterase Variant S7 also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Phosphotriesterase Variant S7
(pdb code 5wms). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Phosphotriesterase Variant S7, PDB code: 5wms:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 1 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2401
b:14.8
occ:1.00
|
O2
|
A:CAC2403
|
1.9
|
12.9
|
0.8
|
|
OQ2
|
A:KCX169
|
2.1
|
16.4
|
1.0
|
|
NE2
|
A:HIS57
|
2.1
|
16.3
|
1.0
|
|
NE2
|
A:HIS55
|
2.1
|
15.9
|
1.0
|
|
OD1
|
A:ASP301
|
2.4
|
17.3
|
1.0
|
|
CE1
|
A:HIS57
|
3.0
|
14.0
|
1.0
|
|
CX
|
A:KCX169
|
3.0
|
16.6
|
1.0
|
|
CD2
|
A:HIS55
|
3.0
|
13.7
|
1.0
|
|
CE1
|
A:HIS55
|
3.1
|
17.3
|
1.0
|
|
CD2
|
A:HIS57
|
3.1
|
11.2
|
1.0
|
|
AS
|
A:CAC2403
|
3.3
|
15.9
|
0.8
|
|
CG
|
A:ASP301
|
3.3
|
18.9
|
1.0
|
|
OQ1
|
A:KCX169
|
3.5
|
19.6
|
1.0
|
|
OD2
|
A:ASP301
|
3.6
|
17.8
|
1.0
|
|
C1
|
A:CAC2403
|
3.6
|
13.9
|
0.8
|
|
ZN
|
A:ZN2402
|
4.0
|
14.9
|
0.8
|
|
O1
|
A:CAC2403
|
4.0
|
13.7
|
0.8
|
|
CG2
|
A:VAL101
|
4.1
|
14.6
|
1.0
|
|
NZ
|
A:KCX169
|
4.1
|
19.0
|
1.0
|
|
ND1
|
A:HIS57
|
4.1
|
13.5
|
1.0
|
|
CG
|
A:HIS55
|
4.2
|
15.2
|
1.0
|
|
ND1
|
A:HIS55
|
4.2
|
13.8
|
1.0
|
|
CE1
|
A:HIS230
|
4.2
|
35.0
|
1.0
|
|
CG
|
A:HIS57
|
4.2
|
11.4
|
1.0
|
|
NE2
|
A:HIS230
|
4.5
|
35.3
|
1.0
|
|
CB
|
A:ASP301
|
4.7
|
13.3
|
1.0
|
|
C2
|
A:CAC2403
|
4.8
|
18.7
|
0.8
|
|
Zinc binding site 2 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 2 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn2402
b:14.9
occ:0.81
|
OQ1
|
A:KCX169
|
2.0
|
19.6
|
1.0
|
|
O1
|
A:CAC2403
|
2.0
|
13.7
|
0.8
|
|
ND1
|
A:HIS201
|
2.0
|
36.1
|
1.0
|
|
NE2
|
A:HIS230
|
2.0
|
35.3
|
1.0
|
|
CE1
|
A:HIS201
|
2.9
|
36.8
|
1.0
|
|
CD2
|
A:HIS230
|
3.0
|
35.8
|
1.0
|
|
CX
|
A:KCX169
|
3.0
|
16.6
|
1.0
|
|
CG
|
A:HIS201
|
3.0
|
36.1
|
1.0
|
|
CE1
|
A:HIS230
|
3.1
|
35.0
|
1.0
|
|
AS
|
A:CAC2403
|
3.1
|
15.9
|
0.8
|
|
O2
|
A:CAC2403
|
3.1
|
12.9
|
0.8
|
|
CB
|
A:HIS201
|
3.4
|
35.5
|
1.0
|
|
OQ2
|
A:KCX169
|
3.4
|
16.4
|
1.0
|
|
NE1
|
A:TRP131
|
3.8
|
19.9
|
1.0
|
|
ZN
|
A:ZN2401
|
4.0
|
14.8
|
1.0
|
|
NE2
|
A:HIS201
|
4.1
|
37.3
|
1.0
|
|
CD2
|
A:HIS201
|
4.1
|
36.9
|
1.0
|
|
CG
|
A:HIS230
|
4.1
|
35.7
|
1.0
|
|
ND1
|
A:HIS230
|
4.2
|
35.2
|
1.0
|
|
NZ
|
A:KCX169
|
4.3
|
19.0
|
1.0
|
|
CE1
|
A:HIS55
|
4.4
|
17.3
|
1.0
|
|
CD1
|
A:TRP131
|
4.4
|
17.4
|
1.0
|
|
CA
|
A:HIS201
|
4.4
|
35.5
|
1.0
|
|
C2
|
A:CAC2403
|
4.5
|
18.7
|
0.8
|
|
C1
|
A:CAC2403
|
4.5
|
13.9
|
0.8
|
|
NE2
|
A:HIS55
|
4.5
|
15.9
|
1.0
|
|
CE
|
A:KCX169
|
4.6
|
20.4
|
1.0
|
|
OD2
|
A:ASP301
|
5.0
|
17.8
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 3 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn2401
b:20.9
occ:0.90
|
NE2
|
G:HIS57
|
2.0
|
28.6
|
1.0
|
|
NE2
|
G:HIS55
|
2.1
|
29.4
|
1.0
|
|
OQ1
|
G:KCX169
|
2.1
|
22.5
|
1.0
|
|
OD1
|
G:ASP301
|
2.2
|
35.0
|
1.0
|
|
O1
|
G:CAC2403
|
2.6
|
13.8
|
0.8
|
|
CE1
|
G:HIS57
|
2.9
|
28.2
|
1.0
|
|
CX
|
G:KCX169
|
3.0
|
19.6
|
1.0
|
|
CD2
|
G:HIS55
|
3.0
|
29.4
|
1.0
|
|
CG
|
G:ASP301
|
3.0
|
35.3
|
1.0
|
|
CE1
|
G:HIS55
|
3.1
|
29.5
|
1.0
|
|
CD2
|
G:HIS57
|
3.1
|
28.7
|
1.0
|
|
OD2
|
G:ASP301
|
3.1
|
35.3
|
1.0
|
|
O2
|
G:CAC2403
|
3.4
|
25.7
|
0.8
|
|
OQ2
|
G:KCX169
|
3.5
|
23.1
|
1.0
|
|
AS
|
G:CAC2403
|
3.6
|
23.2
|
0.8
|
|
CG2
|
G:VAL101
|
3.9
|
28.4
|
1.0
|
|
ZN
|
G:ZN2402
|
3.9
|
21.7
|
0.8
|
|
ND1
|
G:HIS57
|
4.0
|
28.0
|
1.0
|
|
NZ
|
G:KCX169
|
4.0
|
22.8
|
1.0
|
|
CE1
|
G:HIS230
|
4.1
|
34.9
|
1.0
|
|
CG
|
G:HIS55
|
4.2
|
29.6
|
1.0
|
|
CG
|
G:HIS57
|
4.2
|
28.3
|
1.0
|
|
ND1
|
G:HIS55
|
4.2
|
29.6
|
1.0
|
|
NE2
|
G:HIS230
|
4.3
|
34.6
|
1.0
|
|
CB
|
G:ASP301
|
4.5
|
35.7
|
1.0
|
|
C2
|
G:CAC2403
|
4.7
|
33.3
|
0.8
|
|
C1
|
G:CAC2403
|
4.9
|
25.7
|
0.8
|
|
Zinc binding site 4 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 4 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn2402
b:21.7
occ:0.79
|
NE2
|
G:HIS230
|
2.0
|
34.6
|
1.0
|
|
ND1
|
G:HIS201
|
2.0
|
38.5
|
1.0
|
|
OQ2
|
G:KCX169
|
2.1
|
23.1
|
1.0
|
|
C2
|
G:CAC2403
|
2.2
|
33.3
|
0.8
|
|
O1
|
G:CAC2403
|
2.4
|
13.8
|
0.8
|
|
CE1
|
G:HIS201
|
2.8
|
34.3
|
1.0
|
|
CD2
|
G:HIS230
|
2.9
|
35.4
|
1.0
|
|
CE1
|
G:HIS230
|
3.1
|
34.9
|
1.0
|
|
CX
|
G:KCX169
|
3.1
|
19.6
|
1.0
|
|
CG
|
G:HIS201
|
3.2
|
33.8
|
1.0
|
|
AS
|
G:CAC2403
|
3.2
|
23.2
|
0.8
|
|
OQ1
|
G:KCX169
|
3.3
|
22.5
|
1.0
|
|
CB
|
G:HIS201
|
3.7
|
33.5
|
1.0
|
|
NE1
|
G:TRP131
|
3.9
|
20.2
|
1.0
|
|
ZN
|
G:ZN2401
|
3.9
|
20.9
|
0.9
|
|
NE2
|
G:HIS201
|
4.0
|
34.1
|
1.0
|
|
O2
|
G:CAC2403
|
4.1
|
25.7
|
0.8
|
|
CG
|
G:HIS230
|
4.1
|
35.0
|
1.0
|
|
ND1
|
G:HIS230
|
4.1
|
35.1
|
1.0
|
|
CD2
|
G:HIS201
|
4.2
|
33.8
|
1.0
|
|
NZ
|
G:KCX169
|
4.4
|
22.8
|
1.0
|
|
CD1
|
G:TRP131
|
4.5
|
24.4
|
1.0
|
|
OD2
|
G:ASP301
|
4.5
|
35.3
|
1.0
|
|
CE1
|
G:HIS55
|
4.5
|
29.5
|
1.0
|
|
NE2
|
G:HIS55
|
4.6
|
29.4
|
1.0
|
|
CA
|
G:HIS201
|
4.6
|
33.5
|
1.0
|
|
C1
|
G:CAC2403
|
4.8
|
25.7
|
0.8
|
|
CE
|
G:KCX169
|
4.9
|
23.0
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 5 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Zn2401
b:15.4
occ:0.77
|
OQ1
|
Q:KCX169
|
1.9
|
22.4
|
1.0
|
|
O2
|
Q:CAC2403
|
2.0
|
16.9
|
0.8
|
|
NE2
|
Q:HIS57
|
2.0
|
28.4
|
1.0
|
|
NE2
|
Q:HIS55
|
2.1
|
27.7
|
1.0
|
|
OD1
|
Q:ASP301
|
2.1
|
42.3
|
1.0
|
|
CX
|
Q:KCX169
|
2.9
|
20.5
|
1.0
|
|
CD2
|
Q:HIS55
|
3.0
|
26.9
|
1.0
|
|
CE1
|
Q:HIS57
|
3.0
|
27.5
|
1.0
|
|
CD2
|
Q:HIS57
|
3.0
|
28.7
|
1.0
|
|
CE1
|
Q:HIS55
|
3.1
|
27.2
|
1.0
|
|
CG
|
Q:ASP301
|
3.1
|
42.7
|
1.0
|
|
AS
|
Q:CAC2403
|
3.3
|
22.7
|
0.8
|
|
OQ2
|
Q:KCX169
|
3.4
|
21.5
|
1.0
|
|
OD2
|
Q:ASP301
|
3.5
|
43.0
|
1.0
|
|
C1
|
Q:CAC2403
|
3.7
|
18.9
|
0.8
|
|
ZN
|
Q:ZN2402
|
4.0
|
17.5
|
0.8
|
|
CG2
|
Q:VAL101
|
4.0
|
32.6
|
1.0
|
|
O1
|
Q:CAC2403
|
4.0
|
15.5
|
0.8
|
|
NZ
|
Q:KCX169
|
4.0
|
19.7
|
1.0
|
|
CE1
|
Q:HIS230
|
4.1
|
16.8
|
1.0
|
|
ND1
|
Q:HIS57
|
4.1
|
27.3
|
1.0
|
|
CG
|
Q:HIS55
|
4.1
|
25.8
|
1.0
|
|
ND1
|
Q:HIS55
|
4.1
|
26.1
|
1.0
|
|
CG
|
Q:HIS57
|
4.2
|
28.0
|
1.0
|
|
NE2
|
Q:HIS230
|
4.4
|
18.9
|
1.0
|
|
CB
|
Q:ASP301
|
4.4
|
42.9
|
1.0
|
|
C2
|
Q:CAC2403
|
4.9
|
21.0
|
0.8
|
|
CA
|
Q:ASP301
|
5.0
|
42.6
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 6 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Q:Zn2402
b:17.5
occ:0.79
|
OQ2
|
Q:KCX169
|
1.9
|
21.5
|
1.0
|
|
O1
|
Q:CAC2403
|
2.0
|
15.5
|
0.8
|
|
NE2
|
Q:HIS230
|
2.0
|
18.9
|
1.0
|
|
ND1
|
Q:HIS201
|
2.1
|
17.6
|
1.0
|
|
CX
|
Q:KCX169
|
2.9
|
20.5
|
1.0
|
|
CE1
|
Q:HIS201
|
3.0
|
22.6
|
1.0
|
|
CD2
|
Q:HIS230
|
3.0
|
22.4
|
1.0
|
|
AS
|
Q:CAC2403
|
3.1
|
22.7
|
0.8
|
|
CE1
|
Q:HIS230
|
3.1
|
16.8
|
1.0
|
|
CG
|
Q:HIS201
|
3.1
|
18.2
|
1.0
|
|
O2
|
Q:CAC2403
|
3.1
|
16.9
|
0.8
|
|
OQ1
|
Q:KCX169
|
3.4
|
22.4
|
1.0
|
|
CB
|
Q:HIS201
|
3.5
|
19.7
|
1.0
|
|
NE1
|
Q:TRP131
|
3.9
|
26.4
|
1.0
|
|
ZN
|
Q:ZN2401
|
4.0
|
15.4
|
0.8
|
|
NE2
|
Q:HIS201
|
4.1
|
21.8
|
1.0
|
|
NZ
|
Q:KCX169
|
4.1
|
19.7
|
1.0
|
|
CG
|
Q:HIS230
|
4.1
|
22.8
|
1.0
|
|
ND1
|
Q:HIS230
|
4.2
|
22.4
|
1.0
|
|
CD2
|
Q:HIS201
|
4.2
|
17.4
|
1.0
|
|
C2
|
Q:CAC2403
|
4.3
|
21.0
|
0.8
|
|
CE1
|
Q:HIS55
|
4.3
|
27.2
|
1.0
|
|
CA
|
Q:HIS201
|
4.3
|
21.0
|
1.0
|
|
NE2
|
Q:HIS55
|
4.4
|
27.7
|
1.0
|
|
CD1
|
Q:TRP131
|
4.5
|
27.5
|
1.0
|
|
C1
|
Q:CAC2403
|
4.5
|
18.9
|
0.8
|
|
CE
|
Q:KCX169
|
4.6
|
19.4
|
1.0
|
|
OD2
|
Q:ASP301
|
5.0
|
43.0
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 7 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Zn2401
b:20.9
occ:0.87
|
O1
|
S:CAC2403
|
1.8
|
15.9
|
0.8
|
|
OQ2
|
S:KCX169
|
2.0
|
39.9
|
1.0
|
|
NE2
|
S:HIS57
|
2.1
|
25.7
|
1.0
|
|
NE2
|
S:HIS55
|
2.1
|
26.7
|
1.0
|
|
OD1
|
S:ASP301
|
2.2
|
25.1
|
1.0
|
|
CD2
|
S:HIS55
|
3.0
|
27.7
|
1.0
|
|
CX
|
S:KCX169
|
3.0
|
39.9
|
1.0
|
|
CG
|
S:ASP301
|
3.1
|
26.8
|
1.0
|
|
CE1
|
S:HIS57
|
3.1
|
25.7
|
1.0
|
|
CD2
|
S:HIS57
|
3.1
|
27.5
|
1.0
|
|
AS
|
S:CAC2403
|
3.1
|
22.7
|
0.8
|
|
CE1
|
S:HIS55
|
3.2
|
27.1
|
1.0
|
|
OD2
|
S:ASP301
|
3.4
|
27.7
|
1.0
|
|
OQ1
|
S:KCX169
|
3.4
|
39.8
|
1.0
|
|
O2
|
S:CAC2403
|
3.7
|
20.6
|
0.8
|
|
ZN
|
S:ZN2402
|
4.0
|
21.9
|
0.8
|
|
CE1
|
S:HIS230
|
4.0
|
36.9
|
1.0
|
|
ND1
|
S:HIS57
|
4.2
|
25.5
|
1.0
|
|
CG
|
S:HIS55
|
4.2
|
27.2
|
1.0
|
|
CG
|
S:HIS57
|
4.2
|
25.4
|
1.0
|
|
ND1
|
S:HIS55
|
4.2
|
27.4
|
1.0
|
|
C2
|
S:CAC2403
|
4.3
|
15.6
|
0.8
|
|
CG2
|
S:VAL101
|
4.3
|
40.3
|
1.0
|
|
NZ
|
S:KCX169
|
4.3
|
40.0
|
1.0
|
|
NE2
|
S:HIS230
|
4.4
|
36.8
|
1.0
|
|
CB
|
S:ASP301
|
4.4
|
25.4
|
1.0
|
|
C1
|
S:CAC2403
|
4.5
|
10.3
|
0.8
|
|
CA
|
S:ASP301
|
4.9
|
25.2
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5wms
Go back to
Zinc Binding Sites List in 5wms
Zinc binding site 8 out
of 8 in the Phosphotriesterase Variant S7
 Mono view
 Stereo pair view
|
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Phosphotriesterase Variant S7 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
S:Zn2402
b:21.9
occ:0.84
|
OQ1
|
S:KCX169
|
1.8
|
39.8
|
1.0
|
|
ND1
|
S:HIS201
|
2.0
|
36.5
|
1.0
|
|
C1
|
S:CAC2403
|
2.1
|
10.3
|
0.8
|
|
NE2
|
S:HIS230
|
2.1
|
36.8
|
1.0
|
|
O1
|
S:CAC2403
|
2.8
|
15.9
|
0.8
|
|
CG
|
S:HIS201
|
2.9
|
36.4
|
1.0
|
|
CX
|
S:KCX169
|
3.0
|
39.9
|
1.0
|
|
CD2
|
S:HIS230
|
3.0
|
36.7
|
1.0
|
|
AS
|
S:CAC2403
|
3.0
|
22.7
|
0.8
|
|
CE1
|
S:HIS201
|
3.1
|
36.6
|
1.0
|
|
CE1
|
S:HIS230
|
3.2
|
36.9
|
1.0
|
|
CB
|
S:HIS201
|
3.2
|
36.3
|
1.0
|
|
OQ2
|
S:KCX169
|
3.5
|
39.9
|
1.0
|
|
NE1
|
S:TRP131
|
3.9
|
39.5
|
1.0
|
|
ZN
|
S:ZN2401
|
4.0
|
20.9
|
0.9
|
|
NZ
|
S:KCX169
|
4.1
|
40.0
|
1.0
|
|
CD2
|
S:HIS201
|
4.1
|
36.4
|
1.0
|
|
NE2
|
S:HIS201
|
4.1
|
36.5
|
1.0
|
|
CG
|
S:HIS230
|
4.2
|
36.9
|
1.0
|
|
CA
|
S:HIS201
|
4.2
|
36.3
|
1.0
|
|
ND1
|
S:HIS230
|
4.2
|
36.9
|
1.0
|
|
CE1
|
S:HIS55
|
4.2
|
27.1
|
1.0
|
|
O2
|
S:CAC2403
|
4.3
|
20.6
|
0.8
|
|
CE
|
S:KCX169
|
4.3
|
40.0
|
1.0
|
|
C2
|
S:CAC2403
|
4.4
|
15.6
|
0.8
|
|
NE2
|
S:HIS55
|
4.5
|
26.7
|
1.0
|
|
CD1
|
S:TRP131
|
4.5
|
39.6
|
1.0
|
|
Reference:
C.M.Miton,
E.C.Campbell,
C.J.Jackson,
N.Tokuriki.
Phosphotriesterase Variant S7 To Be Published.
Page generated: Mon Oct 28 14:23:16 2024
|
