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Zinc in PDB 2o4q: Structure of Phosphotriesterase Mutant G60A

Enzymatic activity of Structure of Phosphotriesterase Mutant G60A

All present enzymatic activity of Structure of Phosphotriesterase Mutant G60A:
3.1.8.1;

Protein crystallography data

The structure of Structure of Phosphotriesterase Mutant G60A, PDB code: 2o4q was solved by J.Kim, U.A.Ramagopal, P.C.Tsai, F.M.Raushel, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.64 / 1.95
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.295, 68.299, 90.030, 90.05, 100.42, 89.96
R / Rfree (%) 16.4 / 22.6

Other elements in 2o4q:

The structure of Structure of Phosphotriesterase Mutant G60A also contains other interesting chemical elements:

Arsenic (As) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Phosphotriesterase Mutant G60A (pdb code 2o4q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Phosphotriesterase Mutant G60A, PDB code: 2o4q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2o4q

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Zinc binding site 1 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2401

b:16.7
occ:1.00
 O1 A:CAC1 2.0 24.3 0.8
NE2 A:HIS55 2.0 6.1 1.0
OQ1 A:KCX169 2.1 12.4 1.0
NE2 A:HIS57 2.1 13.7 1.0
OD1 A:ASP301 2.1 16.4 1.0
CD2 A:HIS55 2.9 10.3 1.0
CG A:ASP301 3.0 15.6 1.0
CD2 A:HIS57 3.1 11.3 1.0
CE1 A:HIS55 3.1 12.1 1.0
CX A:KCX169 3.1 16.4 1.0
CE1 A:HIS57 3.1 10.9 1.0
OD2 A:ASP301 3.2 17.7 1.0
AS A:CAC1 3.3 22.2 0.8
OQ2 A:KCX169 3.6 17.2 1.0
C2 A:CAC1 3.9 12.0 0.8
O A:HOH2488 4.0 17.5 1.0
ZN A:ZN2402 4.0 18.6 1.0
CG A:HIS55 4.1 13.8 1.0
O2 A:CAC1 4.1 16.0 0.8
ND1 A:HIS55 4.1 10.6 1.0
CE1 A:HIS230 4.1 15.3 1.0
NZ A:KCX169 4.1 14.5 1.0
CG2 A:VAL101 4.2 8.6 1.0
ND1 A:HIS57 4.2 8.9 1.0
CG A:HIS57 4.2 10.0 1.0
CB A:ASP301 4.4 16.5 1.0
NE2 A:HIS230 4.5 14.3 1.0
O A:HOH2593 4.5 22.4 1.0
CA A:ASP301 4.8 14.6 1.0
C1 A:CAC1 5.0 20.1 0.8

Zinc binding site 2 out of 8 in 2o4q

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Zinc binding site 2 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2402

b:18.6
occ:1.00
 OQ2 A:KCX169 1.9 17.2 1.0
O2 A:CAC1 2.1 16.0 0.8
NE2 A:HIS230 2.1 14.3 1.0
ND1 A:HIS201 2.2 14.5 1.0
CX A:KCX169 3.0 16.4 1.0
CE1 A:HIS230 3.1 15.3 1.0
CE1 A:HIS201 3.1 17.9 1.0
CD2 A:HIS230 3.1 17.5 1.0
CG A:HIS201 3.2 13.2 1.0
AS A:CAC1 3.3 22.2 0.8
OQ1 A:KCX169 3.3 12.4 1.0
O1 A:CAC1 3.5 24.3 0.8
CB A:HIS201 3.5 13.8 1.0
O A:HOH2593 3.9 22.4 1.0
ZN A:ZN2401 4.0 16.7 1.0
NE1 A:TRP131 4.0 12.9 1.0
NZ A:KCX169 4.2 14.5 1.0
ND1 A:HIS230 4.2 16.7 1.0
NE2 A:HIS201 4.2 17.7 1.0
CG A:HIS230 4.2 15.8 1.0
CE1 A:HIS55 4.3 12.1 1.0
CD2 A:HIS201 4.3 16.1 1.0
CA A:HIS201 4.3 13.1 1.0
NE2 A:HIS55 4.4 6.1 1.0
OD2 A:ASP301 4.6 17.7 1.0
C2 A:CAC1 4.6 12.0 0.8
CD1 A:TRP131 4.6 14.4 1.0
CE A:KCX169 4.6 14.7 1.0
C1 A:CAC1 4.7 20.1 0.8

Zinc binding site 3 out of 8 in 2o4q

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Zinc binding site 3 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2403

b:18.6
occ:1.00
 O2 B:CAC2 2.1 22.6 0.7
OQ2 B:KCX169 2.1 15.0 1.0
NE2 B:HIS57 2.1 17.2 1.0
NE2 B:HIS55 2.2 14.2 1.0
OD1 B:ASP301 2.2 15.7 1.0
CD2 B:HIS55 3.0 12.4 1.0
CG B:ASP301 3.0 22.3 1.0
CX B:KCX169 3.1 16.6 1.0
CE1 B:HIS57 3.1 14.6 1.0
CD2 B:HIS57 3.1 19.6 1.0
OD2 B:ASP301 3.2 17.0 1.0
CE1 B:HIS55 3.2 18.0 1.0
AS B:CAC2 3.3 21.9 0.7
OQ1 B:KCX169 3.6 14.9 1.0
C1 B:CAC2 3.8 13.6 0.7
ZN B:ZN2404 3.9 22.6 1.0
O B:HOH2469 3.9 21.1 1.0
NZ B:KCX169 4.1 18.1 1.0
O1 B:CAC2 4.1 13.2 0.7
CE1 B:HIS230 4.2 18.4 1.0
CG B:HIS55 4.2 17.2 1.0
CG2 B:VAL101 4.2 15.2 1.0
ND1 B:HIS57 4.2 14.5 1.0
CG B:HIS57 4.3 12.9 1.0
ND1 B:HIS55 4.3 10.5 1.0
CB B:ASP301 4.4 15.6 1.0
NE2 B:HIS230 4.5 17.8 1.0
CA B:ASP301 4.9 15.8 1.0
C2 B:CAC2 5.0 17.7 0.7

Zinc binding site 4 out of 8 in 2o4q

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Zinc binding site 4 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2404

b:22.6
occ:1.00
 OQ1 B:KCX169 2.0 14.9 1.0
NE2 B:HIS230 2.1 17.8 1.0
O1 B:CAC2 2.1 13.2 0.7
ND1 B:HIS201 2.2 18.3 1.0
CX B:KCX169 3.0 16.6 1.0
CD2 B:HIS230 3.1 18.4 1.0
CE1 B:HIS201 3.1 16.9 1.0
CE1 B:HIS230 3.1 18.4 1.0
CG B:HIS201 3.2 24.3 1.0
AS B:CAC2 3.3 21.9 0.7
OQ2 B:KCX169 3.3 15.0 1.0
O2 B:CAC2 3.5 22.6 0.7
CB B:HIS201 3.5 21.4 1.0
ZN B:ZN2403 3.9 18.6 1.0
NE1 B:TRP131 3.9 12.8 1.0
NZ B:KCX169 4.2 18.1 1.0
CG B:HIS230 4.2 15.3 1.0
ND1 B:HIS230 4.2 16.1 1.0
NE2 B:HIS201 4.2 19.8 1.0
CD2 B:HIS201 4.3 19.0 1.0
CA B:HIS201 4.3 21.1 1.0
NE2 B:HIS55 4.4 14.2 1.0
CE1 B:HIS55 4.4 18.0 1.0
OD2 B:ASP301 4.5 17.0 1.0
CD1 B:TRP131 4.5 16.3 1.0
C1 B:CAC2 4.6 13.6 0.7
CE B:KCX169 4.6 17.6 1.0
C2 B:CAC2 4.8 17.7 0.7

Zinc binding site 5 out of 8 in 2o4q

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Zinc binding site 5 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn2405

b:14.1
occ:0.90
 O2 K:CAC3 1.9 25.6 0.8
OQ1 K:KCX169 2.0 13.8 1.0
NE2 K:HIS55 2.0 9.3 1.0
NE2 K:HIS57 2.1 9.1 1.0
OD1 K:ASP301 2.1 12.7 1.0
CD2 K:HIS55 2.9 8.2 1.0
CG K:ASP301 3.0 16.1 1.0
CD2 K:HIS57 3.1 12.4 1.0
CE1 K:HIS57 3.1 8.8 1.0
CX K:KCX169 3.1 13.2 1.0
CE1 K:HIS55 3.1 11.0 1.0
OD2 K:ASP301 3.2 15.2 1.0
AS K:CAC3 3.3 22.5 0.8
OQ2 K:KCX169 3.6 11.6 1.0
C1 K:CAC3 3.9 12.7 0.8
ZN K:ZN2406 3.9 19.0 1.0
NZ K:KCX169 4.1 16.0 1.0
O K:HOH2517 4.1 21.4 1.0
CG K:HIS55 4.1 12.4 1.0
O1 K:CAC3 4.2 12.7 0.8
CE1 K:HIS230 4.2 11.0 1.0
ND1 K:HIS55 4.2 9.1 1.0
ND1 K:HIS57 4.2 7.5 1.0
CG2 K:VAL101 4.2 11.3 1.0
CG K:HIS57 4.2 8.8 1.0
CB K:ASP301 4.4 16.2 1.0
NE2 K:HIS230 4.4 18.6 1.0
O K:HOH2672 4.5 23.2 1.0
CA K:ASP301 4.8 14.8 1.0
C2 K:CAC3 5.0 19.6 0.8

Zinc binding site 6 out of 8 in 2o4q

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Zinc binding site 6 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn2406

b:19.0
occ:1.00
 OQ2 K:KCX169 2.0 11.6 1.0
O1 K:CAC3 2.1 12.7 0.8
NE2 K:HIS230 2.1 18.6 1.0
ND1 K:HIS201 2.2 17.8 1.0
CX K:KCX169 3.0 13.2 1.0
CD2 K:HIS230 3.1 12.1 1.0
CE1 K:HIS201 3.1 17.0 1.0
CE1 K:HIS230 3.2 11.0 1.0
CG K:HIS201 3.2 14.6 1.0
OQ1 K:KCX169 3.3 13.8 1.0
AS K:CAC3 3.3 22.5 0.8
O2 K:CAC3 3.4 25.6 0.8
CB K:HIS201 3.6 13.7 1.0
O K:HOH2672 3.8 23.2 1.0
ZN K:ZN2405 3.9 14.1 0.9
NE1 K:TRP131 3.9 15.6 1.0
NZ K:KCX169 4.2 16.0 1.0
NE2 K:HIS201 4.2 20.7 1.0
CG K:HIS230 4.2 14.3 1.0
ND1 K:HIS230 4.3 15.3 1.0
CD2 K:HIS201 4.3 16.4 1.0
CE1 K:HIS55 4.3 11.0 1.0
CA K:HIS201 4.3 13.2 1.0
NE2 K:HIS55 4.4 9.3 1.0
C1 K:CAC3 4.5 12.7 0.8
OD2 K:ASP301 4.6 15.2 1.0
CE K:KCX169 4.6 13.6 1.0
CD1 K:TRP131 4.6 15.6 1.0
C2 K:CAC3 4.8 19.6 0.8

Zinc binding site 7 out of 8 in 2o4q

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Zinc binding site 7 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn2407

b:14.7
occ:0.80
 O2 P:CAC4 2.0 19.5 0.7
OD1 P:ASP301 2.1 16.2 1.0
NE2 P:HIS57 2.1 19.2 1.0
NE2 P:HIS55 2.1 13.0 1.0
OQ2 P:KCX169 2.2 16.0 1.0
CG P:ASP301 2.9 19.0 1.0
CD2 P:HIS55 3.0 16.6 1.0
CD2 P:HIS57 3.1 15.3 1.0
CX P:KCX169 3.1 11.7 1.0
OD2 P:ASP301 3.2 19.3 1.0
CE1 P:HIS57 3.2 12.4 1.0
CE1 P:HIS55 3.2 16.8 1.0
AS P:CAC4 3.3 20.9 0.7
OQ1 P:KCX169 3.6 16.9 1.0
C1 P:CAC4 3.9 10.9 0.7
O P:HOH2516 3.9 22.4 1.0
ZN P:ZN2408 3.9 19.7 0.9
NZ P:KCX169 4.1 14.6 1.0
CG2 P:VAL101 4.2 15.3 1.0
O1 P:CAC4 4.2 16.3 0.7
CG P:HIS55 4.2 19.2 1.0
CE1 P:HIS230 4.2 17.6 1.0
CG P:HIS57 4.2 12.2 1.0
ND1 P:HIS57 4.2 15.5 1.0
ND1 P:HIS55 4.3 12.7 1.0
CB P:ASP301 4.4 15.0 1.0
NE2 P:HIS230 4.5 18.3 1.0
O P:HOH2566 4.6 26.5 1.0
CA P:ASP301 4.9 15.0 1.0
C2 P:CAC4 4.9 21.5 0.7

Zinc binding site 8 out of 8 in 2o4q

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Zinc binding site 8 out of 8 in the Structure of Phosphotriesterase Mutant G60A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Phosphotriesterase Mutant G60A within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn2408

b:19.7
occ:0.90
 OQ1 P:KCX169 2.0 16.9 1.0
ND1 P:HIS201 2.1 17.2 1.0
O1 P:CAC4 2.1 16.3 0.7
NE2 P:HIS230 2.1 18.3 1.0
CX P:KCX169 3.0 11.7 1.0
CE1 P:HIS201 3.0 16.4 1.0
CE1 P:HIS230 3.1 17.6 1.0
CD2 P:HIS230 3.1 18.9 1.0
CG P:HIS201 3.1 23.2 1.0
AS P:CAC4 3.3 20.9 0.7
O2 P:CAC4 3.3 19.5 0.7
OQ2 P:KCX169 3.3 16.0 1.0
CB P:HIS201 3.5 20.1 1.0
ZN P:ZN2407 3.9 14.7 0.8
NE1 P:TRP131 3.9 13.1 1.0
O P:HOH2566 4.0 26.5 1.0
NE2 P:HIS201 4.1 18.3 1.0
NZ P:KCX169 4.1 14.6 1.0
ND1 P:HIS230 4.2 17.6 1.0
CD2 P:HIS201 4.2 18.3 1.0
CG P:HIS230 4.2 19.6 1.0
CA P:HIS201 4.3 20.5 1.0
CE1 P:HIS55 4.4 16.8 1.0
NE2 P:HIS55 4.4 13.0 1.0
OD2 P:ASP301 4.4 19.3 1.0
CD1 P:TRP131 4.5 15.3 1.0
C1 P:CAC4 4.6 10.9 0.7
CE P:KCX169 4.6 17.3 1.0
C2 P:CAC4 4.8 21.5 0.7

Reference:

J.Kim, P.C.Tsai, S.L.Chen, F.Himo, S.C.Almo, F.M.Raushel. Structure of Diethyl Phosphate Bound to the Binuclear Metal Center of Phosphotriesterase. Biochemistry V. 47 9497 2008.
ISSN: ISSN 0006-2960
PubMed: 18702530
DOI: 10.1021/BI800971V
Page generated: Thu Oct 17 02:26:52 2024

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