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Zinc in PDB 8p7s: The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes

Enzymatic activity of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes

All present enzymatic activity of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes:
3.1.8.1;

Protein crystallography data

The structure of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes, PDB code: 8p7s was solved by O.Dym, N.Aggarwal, Y.Ashani, S.Albeck, T.Unger, S.Hamer Rogotner, I.Silman, J.L.Sussman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.77 / 1.77
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.54, 69.54, 185.84, 90, 90, 90
R / Rfree (%) 15.8 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes (pdb code 8p7s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes, PDB code: 8p7s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8p7s

Go back to Zinc Binding Sites List in 8p7s
Zinc binding site 1 out of 2 in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:13.9
occ:1.00
 O1 A:VX408 1.8 13.6 0.8
O2 A:FMT401 2.0 13.0 1.0
NE2 A:HIS57 2.0 11.9 1.0
NE2 A:HIS55 2.1 10.4 1.0
OD1 A:ASP301 2.3 12.5 1.0
CD2 A:HIS55 3.0 13.2 1.0
CE1 A:HIS57 3.0 12.8 1.0
CD2 A:HIS57 3.0 12.9 1.0
C A:FMT401 3.0 13.5 1.0
CE1 A:HIS55 3.1 13.3 1.0
P1 A:VX408 3.1 27.2 0.8
CG A:ASP301 3.2 12.6 1.0
O2 A:VX408 3.3 29.5 0.8
OD2 A:ASP301 3.4 14.2 1.0
O1 A:FMT401 3.5 11.3 1.0
ZN A:ZN403 3.9 14.9 1.0
CG2 A:VAL101 4.0 10.7 1.0
O3 A:VX408 4.1 9.8 0.8
NZ A:LYS169 4.1 11.8 1.0
ND1 A:HIS57 4.1 13.2 1.0
CG A:HIS55 4.1 11.4 1.0
CE1 A:HIS230 4.1 16.2 1.0
CG A:HIS57 4.2 12.6 1.0
ND1 A:HIS55 4.2 9.6 1.0
C1 A:VX408 4.4 18.9 0.8
NE2 A:HIS230 4.5 12.1 1.0
CB A:ASP301 4.5 12.4 1.0
C2 A:VX408 4.6 33.2 0.8
CA A:ASP301 5.0 11.0 1.0
C3 A:VX408 5.0 28.6 0.8

Zinc binding site 2 out of 2 in 8p7s

Go back to Zinc Binding Sites List in 8p7s
Zinc binding site 2 out of 2 in the The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:14.9
occ:1.00
 O1 A:FMT401 2.0 11.3 1.0
NE2 A:HIS230 2.0 12.1 1.0
O3 A:VX408 2.1 9.8 0.8
ND1 A:HIS201 2.1 12.4 1.0
O1 A:VX408 2.9 13.6 0.8
P1 A:VX408 2.9 27.2 0.8
C A:FMT401 3.0 13.5 1.0
CD2 A:HIS230 3.0 11.7 1.0
CE1 A:HIS201 3.0 15.6 1.0
CE1 A:HIS230 3.0 16.2 1.0
CG A:HIS201 3.1 12.1 1.0
O2 A:FMT401 3.4 13.0 1.0
CB A:HIS201 3.5 10.2 1.0
NE1 A:TRP131 3.8 15.5 1.0
ZN A:ZN402 3.9 13.9 1.0
ND1 A:HIS230 4.1 12.9 1.0
CG A:HIS230 4.1 9.9 1.0
NE2 A:HIS201 4.1 12.5 1.0
C1 A:VX408 4.2 18.9 0.8
NZ A:LYS169 4.2 11.8 1.0
O A:HOH553 4.2 29.8 1.0
O2 A:VX408 4.2 29.5 0.8
CD2 A:HIS201 4.2 13.1 1.0
CE1 A:HIS55 4.3 13.3 1.0
CA A:HIS201 4.3 9.4 1.0
CD1 A:TRP131 4.4 14.6 1.0
NE2 A:HIS55 4.4 10.4 1.0
CE A:LYS169 4.6 11.3 1.0
OD2 A:ASP301 4.8 14.2 1.0
CE2 A:TRP131 4.9 16.2 1.0

Reference:

O.Dym, N.Aggarwal, Y.Ashani, S.Albeck, H.Leader, T.Unger, S.Hamer Rogotner, I.Silman, D.S.Tawfik, J.L.Sussman. The Impact of Molecular Variants, Crystallization Conditions and the Space Group on Ligand–Protein Complexes: A Case Study on Bacterial Phosphotriesterase Acta Crystallogr. V. 79 2023.
ISSN: ISSN 0365-110X
DOI: 10.1107/S2059798323007672
Page generated: Fri Aug 22 12:03:39 2025

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