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Zinc in PDB 8p7m: 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: 8p7m 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) 28.42 / 1.85
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.74, 69.74, 186.76, 90, 90, 90
R / Rfree (%) 16.2 / 18.7

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 8p7m). 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: 8p7m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8p7m

Go back to Zinc Binding Sites List in 8p7m
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:Zn403

b:13.8
occ:1.00
 O3 A:GB407 1.9 13.9 1.0
NE2 A:HIS57 2.0 10.7 1.0
O1 A:FMT402 2.1 12.1 1.0
NE2 A:HIS55 2.1 11.6 1.0
OD1 A:ASP301 2.5 12.3 1.0
CE1 A:HIS57 2.9 12.1 1.0
C A:FMT402 3.0 12.6 1.0
CD2 A:HIS55 3.0 12.4 1.0
CE1 A:HIS55 3.1 12.1 1.0
CD2 A:HIS57 3.1 11.7 1.0
P1 A:GB407 3.2 16.6 1.0
CG A:ASP301 3.3 14.6 1.0
O2 A:FMT402 3.5 12.0 1.0
OD2 A:ASP301 3.5 13.3 1.0
C1 A:GB407 3.6 16.3 1.0
O1 A:GB407 3.8 12.4 1.0
ZN A:ZN404 3.9 13.8 1.0
CG2 A:VAL101 4.0 9.5 1.0
NZ A:LYS169 4.1 9.8 1.0
ND1 A:HIS57 4.1 10.9 1.0
CE1 A:HIS230 4.1 12.3 1.0
ND1 A:HIS55 4.2 9.8 1.0
CG A:HIS55 4.2 10.8 1.0
CG A:HIS57 4.2 11.9 1.0
O2 A:GB407 4.4 14.8 1.0
NE2 A:HIS230 4.4 10.4 1.0
CB A:ASP301 4.6 11.4 1.0

Zinc binding site 2 out of 2 in 8p7m

Go back to Zinc Binding Sites List in 8p7m
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:Zn404

b:13.8
occ:1.00
 O2 A:FMT402 2.0 12.0 1.0
ND1 A:HIS201 2.0 11.3 1.0
NE2 A:HIS230 2.1 10.4 1.0
O1 A:GB407 2.1 12.4 1.0
P1 A:GB407 2.9 16.6 1.0
CE1 A:HIS201 3.0 14.6 1.0
C A:FMT402 3.0 12.6 1.0
CD2 A:HIS230 3.0 12.0 1.0
O3 A:GB407 3.1 13.9 1.0
CE1 A:HIS230 3.1 12.3 1.0
CG A:HIS201 3.1 10.8 1.0
O1 A:FMT402 3.4 12.1 1.0
CB A:HIS201 3.5 10.1 1.0
NE1 A:TRP131 3.8 13.5 1.0
ZN A:ZN403 3.9 13.8 1.0
O2 A:GB407 3.9 14.8 1.0
NE2 A:HIS201 4.1 15.2 1.0
ND1 A:HIS230 4.2 12.9 1.0
CG A:HIS230 4.2 10.7 1.0
CD2 A:HIS201 4.2 15.5 1.0
NZ A:LYS169 4.2 9.8 1.0
CA A:HIS201 4.3 9.7 1.0
CE1 A:HIS55 4.3 12.1 1.0
C1 A:GB407 4.3 16.3 1.0
CD1 A:TRP131 4.4 12.6 1.0
NE2 A:HIS55 4.4 11.6 1.0
CE A:LYS169 4.6 11.2 1.0
O A:HOH723 4.7 27.8 1.0
OD2 A:ASP301 4.9 13.3 1.0

Reference:

O.Dym, N.Aggarwal, Y.Ashani, H.Leader, S.Albeck, 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 12:03:11 2025

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