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Zinc in PDB 8p7t: 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: 8p7t 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) 23.19 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.45, 69.45, 186.97, 90, 90, 90
R / Rfree (%) 15.9 / 18.4

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 8p7t). 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: 8p7t:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8p7t

Go back to Zinc Binding Sites List in 8p7t
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:16.4
occ:1.00
 O1 A:VX404 1.9 18.6 1.0
NE2 A:HIS57 2.1 12.3 1.0
O2 A:FMT401 2.1 12.5 1.0
NE2 A:HIS55 2.1 13.0 1.0
OD1 A:ASP301 2.3 13.7 1.0
CD2 A:HIS55 3.0 12.5 1.0
CE1 A:HIS57 3.0 13.9 1.0
CD2 A:HIS57 3.1 13.8 1.0
C A:FMT401 3.1 14.9 1.0
CG A:ASP301 3.1 15.7 1.0
CE1 A:HIS55 3.2 13.5 1.0
P1 A:VX404 3.2 21.7 1.0
OD2 A:ASP301 3.4 15.9 1.0
C2 A:VX404 3.6 37.7 1.0
O1 A:FMT401 3.6 13.2 1.0
O2 A:VX404 3.7 30.3 1.0
ZN A:ZN403 4.0 15.7 1.0
CG2 A:VAL101 4.0 12.3 1.0
O3 A:VX404 4.1 12.6 1.0
NZ A:LYS169 4.1 12.4 1.0
ND1 A:HIS57 4.1 13.1 1.0
CG A:HIS55 4.1 13.2 1.0
CE1 A:HIS230 4.2 15.5 1.0
CG A:HIS57 4.2 12.2 1.0
ND1 A:HIS55 4.2 11.7 1.0
CB A:ASP301 4.4 14.0 1.0
NE2 A:HIS230 4.5 13.8 1.0
C1 A:VX404 4.5 19.0 1.0
CA A:ASP301 4.9 13.3 1.0

Zinc binding site 2 out of 2 in 8p7t

Go back to Zinc Binding Sites List in 8p7t
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:15.7
occ:1.00
 O1 A:FMT401 1.9 13.2 1.0
NE2 A:HIS230 2.0 13.8 1.0
O3 A:VX404 2.0 12.6 1.0
ND1 A:HIS201 2.1 14.0 1.0
P1 A:VX404 2.9 21.7 1.0
C A:FMT401 3.0 14.9 1.0
CD2 A:HIS230 3.0 14.1 1.0
CE1 A:HIS201 3.0 15.7 1.0
O1 A:VX404 3.0 18.6 1.0
CE1 A:HIS230 3.0 15.5 1.0
CG A:HIS201 3.1 14.6 1.0
O2 A:FMT401 3.4 12.5 1.0
CB A:HIS201 3.5 11.7 1.0
NE1 A:TRP131 3.7 16.4 1.0
ZN A:ZN402 4.0 16.4 1.0
NE2 A:HIS201 4.1 13.9 1.0
CG A:HIS230 4.1 13.0 1.0
ND1 A:HIS230 4.1 16.1 1.0
O2 A:VX404 4.1 30.3 1.0
C1 A:VX404 4.2 19.0 1.0
CD2 A:HIS201 4.2 15.3 1.0
NZ A:LYS169 4.2 12.4 1.0
CD1 A:TRP131 4.3 15.0 1.0
CA A:HIS201 4.3 12.3 1.0
CE1 A:HIS55 4.4 13.5 1.0
NE2 A:HIS55 4.4 13.0 1.0
CE A:LYS169 4.6 13.1 1.0
OD2 A:ASP301 4.8 15.9 1.0
CE2 A:TRP131 4.9 14.8 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 12:04:04 2025

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