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Zinc in PDB 8p7v: 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: 8p7v was solved by O.Dym, N.Aggawal, 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) 25.46 / 1.74
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.7, 69.7, 186.479, 90, 90, 90
R / Rfree (%) 16.7 / 18.6

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 8p7v). 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: 8p7v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8p7v

Go back to Zinc Binding Sites List in 8p7v
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:16.2
occ:1.00
 O2 A:GB406 1.9 15.0 1.0
O2 A:FMT402 2.0 13.1 1.0
NE2 A:HIS57 2.1 13.7 1.0
NE2 A:HIS55 2.1 13.8 1.0
OD1 A:ASP301 2.6 15.0 1.0
C A:FMT402 3.0 15.3 1.0
CD2 A:HIS55 3.0 15.6 1.0
CE1 A:HIS57 3.0 15.0 1.0
CD2 A:HIS57 3.1 14.2 1.0
CE1 A:HIS55 3.1 14.3 1.0
P1 A:GB406 3.2 14.9 1.0
CG A:ASP301 3.3 15.7 1.0
C1 A:GB406 3.4 16.4 1.0
O1 A:FMT402 3.4 13.5 1.0
OD2 A:ASP301 3.5 16.3 1.0
O3 A:GB406 3.8 13.9 1.0
ZN A:ZN404 3.9 16.0 1.0
CG2 A:VAL101 4.0 13.8 1.0
NZ A:LYS169 4.0 11.9 1.0
ND1 A:HIS57 4.1 14.4 1.0
CG A:HIS55 4.2 14.7 1.0
ND1 A:HIS55 4.2 12.3 1.0
CE1 A:HIS230 4.2 16.9 1.0
CG A:HIS57 4.2 14.3 1.0
O1 A:GB406 4.4 19.3 1.0
NE2 A:HIS230 4.5 14.2 1.0
CB A:ASP301 4.6 14.4 1.0

Zinc binding site 2 out of 2 in 8p7v

Go back to Zinc Binding Sites List in 8p7v
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:16.0
occ:1.00
 O1 A:FMT402 2.0 13.5 1.0
NE2 A:HIS230 2.0 14.2 1.0
ND1 A:HIS201 2.0 13.3 1.0
O3 A:GB406 2.1 13.9 1.0
C A:FMT402 2.9 15.3 1.0
CE1 A:HIS201 3.0 15.3 1.0
P1 A:GB406 3.0 14.9 1.0
CD2 A:HIS230 3.0 14.5 1.0
CE1 A:HIS230 3.0 16.9 1.0
O2 A:GB406 3.1 15.0 1.0
CG A:HIS201 3.1 12.6 1.0
O2 A:FMT402 3.4 13.1 1.0
CB A:HIS201 3.4 12.6 1.0
NE1 A:TRP131 3.7 15.6 1.0
ZN A:ZN403 3.9 16.2 1.0
O1 A:GB406 4.0 19.3 1.0
NE2 A:HIS201 4.1 14.6 1.0
CG A:HIS230 4.1 11.9 1.0
ND1 A:HIS230 4.1 15.0 1.0
CD2 A:HIS201 4.2 14.8 1.0
NZ A:LYS169 4.2 11.9 1.0
C1 A:GB406 4.3 16.4 1.0
CD1 A:TRP131 4.3 14.3 1.0
CA A:HIS201 4.3 13.3 1.0
CE1 A:HIS55 4.3 14.3 1.0
NE2 A:HIS55 4.4 13.8 1.0
CE A:LYS169 4.5 12.3 1.0
OD2 A:ASP301 4.9 16.3 1.0
CE2 A:TRP131 4.9 13.3 1.0

Reference:

O.Dym, N.Aggawal, Y.Ashani, S.Albeck, T.Unger, S.Hamer Rogotner, I.Silman, J.L.Sussman. The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes To Be Published.
Page generated: Fri Aug 22 12:04:05 2025

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