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: Thu Oct 31 09:10:11 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy