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Zinc in PDB 8p7f: 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: 8p7f 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) 40.26 / 2.00
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.7, 93.67, 44.59, 90, 90, 90
R / Rfree (%) 20.4 / 24

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 8p7f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was 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: 8p7f:

Zinc binding site 1 out of 1 in 8p7f

Go back to Zinc Binding Sites List in 8p7f
Zinc binding site 1 out of 1 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:Zn401

b:33.5
occ:0.80
 OD2 A:ASP301 1.8 36.0 1.0
NE2 A:HIS57 2.1 37.2 1.0
ND1 A:HIS55 2.2 33.2 1.0
O A:HIS55 2.3 32.2 1.0
CG A:ASP301 2.7 39.3 1.0
OD1 A:ASP301 2.9 39.0 1.0
CD2 A:HIS57 3.0 38.1 1.0
CE1 A:HIS55 3.1 35.4 1.0
CE1 A:HIS57 3.1 38.1 1.0
CG A:HIS55 3.2 31.3 1.0
C A:HIS55 3.3 33.3 1.0
CB A:HIS55 3.6 30.4 1.0
O A:PHE306 4.0 47.8 1.0
CA A:HIS55 4.0 31.3 1.0
CB A:ASP301 4.1 39.0 1.0
CG A:HIS57 4.2 40.8 1.0
ND1 A:HIS57 4.2 38.3 1.0
NE2 A:HIS55 4.2 37.9 1.0
N A:GLU56 4.3 31.4 1.0
O A:HOH540 4.3 39.4 1.0
CD2 A:HIS55 4.3 33.8 1.0
OG A:SER299 4.4 36.0 1.0
CG2 A:VAL101 4.5 28.5 1.0
CA A:GLU56 4.6 33.2 1.0
C A:PHE306 4.7 46.9 1.0
C A:GLU56 4.9 34.4 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 D Struct 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37860961
DOI: 10.1107/S2059798323007672
Page generated: Thu Dec 28 13:32:16 2023

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