Zinc in PDB 8p7h: The Impact of Molecular Variants, Crystallization Conditions and Space Group on Structure-Ligand Complexes: A Case Study on Bacterial Phosphotriesterase Variants and Complexes

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: 8p7h 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)	25.92 / 1.77
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	69.669, 69.669, 186.83, 90, 90, 90
R / Rfree (%)	15.8 / 18.9

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 8p7h). 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: 8p7h:
Jump to Zinc binding site number: 1; 2;

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:15.2 occ:1.00 O09 A:X3B408 2.0 13.1 1.0 NE2 A:HIS57 2.0 10.2 1.0 NE2 A:HIS55 2.1 12.3 1.0 O2 A:FMT401 2.1 12.6 1.0 OD1 A:ASP301 2.3 13.5 1.0 CD2 A:HIS55 3.0 13.1 1.0 CE1 A:HIS57 3.0 12.2 1.0 C07 A:X3B408 3.0 9.8 1.0 C02 A:X3B408 3.0 20.0 1.0 CD2 A:HIS57 3.1 13.5 1.0 C A:FMT401 3.1 14.5 1.0 CG A:ASP301 3.1 14.8 1.0 CE1 A:HIS55 3.2 11.4 1.0 OD2 A:ASP301 3.4 15.1 1.0 O1 A:FMT401 3.5 12.2 1.0 ZN A:ZN403 3.8 14.9 1.0 O01 A:X3B408 3.9 14.2 1.0 CG2 A:VAL101 4.0 11.3 1.0 O03 A:X3B408 4.0 20.0 1.0 NZ A:LYS169 4.1 11.5 1.0 ND1 A:HIS57 4.1 12.5 1.0 CG A:HIS55 4.2 12.0 1.0 CE1 A:HIS230 4.2 13.9 1.0 CG A:HIS57 4.2 14.0 1.0 ND1 A:HIS55 4.2 9.6 1.0 C06 A:X3B408 4.2 26.4 1.0 C04 A:X3B408 4.3 33.6 1.0 NE2 A:HIS230 4.4 12.0 1.0 CB A:ASP301 4.5 10.8 1.0 O05 A:X3B408 4.5 39.4 1.0 C08 A:X3B408 4.9 30.2 1.0 CA A:ASP301 5.0 12.3 1.0

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:14.9 occ:1.00 O1 A:FMT401 1.9 12.2 1.0 NE2 A:HIS230 2.1 12.0 1.0 O01 A:X3B408 2.1 14.2 1.0 ND1 A:HIS201 2.1 12.5 1.0 O09 A:X3B408 2.5 13.1 1.0 C02 A:X3B408 2.8 20.0 1.0 C A:FMT401 2.9 14.5 1.0 CE1 A:HIS201 3.0 14.0 1.0 CD2 A:HIS230 3.0 12.5 1.0 CE1 A:HIS230 3.1 13.9 1.0 CG A:HIS201 3.1 12.7 1.0 O2 A:FMT401 3.3 12.6 1.0 CB A:HIS201 3.5 11.0 1.0 O03 A:X3B408 3.7 20.0 1.0 C07 A:X3B408 3.8 9.8 1.0 ZN A:ZN402 3.8 15.2 1.0 NE1 A:TRP131 3.9 18.4 1.0 NE2 A:HIS201 4.1 15.2 1.0 ND1 A:HIS230 4.2 14.4 1.0 CG A:HIS230 4.2 11.2 1.0 O A:HOH502 4.2 25.2 1.0 NZ A:LYS169 4.2 11.5 1.0 CD2 A:HIS201 4.2 15.1 1.0 CE1 A:HIS55 4.2 11.4 1.0 NE2 A:HIS55 4.3 12.3 1.0 CA A:HIS201 4.3 10.8 1.0 CD1 A:TRP131 4.5 18.1 1.0 CE A:LYS169 4.6 10.6 1.0 OD2 A:ASP301 4.6 15.1 1.0

O.Dym, N.Aggarwal, 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.