Zinc in PDB 7z00: Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr

The structure of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr, PDB code: 7z00 was solved by S.Markusson, J.G.Hjorleifsson, P.Kursula, B.Asgeirsson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.39 / 2.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.25, 118.12, 84.4, 90, 90, 90
R / Rfree (%)	24.2 / 29.1

The structure of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr (pdb code 7z00). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr, PDB code: 7z00:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:67.4 occ:1.00 OD1 B:ASP273 1.8 64.2 1.0 O2 B:PO4606 2.0 69.5 1.0 OD2 B:ASP273 2.0 64.6 1.0 CG B:ASP273 2.1 66.1 1.0 O3 B:PO4606 2.2 64.0 1.0 NE2 B:HIS465 2.3 62.6 1.0 NE2 B:HIS277 2.3 59.5 1.0 P B:PO4606 2.6 66.8 1.0 CE1 B:HIS465 3.0 63.7 1.0 CD2 B:HIS277 3.1 61.4 1.0 HE1 B:HIS465 3.1 76.5 1.0 HD2 B:HIS277 3.1 73.8 1.0 HE1 B:HIS316 3.1 78.5 1.0 CD2 B:HIS465 3.3 61.1 1.0 CE1 B:HIS277 3.4 60.4 1.0 CB B:ASP273 3.5 63.5 1.0 O4 B:PO4606 3.5 66.3 1.0 HD2 B:HIS465 3.6 73.4 1.0 HE2 B:HIS316 3.6 81.3 1.0 HE1 B:HIS277 3.7 72.6 1.0 HB2 B:ASP273 3.7 76.2 1.0 O1 B:PO4606 3.7 64.9 1.0 CE1 B:HIS316 3.8 65.3 1.0 ZN B:ZN602 3.8 64.9 1.0 HG1 B:THR318 3.8 75.8 1.0 OD2 B:ASP12 3.8 68.6 1.0 HB3 B:ASP273 3.9 76.2 1.0 NE2 B:HIS316 4.0 67.7 1.0 ND1 B:HIS465 4.2 60.1 1.0 CG B:HIS277 4.3 59.5 1.0 HG21 B:THR318 4.3 74.3 1.0 OG1 B:THR318 4.3 63.1 1.0 CG B:HIS465 4.3 60.0 1.0 OG B:SER65 4.4 71.2 1.0 ND1 B:HIS277 4.4 58.5 1.0 CA B:ASP273 4.5 64.2 1.0 HA B:ASP273 4.6 77.1 1.0 O B:ASP273 4.7 65.9 1.0 C B:ASP273 4.7 64.4 1.0 HD1 B:TRP274 4.7 83.1 1.0 HG23 B:THR318 4.8 74.3 1.0 HD1 B:HIS465 4.9 72.2 1.0 CG2 B:THR318 4.9 61.9 1.0 ND1 B:HIS316 5.0 61.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Kbr within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:64.9 occ:1.00 OD2 B:ASP12 1.8 68.6 1.0 OG B:SER65 1.9 71.2 1.0 HE2 B:HIS316 1.9 81.3 1.0 OD2 B:ASP315 2.0 67.8 1.0 O3 B:PO4606 2.1 64.0 1.0 NE2 B:HIS316 2.3 67.7 1.0 CG B:ASP12 2.4 65.6 1.0 OD1 B:ASP12 2.6 63.4 1.0 CE1 B:HIS316 2.7 65.3 1.0 HE1 B:HIS316 2.7 78.5 1.0 CG B:ASP315 2.9 67.4 1.0 OD1 B:ASP315 3.2 66.1 1.0 CD2 B:HIS316 3.3 65.2 1.0 CB B:SER65 3.3 71.7 1.0 HB2 B:ASP273 3.4 76.2 1.0 P B:PO4606 3.5 66.8 1.0 HA B:ASP12 3.6 75.9 1.0 HA B:SER65 3.6 82.1 1.0 CB B:ASP12 3.6 63.0 1.0 HB3 B:SER65 3.7 86.2 1.0 HD2 B:HIS316 3.7 78.3 1.0 ND1 B:HIS316 3.7 61.8 1.0 ZN B:ZN601 3.8 67.4 1.0 HB2 B:SER65 3.9 86.2 1.0 CG B:ASP273 3.9 66.1 1.0 CA B:SER65 3.9 68.4 1.0 H B:GLY13 3.9 75.4 1.0 OD1 B:ASP273 3.9 64.2 1.0 CA B:ASP12 4.0 63.2 1.0 H B:SER65 4.0 81.3 1.0 CB B:ASP273 4.0 63.5 1.0 HB3 B:ASP12 4.0 75.7 1.0 CG B:HIS316 4.1 62.0 1.0 N B:GLY13 4.1 62.8 1.0 O4 B:PO4606 4.1 66.3 1.0 O1 B:PO4606 4.1 64.9 1.0 C B:ASP12 4.1 61.8 1.0 HB3 B:ASP273 4.1 76.2 1.0 HE1 B:HIS465 4.2 76.5 1.0 N B:SER65 4.2 67.7 1.0 CB B:ASP315 4.3 66.1 1.0 HB2 B:ASP12 4.3 75.7 1.0 MG B:MG604 4.4 62.5 1.0 OD2 B:ASP273 4.4 64.6 1.0 CE1 B:HIS465 4.4 63.7 1.0 HB2 B:ASP315 4.4 79.3 1.0 HG1 B:THR118 4.5 81.5 1.0 O2 B:PO4606 4.6 69.5 1.0 NE2 B:HIS465 4.6 62.6 1.0 HB3 B:ASP315 4.7 79.3 1.0 HG1 B:THR318 4.7 75.8 1.0 HA2 B:GLY13 4.8 74.0 1.0 O B:ASP12 4.8 62.4 1.0 OG1 B:THR118 4.8 67.8 1.0 CA B:GLY13 4.9 61.6 1.0 HA3 B:GLY13 4.9 74.0 1.0

S.Markusson, J.G.Hjorleifsson, P.Kursula, B.Asgeirsson. Structural Characterization of Functionally Important Chloride Binding Sites in the Marine Vibrio Alkaline Phosphatase. Biochemistry V. 61 2248 2022.
ISSN: ISSN 0006-2960
PubMed: 36194497
DOI: 10.1021/ACS.BIOCHEM.2C00438