Zinc in PDB 7qow: Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl

The structure of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl, PDB code: 7qow 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)	43.00 / 1.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.202, 85.993, 85.139, 90, 113.37, 90
R / Rfree (%)	13.1 / 16

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

Chlorine	(Cl)	3 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Zinc atom in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl (pdb code 7qow). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl, PDB code: 7qow:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl


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 Nacl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:14.9 occ:1.00 O3 A:PO4604 2.0 16.0 1.0 NE2 A:HIS277 2.1 14.6 1.0 NE2 A:HIS465 2.1 13.7 1.0 OD1 A:ASP273 2.1 14.5 1.0 OD2 A:ASP273 2.5 15.2 1.0 O4 A:PO4604 2.6 16.6 1.0 CG A:ASP273 2.6 14.6 1.0 P A:PO4604 2.9 15.4 1.0 CE1 A:HIS277 3.0 14.3 1.0 CD2 A:HIS277 3.1 14.6 1.0 CE1 A:HIS465 3.1 14.1 1.0 CD2 A:HIS465 3.1 14.5 1.0 HE1 A:HIS277 3.2 17.1 1.0 HE1 A:HIS465 3.2 16.9 1.0 HD2 A:HIS277 3.2 17.5 1.0 HD2 A:HIS465 3.3 17.3 1.0 HE1 A:HIS316 3.5 17.4 1.0 HO2 A:EDO605 3.5 27.8 1.0 O2 A:PO4604 3.8 14.7 1.0 H22 A:EDO605 3.8 30.0 1.0 HG1 A:THR318 4.0 17.8 1.0 O1 A:PO4604 4.0 16.0 1.0 ZN A:ZN602 4.0 15.4 1.0 CE1 A:HIS316 4.1 14.5 1.0 ND1 A:HIS277 4.1 14.5 1.0 CB A:ASP273 4.2 14.2 1.0 CG A:HIS277 4.2 14.1 1.0 ND1 A:HIS465 4.2 14.7 1.0 O2 A:EDO605 4.2 23.2 1.0 HG21 A:THR318 4.2 19.7 1.0 CG A:HIS465 4.3 14.5 1.0 NE2 A:HIS316 4.3 14.5 1.0 OG1 A:THR318 4.3 14.9 1.0 HB2 A:ASP273 4.4 17.1 1.0 O B:HOH1416 4.5 17.5 1.0 C2 A:EDO605 4.5 25.0 1.0 HG23 A:THR318 4.6 19.7 1.0 HB3 A:ASP273 4.6 17.1 1.0 OH B:TYR325 4.6 16.8 1.0 OD1 A:ASP12 4.7 14.3 1.0 CG2 A:THR318 4.8 16.5 1.0 O A:ASP273 4.9 15.1 1.0 HD1 A:TRP274 4.9 17.5 1.0 HD1 A:HIS277 4.9 17.4 1.0 OG A:SER65 4.9 16.5 0.4 HD1 A:HIS465 5.0 17.6 1.0 HH B:TYR325 5.0 20.1 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl


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 Nacl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:15.4 occ:1.00 O4 A:PO4604 1.9 16.6 1.0 OD1 A:ASP12 1.9 14.3 1.0 NE2 A:HIS316 2.1 14.5 1.0 OD2 A:ASP315 2.1 14.8 1.0 OG A:SER65 2.3 16.5 0.4 HB2 A:SER65 2.4 19.3 0.6 CG A:ASP12 2.7 14.0 1.0 OD2 A:ASP12 2.9 14.9 1.0 CG A:ASP315 3.0 14.2 1.0 CE1 A:HIS316 3.0 14.5 1.0 CD2 A:HIS316 3.0 13.9 1.0 OD1 A:ASP315 3.2 14.8 1.0 HE1 A:HIS316 3.2 17.4 1.0 HD2 A:HIS316 3.2 16.6 1.0 CB A:SER65 3.3 16.1 0.6 P A:PO4604 3.3 15.4 1.0 CB A:SER65 3.5 14.5 0.4 HA A:SER65 3.5 17.1 0.4 HE1 A:HIS465 3.6 16.9 1.0 OD1 A:ASP273 3.7 14.5 1.0 OG A:SER65 3.7 18.0 0.6 HG A:SER65 3.8 21.6 0.6 HA A:SER65 3.8 18.5 0.6 H A:SER65 3.9 17.6 0.6 O2 A:PO4604 3.9 14.7 1.0 H A:SER65 3.9 17.0 0.4 CA A:SER65 3.9 14.2 0.4 HB2 A:ASP273 3.9 17.1 1.0 CE1 A:HIS465 4.0 14.1 1.0 H A:GLY13 4.0 16.4 1.0 HB3 A:SER65 4.0 19.3 0.6 CA A:SER65 4.0 15.4 0.6 CG A:ASP273 4.0 14.6 1.0 O1 A:PO4604 4.0 16.0 1.0 ZN A:ZN601 4.0 14.9 1.0 HB3 A:SER65 4.0 17.3 0.4 HB2 A:SER65 4.1 17.3 0.4 N A:SER65 4.1 14.7 0.6 CB A:ASP12 4.1 12.7 1.0 ND1 A:HIS316 4.1 14.0 1.0 N A:SER65 4.1 14.2 0.4 HA A:ASP12 4.1 15.8 1.0 CG A:HIS316 4.1 13.9 1.0 NE2 A:HIS465 4.2 13.7 1.0 N A:GLY13 4.3 13.7 1.0 O3 A:PO4604 4.3 16.0 1.0 CB A:ASP315 4.3 13.8 1.0 HB2 A:ASP315 4.4 16.5 1.0 OD2 A:ASP273 4.4 15.2 1.0 CB A:ASP273 4.5 14.2 1.0 CA A:ASP12 4.5 13.2 1.0 HB3 A:ASP12 4.6 15.2 1.0 C A:ASP12 4.6 13.1 1.0 O A:HOH888 4.6 14.8 1.0 HB2 A:ASP12 4.7 15.2 1.0 MG A:MG603 4.7 14.6 1.0 HB3 A:ASP273 4.7 17.1 1.0 HA2 A:GLY13 4.8 16.2 1.0 HB3 A:ASP315 4.8 16.5 1.0 ND1 A:HIS465 4.8 14.7 1.0 HD1 A:HIS316 4.9 16.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:15.7 occ:1.00 O4 B:PO41104 2.0 17.1 1.0 OD1 B:ASP273 2.1 15.7 1.0 NE2 B:HIS277 2.1 15.0 1.0 NE2 B:HIS465 2.1 14.7 1.0 OD2 B:ASP273 2.5 16.8 1.0 O1 B:PO41104 2.6 17.0 1.0 CG B:ASP273 2.6 15.8 1.0 P B:PO41104 2.9 15.9 1.0 CD2 B:HIS277 3.0 14.6 1.0 CE1 B:HIS277 3.1 15.8 1.0 CE1 B:HIS465 3.1 15.1 1.0 CD2 B:HIS465 3.1 15.0 1.0 HD2 B:HIS277 3.2 17.4 1.0 HE1 B:HIS465 3.2 18.0 1.0 HE1 B:HIS277 3.3 18.9 1.0 HD2 B:HIS465 3.3 17.9 1.0 HE1 B:HIS316 3.4 17.5 1.0 O3 B:PO41104 3.8 15.7 1.0 HO2 B:EDO1105 3.8 26.1 1.0 HG1 B:THR318 3.9 19.3 1.0 H22 B:EDO1105 4.0 28.3 1.0 ZN B:ZN1103 4.0 16.4 1.0 CE1 B:HIS316 4.1 14.6 1.0 O2 B:PO41104 4.1 16.5 1.0 CB B:ASP273 4.1 16.0 1.0 ND1 B:HIS277 4.1 15.9 1.0 O2 B:EDO1105 4.2 21.8 1.0 CG B:HIS277 4.2 16.1 1.0 ND1 B:HIS465 4.2 14.9 1.0 O B:HOH1334 4.2 15.9 1.0 CG B:HIS465 4.2 15.0 1.0 HG22 B:THR318 4.3 19.3 1.0 NE2 B:HIS316 4.3 14.6 1.0 OG1 B:THR318 4.3 16.1 1.0 H31 B:TRS1106 4.4 62.9 0.6 H31 B:TRS1106 4.4 64.2 0.4 HG21 B:THR318 4.4 19.3 1.0 HB2 B:ASP273 4.4 19.1 1.0 O A:HOH920 4.5 18.1 1.0 HB3 B:ASP273 4.6 19.1 1.0 C2 B:EDO1105 4.6 23.6 1.0 OH A:TYR325 4.6 17.5 1.0 OD1 B:ASP12 4.7 15.6 1.0 CG2 B:THR318 4.7 16.1 1.0 O B:ASP273 4.8 15.5 1.0 HD1 B:HIS277 4.9 19.0 1.0 HD1 B:TRP274 4.9 21.0 1.0 OG B:SER65 4.9 17.7 0.5 HD1 B:HIS465 5.0 17.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1103 b:16.4 occ:1.00 O1 B:PO41104 1.9 17.0 1.0 OD1 B:ASP12 1.9 15.6 1.0 NE2 B:HIS316 2.1 14.6 1.0 OD2 B:ASP315 2.1 15.8 1.0 OG B:SER65 2.2 17.7 0.5 HB2 B:SER65 2.3 18.8 0.5 CG B:ASP12 2.7 15.7 1.0 OD2 B:ASP12 2.9 15.8 1.0 CG B:ASP315 3.0 15.3 1.0 CE1 B:HIS316 3.0 14.6 1.0 CD2 B:HIS316 3.1 14.3 1.0 HE1 B:HIS316 3.2 17.5 1.0 OD1 B:ASP315 3.2 15.6 1.0 CB B:SER65 3.2 15.7 0.5 HD2 B:HIS316 3.3 17.1 1.0 P B:PO41104 3.3 15.9 1.0 CB B:SER65 3.5 16.3 0.5 HA B:SER65 3.6 19.1 0.5 HE1 B:HIS465 3.6 18.0 1.0 OG B:SER65 3.6 17.0 0.5 HG B:SER65 3.7 20.4 0.5 OD1 B:ASP273 3.7 15.7 1.0 HA B:SER65 3.8 18.2 0.5 O3 B:PO41104 3.8 15.7 1.0 HB3 B:SER65 3.9 18.8 0.5 H B:SER65 3.9 18.4 0.5 CA B:SER65 3.9 15.9 0.5 H B:SER65 3.9 18.0 0.5 HB2 B:ASP273 3.9 19.1 1.0 H B:GLY13 3.9 17.6 1.0 CE1 B:HIS465 3.9 15.1 1.0 CA B:SER65 4.0 15.2 0.5 CG B:ASP273 4.0 15.8 1.0 O2 B:PO41104 4.0 16.5 1.0 ZN B:ZN1102 4.0 15.7 1.0 HB2 B:SER65 4.0 19.5 0.5 HB3 B:SER65 4.0 19.5 0.5 ND1 B:HIS316 4.1 14.4 1.0 N B:SER65 4.1 15.4 0.5 CB B:ASP12 4.1 14.8 1.0 N B:SER65 4.1 15.1 0.5 HA B:ASP12 4.1 17.1 1.0 CG B:HIS316 4.2 14.7 1.0 NE2 B:HIS465 4.2 14.7 1.0 N B:GLY13 4.3 14.7 1.0 O4 B:PO41104 4.3 17.1 1.0 CB B:ASP315 4.3 14.6 1.0 HB2 B:ASP315 4.4 17.4 1.0 CB B:ASP273 4.4 16.0 1.0 OD2 B:ASP273 4.4 16.8 1.0 CA B:ASP12 4.5 14.3 1.0 O B:HOH1201 4.5 19.6 0.6 HB3 B:ASP12 4.6 17.7 1.0 C B:ASP12 4.6 14.6 1.0 O B:HOH1327 4.6 15.2 1.0 HB2 B:ASP12 4.7 17.7 1.0 HB3 B:ASP273 4.7 19.1 1.0 MG B:MG1109 4.7 15.3 1.0 O B:HOH1334 4.8 15.9 1.0 ND1 B:HIS465 4.8 14.9 1.0 HA2 B:GLY13 4.8 17.6 1.0 HB3 B:ASP315 4.8 17.4 1.0 HD1 B:HIS316 4.9 17.3 1.0 HG1 B:THR318 4.9 19.3 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