Zinc in PDB 7yzz: Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 M Nacl

The structure of Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 M Nacl, PDB code: 7yzz 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)	39.31 / 1.29
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.08, 84.74, 85.23, 90, 113.48, 90
R / Rfree (%)	12.1 / 13.9

The structure of Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 M Nacl also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 M Nacl (pdb code 7yzz). 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 0.5 M Nacl, PDB code: 7yzz:
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 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:16.5 occ:1.00 O4 A:PO4613 2.0 18.8 1.0 NE2 A:HIS277 2.1 15.5 1.0 NE2 A:HIS465 2.1 14.8 1.0 OD1 A:ASP273 2.1 16.6 1.0 OD2 A:ASP273 2.5 17.9 1.0 CG A:ASP273 2.6 16.0 1.0 O3 A:PO4613 2.7 18.4 1.0 P A:PO4613 2.9 16.7 1.0 CD2 A:HIS277 3.0 15.6 1.0 CE1 A:HIS465 3.0 14.4 1.0 CE1 A:HIS277 3.1 16.3 1.0 CD2 A:HIS465 3.1 15.4 1.0 HD2 A:HIS277 3.2 18.7 1.0 HE1 A:HIS465 3.2 17.2 1.0 HE1 A:HIS277 3.3 19.6 1.0 HD2 A:HIS465 3.3 18.4 1.0 HO1 A:EDO605 3.4 41.0 1.0 HE1 A:HIS316 3.5 20.0 1.0 H11 A:EDO605 3.8 43.6 1.0 HG1 A:THR318 3.8 22.1 1.0 O2 A:PO4613 3.8 16.8 1.0 HH B:TYR325 3.9 22.3 1.0 ZN A:ZN602 4.1 17.6 1.0 CE1 A:HIS316 4.1 16.7 1.0 O1 A:PO4613 4.1 17.8 1.0 O1 A:EDO605 4.1 34.2 1.0 CB A:ASP273 4.2 15.6 1.0 ND1 A:HIS465 4.2 15.7 1.0 ND1 A:HIS277 4.2 15.3 1.0 CG A:HIS277 4.2 15.0 1.0 CG A:HIS465 4.2 15.8 1.0 O A:HOH765 4.2 16.9 1.0 HG21 A:THR318 4.2 21.2 1.0 NE2 A:HIS316 4.3 17.0 1.0 OG1 A:THR318 4.3 18.4 1.0 C1 A:EDO605 4.4 36.4 1.0 O B:HOH923 4.4 22.3 1.0 HB2 A:ASP273 4.4 18.7 1.0 HG23 A:THR318 4.5 21.2 1.0 H12 A:EDO605 4.6 43.6 1.0 HB3 A:ASP273 4.6 18.7 1.0 OH B:TYR325 4.7 18.6 1.0 OD1 A:ASP12 4.7 15.9 1.0 CG2 A:THR318 4.8 17.7 1.0 O A:ASP273 4.9 15.7 1.0 HD1 A:TRP274 4.9 20.2 1.0 HD1 A:HIS465 4.9 18.8 1.0 HD1 A:HIS277 4.9 18.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:17.6 occ:1.00 O3 A:PO4613 1.9 18.4 1.0 OD1 A:ASP12 2.0 15.9 1.0 OD2 A:ASP315 2.0 18.1 1.0 NE2 A:HIS316 2.1 17.0 1.0 HB2 A:SER65 2.5 23.9 1.0 CG A:ASP12 2.7 15.7 1.0 OD2 A:ASP12 2.9 16.2 1.0 CG A:ASP315 2.9 17.5 1.0 CE1 A:HIS316 3.0 16.7 1.0 CD2 A:HIS316 3.0 16.8 1.0 OD1 A:ASP315 3.1 16.8 1.0 HE1 A:HIS316 3.2 20.0 1.0 HD2 A:HIS316 3.2 20.1 1.0 P A:PO4613 3.3 16.7 1.0 CB A:SER65 3.4 19.9 1.0 HE1 A:HIS465 3.7 17.2 1.0 OD1 A:ASP273 3.7 16.6 1.0 OG A:SER65 3.7 24.2 1.0 HA A:SER65 3.8 21.5 1.0 HG A:SER65 3.8 29.0 0.5 O2 A:PO4613 3.9 16.8 1.0 HB2 A:ASP273 3.9 18.7 1.0 H A:SER65 3.9 21.2 1.0 CG A:ASP273 4.0 16.0 1.0 H A:GLY13 4.0 18.5 1.0 CA A:SER65 4.0 17.9 1.0 CE1 A:HIS465 4.0 14.4 1.0 O1 A:PO4613 4.0 17.8 1.0 HB3 A:SER65 4.1 23.9 1.0 ZN A:ZN601 4.1 16.5 1.0 ND1 A:HIS316 4.1 16.7 1.0 CB A:ASP12 4.1 15.4 1.0 HA A:ASP12 4.1 18.0 1.0 CG A:HIS316 4.1 16.9 1.0 N A:SER65 4.1 17.7 1.0 NE2 A:HIS465 4.2 14.8 1.0 N A:GLY13 4.3 15.4 1.0 CB A:ASP315 4.3 17.3 1.0 O4 A:PO4613 4.3 18.8 1.0 HB2 A:ASP315 4.4 20.7 1.0 CB A:ASP273 4.4 15.6 1.0 OD2 A:ASP273 4.5 17.9 1.0 CA A:ASP12 4.5 15.0 1.0 C A:ASP12 4.5 15.1 1.0 HB3 A:ASP12 4.5 18.4 1.0 O A:HOH799 4.6 16.7 1.0 O A:HOH701 4.6 24.2 0.5 HB2 A:ASP12 4.7 18.4 1.0 HB3 A:ASP273 4.7 18.7 1.0 HB3 A:ASP315 4.7 20.7 1.0 MG A:MG603 4.7 16.4 1.0 HA2 A:GLY13 4.7 18.2 1.0 O A:HOH765 4.7 16.9 1.0 HG1 A:THR318 4.8 22.1 1.0 ND1 A:HIS465 4.8 15.7 1.0 HD1 A:HIS316 4.9 20.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:15.6 occ:1.00 O4 B:PO4606 2.0 17.4 1.0 OD1 B:ASP273 2.1 16.9 1.0 NE2 B:HIS277 2.1 14.1 1.0 NE2 B:HIS465 2.1 15.0 1.0 OD2 B:ASP273 2.6 17.4 1.0 CG B:ASP273 2.6 16.8 1.0 O1 B:PO4606 2.7 17.5 1.0 P B:PO4606 2.9 16.0 1.0 CE1 B:HIS277 3.0 15.9 1.0 CD2 B:HIS277 3.0 14.0 1.0 CE1 B:HIS465 3.1 13.4 1.0 CD2 B:HIS465 3.1 14.3 1.0 HE1 B:HIS277 3.2 19.1 1.0 HE1 B:HIS465 3.2 16.1 1.0 HD2 B:HIS277 3.2 16.8 1.0 HD2 B:HIS465 3.3 17.1 1.0 HE1 B:HIS316 3.4 19.0 1.0 HG1 B:THR318 3.8 20.7 1.0 O3 B:PO4606 3.8 15.4 1.0 ZN B:ZN602 4.0 16.8 1.0 CE1 B:HIS316 4.1 15.8 1.0 O2 B:PO4606 4.1 16.0 1.0 O B:HOH741 4.1 31.7 1.0 ND1 B:HIS277 4.1 15.1 1.0 CB B:ASP273 4.1 16.3 1.0 HG21 B:THR318 4.2 20.2 1.0 CG B:HIS277 4.2 14.0 1.0 ND1 B:HIS465 4.2 14.2 1.0 O B:HOH768 4.2 16.1 1.0 CG B:HIS465 4.2 14.0 1.0 OG1 B:THR318 4.3 17.3 1.0 NE2 B:HIS316 4.3 15.7 1.0 HB2 B:ASP273 4.4 19.5 1.0 O A:HOH861 4.4 20.4 1.0 HG23 B:THR318 4.5 20.2 1.0 HB3 B:ASP273 4.6 19.5 1.0 OD1 B:ASP12 4.6 15.3 1.0 CG2 B:THR318 4.7 16.9 1.0 OH A:TYR325 4.7 17.9 1.0 O B:ASP273 4.8 15.6 1.0 HD1 B:HIS277 4.9 18.1 1.0 HD1 B:HIS465 4.9 17.0 1.0 HD1 B:TRP274 5.0 20.3 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:16.8 occ:1.00 O1 B:PO4606 1.8 17.5 1.0 OD1 B:ASP12 1.9 15.3 1.0 OD2 B:ASP315 2.0 16.5 1.0 NE2 B:HIS316 2.1 15.7 1.0 HB2 B:SER65 2.5 23.3 1.0 CG B:ASP12 2.7 15.0 1.0 OD2 B:ASP12 2.9 15.4 1.0 CG B:ASP315 2.9 16.3 1.0 CE1 B:HIS316 3.0 15.8 1.0 CD2 B:HIS316 3.1 15.0 1.0 OD1 B:ASP315 3.1 15.8 1.0 HE1 B:HIS316 3.2 19.0 1.0 HD2 B:HIS316 3.3 17.9 1.0 P B:PO4606 3.3 16.0 1.0 CB B:SER65 3.4 19.4 1.0 OD1 B:ASP273 3.6 16.9 1.0 HE1 B:HIS465 3.7 16.1 1.0 HG B:SER65 3.7 28.7 0.3 OG B:SER65 3.7 23.9 1.0 HA B:SER65 3.8 19.7 1.0 HB2 B:ASP273 3.9 19.5 1.0 O3 B:PO4606 3.9 15.4 1.0 H B:GLY13 3.9 18.0 1.0 CG B:ASP273 4.0 16.8 1.0 H B:SER65 4.0 19.7 1.0 CE1 B:HIS465 4.0 13.4 1.0 CA B:SER65 4.0 16.4 1.0 O2 B:PO4606 4.0 16.0 1.0 ZN B:ZN601 4.0 15.6 1.0 ND1 B:HIS316 4.1 15.9 1.0 HA B:ASP12 4.1 17.0 1.0 CB B:ASP12 4.1 15.0 1.0 HB3 B:SER65 4.1 23.3 1.0 CG B:HIS316 4.1 15.2 1.0 N B:SER65 4.2 16.4 1.0 NE2 B:HIS465 4.2 15.0 1.0 N B:GLY13 4.2 15.0 1.0 O4 B:PO4606 4.3 17.4 1.0 CB B:ASP315 4.3 16.1 1.0 HB2 B:ASP315 4.4 19.3 1.0 CB B:ASP273 4.4 16.3 1.0 CA B:ASP12 4.5 14.2 1.0 OD2 B:ASP273 4.5 17.4 1.0 O B:HOH701 4.5 25.4 0.5 C B:ASP12 4.5 14.1 1.0 HB3 B:ASP12 4.6 17.9 1.0 O B:HOH772 4.6 15.7 1.0 HB3 B:ASP273 4.6 19.5 1.0 HB2 B:ASP12 4.7 17.9 1.0 MG B:MG603 4.7 15.4 1.0 HG1 B:THR318 4.7 20.7 1.0 HB3 B:ASP315 4.7 19.3 1.0 HA2 B:GLY13 4.7 17.9 1.0 O B:HOH768 4.8 16.1 1.0 ND1 B:HIS465 4.8 14.2 1.0 HD1 B:HIS316 4.9 19.1 1.0 CA B:GLY13 5.0 15.0 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