Zinc in PDB 7qp8: Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes

The structure of Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes, PDB code: 7qp8 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)	44.10 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.81, 85.05, 85.5, 90, 113.9, 90
R / Rfree (%)	15 / 18.1

The structure of Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Magnesium	(Mg)	6 atoms

The binding sites of Zinc atom in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes (pdb code 7qp8). 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 with Bound Hepes, PDB code: 7qp8:
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 with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:24.8 occ:1.00 O2 A:PO4612 2.0 25.6 1.0 OD1 A:ASP273 2.1 23.6 1.0 NE2 A:HIS465 2.2 24.6 1.0 NE2 A:HIS277 2.2 24.4 1.0 OD2 A:ASP273 2.5 24.5 1.0 CG A:ASP273 2.6 23.7 1.0 O4 A:PO4612 2.6 24.9 1.0 P A:PO4612 2.8 25.5 1.0 CD2 A:HIS277 3.0 24.4 1.0 HD2 A:HIS277 3.0 29.4 1.0 CD2 A:HIS465 3.1 24.1 1.0 CE1 A:HIS465 3.2 24.7 1.0 HD2 A:HIS465 3.3 29.0 1.0 HE1 A:HIS316 3.3 28.6 1.0 CE1 A:HIS277 3.3 24.3 1.0 HE1 A:HIS465 3.4 29.6 1.0 HE1 A:HIS277 3.6 29.3 1.0 HG1 A:THR318 3.6 28.2 1.0 H31 A:EPE609 3.6 43.5 1.0 O3 A:PO4612 3.7 25.1 1.0 CE1 A:HIS316 4.0 23.8 1.0 H32 A:EPE609 4.0 43.5 1.0 O1 A:PO4612 4.0 25.8 1.0 H71 A:EPE609 4.0 45.5 1.0 CB A:ASP273 4.1 23.9 1.0 ZN A:ZN602 4.1 25.8 1.0 OG1 A:THR318 4.1 23.4 1.0 HG21 A:THR318 4.1 28.2 1.0 NE2 A:HIS316 4.2 24.3 1.0 CG A:HIS277 4.2 23.6 1.0 ND1 A:HIS465 4.3 23.9 1.0 O A:HOH803 4.3 25.1 1.0 CG A:HIS465 4.3 24.0 1.0 HB2 A:ASP273 4.3 28.7 1.0 C3 A:EPE609 4.3 36.2 1.0 ND1 A:HIS277 4.4 24.1 1.0 O A:HOH950 4.4 47.8 1.0 O A:HOH825 4.4 24.0 1.0 HB3 A:ASP273 4.5 28.7 1.0 HG23 A:THR318 4.6 28.2 1.0 OD1 A:ASP12 4.6 23.4 1.0 CG2 A:THR318 4.7 23.5 1.0 O A:ASP273 4.8 23.5 1.0 OH B:TYR325 4.9 23.5 1.0 HD1 A:TRP274 4.9 30.5 1.0 H22 A:EPE609 4.9 43.5 1.0 CA A:ASP273 5.0 23.6 1.0 OG A:SER65 5.0 30.1 1.0 HA A:ASP273 5.0 28.4 1.0 C A:ASP273 5.0 23.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:25.8 occ:1.00 O4 A:PO4612 1.9 24.9 1.0 OD1 A:ASP12 1.9 23.4 1.0 OG A:SER65 2.0 30.1 1.0 OD2 A:ASP315 2.0 25.8 1.0 NE2 A:HIS316 2.2 24.3 1.0 CG A:ASP12 2.7 22.8 1.0 OD2 A:ASP12 2.9 22.5 1.0 CG A:ASP315 2.9 24.8 1.0 CE1 A:HIS316 3.0 23.8 1.0 CD2 A:HIS316 3.1 23.7 1.0 HE1 A:HIS316 3.2 28.6 1.0 OD1 A:ASP315 3.2 24.6 1.0 CB A:SER65 3.3 27.4 1.0 P A:PO4612 3.3 25.5 1.0 HD2 A:HIS316 3.4 28.5 1.0 HA A:SER65 3.5 30.6 1.0 HB2 A:SER65 3.7 32.9 1.0 OD1 A:ASP273 3.7 23.6 1.0 CA A:SER65 3.8 25.4 1.0 H A:SER65 3.9 30.0 1.0 HB3 A:SER65 3.9 32.9 1.0 O3 A:PO4612 3.9 25.1 1.0 HE1 A:HIS465 3.9 29.6 1.0 O1 A:PO4612 3.9 25.8 1.0 HB2 A:ASP273 3.9 28.7 1.0 H A:GLY13 3.9 26.9 1.0 N A:SER65 4.0 25.0 1.0 CG A:ASP273 4.0 23.7 1.0 ND1 A:HIS316 4.1 23.1 1.0 ZN A:ZN601 4.1 24.8 1.0 CB A:ASP12 4.1 22.6 1.0 HA A:ASP12 4.1 26.5 1.0 CG A:HIS316 4.1 23.2 1.0 CE1 A:HIS465 4.2 24.7 1.0 N A:GLY13 4.3 22.4 1.0 CB A:ASP315 4.3 24.7 1.0 O A:HOH781 4.3 33.7 1.0 O2 A:PO4612 4.4 25.6 1.0 HB2 A:ASP315 4.4 29.7 1.0 CB A:ASP273 4.4 23.9 1.0 NE2 A:HIS465 4.4 24.6 1.0 O A:HOH866 4.5 20.8 1.0 CA A:ASP12 4.5 22.0 1.0 OD2 A:ASP273 4.5 24.5 1.0 HB3 A:ASP12 4.6 27.2 1.0 C A:ASP12 4.6 21.7 1.0 HB3 A:ASP273 4.6 28.7 1.0 HB2 A:ASP12 4.7 27.2 1.0 HB3 A:ASP315 4.7 29.7 1.0 HG1 A:THR318 4.8 28.2 1.0 MG A:MG603 4.8 22.4 1.0 HD1 A:HIS316 4.8 27.8 1.0 O A:HOH803 4.8 25.1 1.0 HA2 A:GLY13 4.8 26.7 1.0 C A:ASP64 4.9 24.4 1.0 ND1 A:HIS465 4.9 23.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:28.1 occ:1.00 OD1 B:ASP12 1.9 21.8 1.0 O1 B:PO4609 1.9 29.8 1.0 OG B:SER65 2.0 32.1 1.0 OD2 B:ASP315 2.1 23.5 1.0 NE2 B:HIS316 2.2 27.7 1.0 CG B:ASP12 2.7 22.1 1.0 OD2 B:ASP12 2.9 23.7 1.0 CE1 B:HIS316 3.0 27.5 1.0 CG B:ASP315 3.0 22.9 1.0 HE1 B:HIS316 3.1 33.0 1.0 CD2 B:HIS316 3.1 27.1 1.0 OD1 B:ASP315 3.3 21.8 1.0 CB B:SER65 3.3 30.1 1.0 P B:PO4609 3.3 29.1 1.0 HD2 B:HIS316 3.4 32.6 1.0 HA B:SER65 3.5 33.9 1.0 HB2 B:SER65 3.8 36.2 1.0 CA B:SER65 3.8 28.2 1.0 OD1 B:ASP273 3.9 27.4 1.0 H B:SER65 3.9 31.9 1.0 HE1 B:HIS465 3.9 30.6 1.0 HB3 B:SER65 3.9 36.2 1.0 O3 B:PO4609 3.9 28.6 1.0 HB2 B:ASP273 3.9 31.4 1.0 O4 B:PO4609 3.9 29.6 1.0 H B:GLY13 4.0 29.7 1.0 ZN B:ZN602 4.0 26.6 1.0 N B:SER65 4.0 26.5 1.0 CG B:ASP273 4.0 26.9 1.0 ND1 B:HIS316 4.1 26.6 1.0 CB B:ASP12 4.1 22.9 1.0 CG B:HIS316 4.2 26.1 1.0 CE1 B:HIS465 4.2 25.4 1.0 HA B:ASP12 4.2 27.6 1.0 N B:GLY13 4.3 24.7 1.0 CB B:ASP315 4.4 23.8 1.0 O2 B:PO4609 4.4 28.4 1.0 HB2 B:ASP315 4.4 28.6 1.0 NE2 B:HIS465 4.4 25.0 1.0 O B:HOH882 4.4 32.4 1.0 CB B:ASP273 4.4 26.2 1.0 O B:HOH894 4.4 24.0 1.0 OD2 B:ASP273 4.5 26.9 1.0 HB3 B:ASP12 4.5 27.5 1.0 CA B:ASP12 4.5 23.0 1.0 HB3 B:ASP273 4.6 31.4 1.0 C B:ASP12 4.6 24.1 1.0 O B:HOH790 4.6 23.4 1.0 MG B:MG603 4.7 24.6 1.0 HB2 B:ASP12 4.7 27.5 1.0 HD1 B:HIS316 4.8 32.0 1.0 HB3 B:ASP315 4.8 28.6 1.0 HG1 B:THR318 4.8 29.3 1.0 HA2 B:GLY13 4.8 30.2 1.0 ND1 B:HIS465 4.9 24.4 1.0 C B:ASP64 5.0 25.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:26.6 occ:1.00 O2 B:PO4609 2.0 28.4 1.0 OD1 B:ASP273 2.0 27.4 1.0 NE2 B:HIS277 2.2 24.6 1.0 NE2 B:HIS465 2.2 25.0 1.0 OD2 B:ASP273 2.5 26.9 1.0 CG B:ASP273 2.6 26.9 1.0 O1 B:PO4609 2.6 29.8 1.0 P B:PO4609 2.8 29.1 1.0 CD2 B:HIS277 3.0 24.4 1.0 HD2 B:HIS277 3.0 29.4 1.0 CD2 B:HIS465 3.2 24.7 1.0 CE1 B:HIS465 3.2 25.4 1.0 HE1 B:HIS316 3.3 33.0 1.0 HD2 B:HIS465 3.3 29.6 1.0 CE1 B:HIS277 3.3 25.6 1.0 HE1 B:HIS465 3.4 30.6 1.0 H31 B:EPE607 3.6 51.0 1.0 HE1 B:HIS277 3.6 30.8 1.0 O3 B:PO4609 3.7 28.6 1.0 HG1 B:THR318 3.7 29.3 1.0 O B:HOH883 3.9 38.6 1.0 CE1 B:HIS316 4.0 27.5 1.0 ZN B:ZN601 4.0 28.1 1.0 H71 B:EPE607 4.0 52.4 1.0 O4 B:PO4609 4.1 29.6 1.0 CB B:ASP273 4.1 26.2 1.0 HG21 B:THR318 4.1 30.1 1.0 OG1 B:THR318 4.2 24.4 1.0 NE2 B:HIS316 4.2 27.7 1.0 CG B:HIS277 4.2 25.1 1.0 H32 B:EPE607 4.2 51.0 1.0 O B:HOH790 4.2 23.4 1.0 ND1 B:HIS465 4.3 24.4 1.0 CG B:HIS465 4.3 24.0 1.0 HB2 B:ASP273 4.3 31.4 1.0 ND1 B:HIS277 4.3 25.5 1.0 O B:HOH768 4.4 26.4 1.0 C3 B:EPE607 4.4 42.5 1.0 HB3 B:ASP273 4.5 31.4 1.0 HG23 B:THR318 4.6 30.1 1.0 OD1 B:ASP12 4.7 21.8 1.0 CG2 B:THR318 4.7 25.1 1.0 O B:ASP273 4.8 25.6 1.0 H22 B:EPE607 4.9 50.6 1.0 OH A:TYR325 4.9 26.7 1.0 OG B:SER65 4.9 32.1 1.0 HD1 B:TRP274 4.9 32.1 1.0 CA B:ASP273 5.0 25.5 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