Magnesium 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:

Zinc	(Zn)	4 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Vibrio Alkaline Phosphatase in 1.0 M Nacl, PDB code: 7qow:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg603 b:14.6 occ:1.00 OD2 A:ASP12 2.0 14.9 1.0 OE2 A:GLU268 2.0 14.1 1.0 O A:HOH888 2.1 14.8 1.0 O A:HOH905 2.1 14.6 1.0 O A:HOH769 2.1 14.2 1.0 OG1 A:THR118 2.2 13.6 1.0 HG A:SER65 3.0 21.6 0.6 CD A:GLU268 3.1 13.7 1.0 CG A:ASP12 3.1 14.0 1.0 HB A:THR118 3.1 16.9 1.0 CB A:THR118 3.2 14.1 1.0 HB2 A:ASP12 3.3 15.2 1.0 H A:THR118 3.5 17.7 1.0 OE1 A:GLU268 3.5 14.5 1.0 CB A:ASP12 3.6 12.7 1.0 OG A:SER65 3.8 16.5 0.4 OG A:SER65 3.8 18.0 0.6 HB3 A:ASP12 3.9 15.2 1.0 HB3 A:SER65 3.9 17.3 0.4 HG21 A:THR118 3.9 18.1 1.0 ND1 A:HIS116 4.1 15.8 1.0 HA2 A:GLY270 4.1 17.2 1.0 N A:THR118 4.1 14.8 1.0 CG2 A:THR118 4.1 15.1 1.0 OD1 A:ASP12 4.2 14.3 1.0 HB2 A:SER65 4.2 19.3 0.6 HA3 A:GLY270 4.2 17.2 1.0 HG23 A:THR112 4.2 19.4 1.0 HB3 A:SER65 4.2 19.3 0.6 CA A:THR118 4.3 14.9 1.0 CB A:SER65 4.3 16.1 0.6 CB A:SER65 4.4 14.5 0.4 CG A:GLU268 4.4 14.1 1.0 O1 A:PO4604 4.4 16.0 1.0 HG3 A:GLU268 4.4 16.9 1.0 O A:GLY270 4.5 14.5 1.0 HD2 A:PRO119 4.6 18.1 1.0 HG23 A:THR118 4.6 18.1 1.0 CA A:GLY270 4.6 14.4 1.0 HB3 A:HIS116 4.6 17.5 1.0 HE1 A:HIS116 4.6 18.3 1.0 HB3 A:ALA117 4.7 19.1 1.0 CE1 A:HIS116 4.7 15.3 1.0 HA A:THR118 4.7 17.8 1.0 ZN A:ZN602 4.7 15.4 1.0 HB2 A:SER65 4.7 17.3 0.4 HG2 A:GLU268 4.7 16.9 1.0 OD2 A:ASP315 4.8 14.8 1.0 HD3 A:PRO119 4.8 18.1 1.0 OG1 A:THR112 4.9 15.0 1.0 HG22 A:THR118 4.9 18.1 1.0 H A:ALA117 5.0 17.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg613 b:16.9 occ:1.00 O B:SER485 2.2 14.9 1.0 O A:GLY48 2.3 16.2 1.0 O A:ALA45 2.4 15.6 1.0 O A:GLN46 2.4 16.5 1.0 O B:HOH1436 2.4 23.5 1.0 C A:GLN46 3.1 15.8 1.0 O B:HOH1588 3.1 31.5 1.0 HA A:GLN46 3.1 18.6 1.0 HB3 B:LYS486 3.1 18.8 1.0 C A:GLY48 3.2 16.0 1.0 C B:SER485 3.4 14.7 1.0 HA A:VAL49 3.5 18.0 1.0 C A:ALA45 3.5 15.0 1.0 CA A:GLN46 3.6 15.5 1.0 HA B:LYS486 3.7 17.4 1.0 HB3 B:SER485 3.8 18.0 1.0 N A:GLY48 3.8 15.9 1.0 O A:HOH960 3.8 21.3 1.0 H A:GLY48 3.8 19.1 1.0 CB B:LYS486 3.9 15.7 1.0 C A:GLU47 4.0 16.9 1.0 N A:GLN46 4.0 15.6 1.0 N A:GLU47 4.0 15.8 1.0 N A:VAL49 4.1 15.3 1.0 CA B:LYS486 4.1 14.6 1.0 CA A:GLY48 4.1 16.1 1.0 N B:LYS486 4.2 14.8 1.0 CA A:VAL49 4.2 15.0 1.0 HB2 B:LYS486 4.2 18.8 1.0 HG12 A:VAL49 4.3 19.1 1.0 CA B:SER485 4.4 14.1 1.0 O A:GLU47 4.5 17.9 1.0 CB B:SER485 4.5 15.0 1.0 CA A:GLU47 4.5 16.8 1.0 HG3 A:GLN46 4.6 28.4 1.0 HA A:GLU47 4.6 20.1 1.0 H A:GLU47 4.7 18.9 1.0 HA2 A:GLY48 4.7 19.2 1.0 HA A:ALA45 4.8 17.6 1.0 CA A:ALA45 4.8 14.7 1.0 HA3 A:GLY48 4.8 19.2 1.0 O B:LEU482 4.8 16.3 1.0 H B:SER485 4.8 17.7 1.0 H A:VAL49 4.9 18.3 1.0 H A:GLN46 4.9 18.7 1.0 OG B:SER485 4.9 14.7 1.0 HG13 A:ILE50 4.9 19.0 1.0 N B:SER485 4.9 14.8 1.0 CB A:GLN46 5.0 18.4 1.0 HG13 A:VAL49 5.0 19.1 1.0 H B:LYS486 5.0 17.8 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1109 b:15.3 occ:1.00 OD2 B:ASP12 2.0 15.8 1.0 OE2 B:GLU268 2.0 14.6 1.0 O B:HOH1327 2.1 15.2 1.0 O B:HOH1398 2.1 15.5 1.0 O B:HOH1262 2.1 16.0 1.0 OG1 B:THR118 2.1 14.7 1.0 HG B:SER65 2.9 20.4 0.5 CD B:GLU268 3.1 14.9 1.0 HB B:THR118 3.1 17.9 1.0 CG B:ASP12 3.1 15.7 1.0 CB B:THR118 3.2 15.0 1.0 HB2 B:ASP12 3.2 17.7 1.0 H B:THR118 3.4 17.7 1.0 OE1 B:GLU268 3.4 15.9 1.0 HD1 B:HIS116 3.5 20.0 1.0 CB B:ASP12 3.6 14.8 1.0 OG B:SER65 3.8 17.0 0.5 OG B:SER65 3.8 17.7 0.5 HB3 B:ASP12 3.9 17.7 1.0 HG23 B:THR118 3.9 19.0 1.0 HB3 B:SER65 4.0 19.5 0.5 HA2 B:GLY270 4.0 18.0 1.0 O B:HOH1334 4.1 15.9 1.0 N B:THR118 4.1 14.8 1.0 ND1 B:HIS116 4.1 16.7 1.0 OD1 B:ASP12 4.1 15.6 1.0 CG2 B:THR118 4.1 15.8 1.0 HG23 B:THR112 4.2 19.9 1.0 HA3 B:GLY270 4.2 18.0 1.0 CA B:THR118 4.2 14.7 1.0 HB2 B:SER65 4.3 18.8 0.5 HB3 B:SER65 4.3 18.8 0.5 O B:HOH1201 4.3 19.6 0.6 CG B:GLU268 4.4 15.8 1.0 CB B:SER65 4.4 15.7 0.5 CB B:SER65 4.4 16.3 0.5 HG3 B:GLU268 4.4 18.9 1.0 O2 B:PO41104 4.4 16.5 1.0 O B:GLY270 4.5 15.9 1.0 HD2 B:PRO119 4.5 19.0 1.0 HG22 B:THR118 4.6 19.0 1.0 CA B:GLY270 4.6 15.0 1.0 HB3 B:HIS116 4.6 19.5 1.0 HE1 B:HIS116 4.6 20.0 1.0 HA B:THR118 4.7 17.6 1.0 HG2 B:GLU268 4.7 18.9 1.0 CE1 B:HIS116 4.7 16.7 1.0 HB2 B:SER65 4.7 19.5 0.5 ZN B:ZN1103 4.7 16.4 1.0 HB1 B:ALA117 4.7 19.5 1.0 HD3 B:PRO119 4.8 19.0 1.0 OD2 B:ASP315 4.8 15.8 1.0 OG1 B:THR112 4.9 16.6 1.0 HG1 B:THR112 4.9 19.9 1.0 HG21 B:THR118 4.9 19.0 1.0 H B:ALA117 5.0 18.7 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1110 b:17.4 occ:1.00 O A:SER485 2.2 16.0 1.0 O B:GLY48 2.3 15.7 1.0 O A:HOH1019 2.4 23.8 1.0 O B:ALA45 2.4 17.7 1.0 O B:GLN46 2.4 16.2 1.0 C B:GLN46 3.1 15.9 1.0 HB3 A:LYS486 3.1 19.3 1.0 HA B:GLN46 3.2 19.1 1.0 C B:GLY48 3.2 15.6 1.0 C A:SER485 3.4 15.3 1.0 HA B:VAL49 3.5 17.6 1.0 C B:ALA45 3.5 16.1 1.0 CA B:GLN46 3.6 16.0 1.0 O B:HOH1243 3.6 28.5 1.0 HA A:LYS486 3.7 17.6 1.0 O A:HOH1054 3.7 34.8 1.0 N B:GLY48 3.8 15.8 1.0 H B:GLY48 3.8 18.9 1.0 O B:HOH1442 3.8 21.8 1.0 HB3 A:SER485 3.8 18.6 1.0 CB A:LYS486 3.9 16.1 1.0 N B:GLN46 4.0 15.7 1.0 N B:GLU47 4.0 16.4 1.0 C B:GLU47 4.1 16.3 1.0 N B:VAL49 4.1 15.0 1.0 CA A:LYS486 4.1 14.7 1.0 CA B:GLY48 4.1 15.4 1.0 N A:LYS486 4.2 15.1 1.0 HB2 A:LYS486 4.2 19.3 1.0 CA B:VAL49 4.2 14.7 1.0 HG12 B:VAL49 4.4 18.9 1.0 CA A:SER485 4.4 15.2 1.0 CB A:SER485 4.5 15.5 1.0 CA B:GLU47 4.5 16.9 1.0 O B:GLU47 4.6 19.1 1.0 HA B:GLU47 4.6 20.3 1.0 H B:GLU47 4.7 19.7 1.0 HA2 B:GLY48 4.7 18.4 1.0 HA B:ALA45 4.7 19.4 1.0 HA3 B:GLY48 4.8 18.4 1.0 O A:LEU482 4.8 16.8 1.0 CA B:ALA45 4.8 16.2 1.0 H A:SER485 4.8 18.5 1.0 H B:VAL49 4.9 18.0 1.0 H B:GLN46 4.9 18.8 1.0 OG A:SER485 4.9 15.2 1.0 HG2 B:GLN46 4.9 24.3 1.0 CB B:GLN46 5.0 17.5 1.0 N A:SER485 5.0 15.4 1.0 HG13 B:ILE50 5.0 18.2 1.0 H A:LYS486 5.0 18.0 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