Magnesium 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:

Zinc	(Zn)	4 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 M Nacl, PDB code: 7yzz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:16.4 occ:1.00 OE2 A:GLU268 2.0 15.7 1.0 OD2 A:ASP12 2.0 16.2 1.0 O A:HOH799 2.1 16.7 1.0 O A:HOH827 2.1 16.9 1.0 OG1 A:THR118 2.1 16.7 1.0 O A:HOH739 2.1 17.3 1.0 HG A:SER65 2.9 29.0 0.5 CD A:GLU268 3.1 15.6 1.0 CG A:ASP12 3.1 15.7 1.0 HB A:THR118 3.1 18.9 1.0 CB A:THR118 3.2 15.8 1.0 HB2 A:ASP12 3.3 18.4 1.0 H A:THR118 3.4 19.6 1.0 OE1 A:GLU268 3.5 16.9 1.0 CB A:ASP12 3.6 15.4 1.0 OG A:SER65 3.7 24.2 1.0 HB3 A:ASP12 3.9 18.4 1.0 HG21 A:THR118 3.9 21.2 1.0 HA2 A:GLY270 4.0 19.4 1.0 O A:HOH765 4.1 16.9 1.0 ND1 A:HIS116 4.1 18.4 1.0 N A:THR118 4.1 16.3 1.0 OD1 A:ASP12 4.1 15.9 1.0 HG21 A:THR112 4.1 21.7 1.0 CG2 A:THR118 4.1 17.7 1.0 HA3 A:GLY270 4.2 19.4 1.0 HB2 A:SER65 4.2 23.9 1.0 CA A:THR118 4.3 15.6 1.0 HB3 A:SER65 4.3 23.9 1.0 CB A:SER65 4.3 19.9 1.0 CG A:GLU268 4.4 16.3 1.0 HG3 A:GLU268 4.4 19.6 1.0 O A:HOH701 4.4 24.2 0.5 O1 A:PO4613 4.4 17.8 1.0 O A:GLY270 4.5 16.8 1.0 CA A:GLY270 4.5 16.2 1.0 HD2 A:PRO119 4.6 20.0 1.0 HG23 A:THR118 4.6 21.2 1.0 HE1 A:HIS116 4.6 22.3 1.0 HB3 A:HIS116 4.6 20.7 1.0 CE1 A:HIS116 4.7 18.6 1.0 HG2 A:GLU268 4.7 19.6 1.0 HA A:THR118 4.7 18.8 1.0 HB3 A:ALA117 4.7 21.3 1.0 ZN A:ZN602 4.7 17.6 1.0 HD3 A:PRO119 4.8 20.0 1.0 OD2 A:ASP315 4.8 18.1 1.0 OG1 A:THR112 4.9 17.2 1.0 HG22 A:THR118 4.9 21.2 1.0 O3 A:PO4613 4.9 18.4 1.0 HG1 A:THR112 5.0 20.7 1.0 H A:ALA117 5.0 19.3 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg615 b:20.9 occ:1.00 O B:SER485 2.2 18.1 1.0 O A:GLY48 2.2 19.6 1.0 O A:ALA45 2.4 19.4 1.0 O B:HOH867 2.4 26.4 1.0 O A:GLN46 2.5 20.5 1.0 C A:GLN46 3.1 19.8 1.0 HB3 B:LYS486 3.1 22.6 1.0 HA A:GLN46 3.2 23.8 1.0 O B:HOH922 3.2 36.3 1.0 C A:GLY48 3.2 19.5 1.0 C B:SER485 3.4 17.5 1.0 HA A:VAL49 3.5 22.5 1.0 C A:ALA45 3.5 18.6 1.0 CA A:GLN46 3.6 19.8 1.0 HA B:LYS486 3.7 20.4 1.0 O A:HOH902 3.8 27.5 1.0 HB3 B:SER485 3.8 22.0 1.0 N A:GLY48 3.8 20.6 1.0 H A:GLY48 3.9 24.7 1.0 CB B:LYS486 3.9 18.9 1.0 N A:GLN46 4.0 19.1 1.0 N A:GLU47 4.0 19.5 1.0 C A:GLU47 4.1 21.0 1.0 N A:VAL49 4.1 18.6 1.0 CA B:LYS486 4.1 17.1 1.0 CA A:GLY48 4.1 20.2 1.0 N B:LYS486 4.2 17.2 1.0 CA A:VAL49 4.2 18.8 1.0 HB2 B:LYS486 4.2 22.6 1.0 HG12 A:VAL49 4.3 25.0 1.0 CA B:SER485 4.4 17.6 1.0 CB B:SER485 4.5 18.3 1.0 CA A:GLU47 4.5 20.8 1.0 O A:GLU47 4.5 24.0 1.0 HA A:GLU47 4.6 24.9 1.0 HG3 A:GLN46 4.6 33.9 1.0 H A:GLU47 4.7 23.4 1.0 HA2 A:GLY48 4.7 24.3 1.0 HA A:ALA45 4.7 22.6 1.0 O B:LEU482 4.7 20.2 1.0 H B:SER485 4.8 21.3 1.0 CA A:ALA45 4.8 18.9 1.0 HA3 A:GLY48 4.8 24.3 1.0 H A:GLN46 4.9 22.9 1.0 H A:VAL49 4.9 22.2 1.0 N B:SER485 4.9 17.8 1.0 HG13 A:VAL49 4.9 25.0 1.0 OG B:SER485 4.9 18.3 1.0 CG1 A:VAL49 5.0 20.9 1.0 CB A:GLN46 5.0 22.8 1.0 H B:LYS486 5.0 20.6 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg616 b:26.4 occ:1.00 O A:HOH1068 2.1 32.7 1.0 O A:HOH912 2.1 28.7 1.0 O A:HOH1011 2.3 26.4 1.0 HZ3 A:LYS236 3.8 47.5 1.0 HG22 A:ILE33 4.0 28.8 1.0 HG21 A:ILE33 4.0 28.8 1.0 O A:HOH866 4.2 33.9 1.0 O A:HOH1014 4.3 44.4 1.0 HZ1 A:LYS236 4.4 47.5 1.0 NZ A:LYS236 4.4 39.6 1.0 OH A:TYR362 4.4 21.9 1.0 CG2 A:ILE33 4.5 24.0 1.0 O A:HOH872 4.5 22.7 1.0 HZ2 A:LYS236 4.5 47.5 1.0 HH A:TYR362 4.7 26.2 1.0 HB A:ILE33 4.8 27.4 1.0 HG2 A:LYS236 4.9 30.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 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 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:15.4 occ:1.00 OD2 B:ASP12 2.0 15.4 1.0 OE2 B:GLU268 2.0 15.2 1.0 O B:HOH772 2.1 15.7 1.0 O B:HOH854 2.1 15.6 1.0 O B:HOH739 2.1 16.7 1.0 OG1 B:THR118 2.2 15.4 1.0 HG B:SER65 2.9 28.7 0.3 CD B:GLU268 3.0 15.3 1.0 CG B:ASP12 3.1 15.0 1.0 HB B:THR118 3.1 19.0 1.0 CB B:THR118 3.2 15.8 1.0 HB2 B:ASP12 3.2 17.9 1.0 H B:THR118 3.4 18.2 1.0 OE1 B:GLU268 3.5 16.2 1.0 HD1 B:HIS116 3.5 21.2 1.0 CB B:ASP12 3.6 15.0 1.0 OG B:SER65 3.8 23.9 1.0 HB3 B:ASP12 3.9 17.9 1.0 HG21 B:THR118 4.0 20.6 1.0 HA2 B:GLY270 4.0 18.7 1.0 O B:HOH768 4.0 16.1 1.0 N B:THR118 4.1 15.2 1.0 ND1 B:HIS116 4.1 17.7 1.0 OD1 B:ASP12 4.1 15.3 1.0 HG21 B:THR112 4.2 20.8 1.0 HA3 B:GLY270 4.2 18.7 1.0 CG2 B:THR118 4.2 17.2 1.0 HB2 B:SER65 4.2 23.3 1.0 CA B:THR118 4.3 15.3 1.0 HB3 B:SER65 4.3 23.3 1.0 CB B:SER65 4.4 19.4 1.0 O B:HOH701 4.4 25.4 0.5 CG B:GLU268 4.4 15.3 1.0 O2 B:PO4606 4.4 16.0 1.0 HG3 B:GLU268 4.4 18.3 1.0 O B:GLY270 4.5 15.8 1.0 HD2 B:PRO119 4.5 19.8 1.0 CA B:GLY270 4.5 15.6 1.0 HB3 B:HIS116 4.6 19.5 1.0 HG23 B:THR118 4.6 20.6 1.0 HE1 B:HIS116 4.6 20.5 1.0 HG2 B:GLU268 4.7 18.3 1.0 HA B:THR118 4.7 18.3 1.0 ZN B:ZN602 4.7 16.8 1.0 HB3 B:ALA117 4.7 19.9 1.0 CE1 B:HIS116 4.7 17.1 1.0 HD3 B:PRO119 4.7 19.8 1.0 OD2 B:ASP315 4.8 16.5 1.0 OG1 B:THR112 4.8 16.1 1.0 O1 B:PO4606 4.9 17.5 1.0 HG22 B:THR118 4.9 20.6 1.0 H B:ALA117 5.0 18.4 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 M Nacl


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Vibrio Alkaline Phosphatase in 0.5 M Nacl within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:20.8 occ:1.00 O A:SER485 2.2 19.9 1.0 O B:GLY48 2.3 19.1 1.0 O A:HOH899 2.3 28.3 1.0 O B:ALA45 2.4 21.1 1.0 O B:GLN46 2.4 20.9 0.5 O B:GLN46 2.4 19.7 0.5 C B:GLN46 3.1 20.6 0.5 HA B:GLN46 3.1 25.6 0.5 C B:GLN46 3.1 19.7 0.5 HB3 A:LYS486 3.2 23.1 1.0 C B:GLY48 3.2 18.4 1.0 HA B:GLN46 3.3 24.1 0.5 C A:SER485 3.4 18.1 1.0 CA B:GLN46 3.5 21.3 0.5 C B:ALA45 3.5 20.6 1.0 HA B:VAL49 3.5 20.2 1.0 CA B:GLN46 3.6 20.1 0.5 HA A:LYS486 3.7 21.6 1.0 O B:HOH883 3.7 27.4 1.0 N B:GLY48 3.8 19.4 1.0 H B:GLY48 3.8 23.3 1.0 HB3 A:SER485 3.8 22.8 1.0 CB A:LYS486 3.9 19.2 1.0 N B:GLN46 4.0 20.4 0.5 N B:GLU47 4.0 19.9 1.0 N B:GLN46 4.0 19.7 0.5 C B:GLU47 4.0 20.8 1.0 CA B:GLY48 4.1 19.3 1.0 N B:VAL49 4.1 17.0 1.0 CA A:LYS486 4.1 18.0 1.0 HB2 A:LYS486 4.2 23.1 1.0 N A:LYS486 4.2 18.2 1.0 CA B:VAL49 4.3 16.9 1.0 HG12 B:VAL49 4.4 22.8 1.0 CA A:SER485 4.5 18.5 1.0 CA B:GLU47 4.5 21.0 1.0 CB A:SER485 4.5 19.0 1.0 OE1 B:GLN46 4.5 27.2 0.5 O B:GLU47 4.6 22.9 1.0 HA B:GLU47 4.6 25.2 1.0 HA2 B:GLY48 4.7 23.1 1.0 HA B:ALA45 4.7 24.1 1.0 O A:LEU482 4.7 21.9 1.0 HA3 B:GLY48 4.8 23.1 1.0 CA B:ALA45 4.8 20.1 1.0 H A:SER485 4.8 22.8 1.0 HG2 B:GLN46 4.8 29.4 0.5 H B:GLN46 4.9 24.5 0.5 H B:VAL49 4.9 20.4 1.0 CB B:GLN46 4.9 22.5 0.5 H B:GLN46 4.9 23.6 0.5 HG3 B:GLN46 4.9 29.4 0.5 N A:SER485 5.0 19.1 1.0 OG A:SER485 5.0 18.7 1.0 HG13 B:VAL49 5.0 22.8 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