Magnesium 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
Zinc	(Zn)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes, PDB code: 7qp8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:22.4 occ:1.00 OE2 A:GLU268 1.9 24.1 1.0 O A:HOH866 2.0 20.8 1.0 O A:HOH876 2.1 24.7 1.0 O A:HOH774 2.1 21.7 1.0 OD2 A:ASP12 2.1 22.5 1.0 OG1 A:THR118 2.2 23.7 1.0 CD A:GLU268 3.0 24.4 1.0 HB A:THR118 3.1 29.2 1.0 CG A:ASP12 3.2 22.8 1.0 CB A:THR118 3.2 24.3 1.0 HB2 A:ASP12 3.3 27.2 1.0 OE1 A:GLU268 3.4 24.8 1.0 H A:THR118 3.4 30.7 1.0 CB A:ASP12 3.7 22.6 1.0 OG A:SER65 3.8 30.1 1.0 HB3 A:SER65 3.8 32.9 1.0 HG21 A:THR118 4.0 29.4 1.0 HB3 A:ASP12 4.0 27.2 1.0 ND1 A:HIS116 4.0 25.2 1.0 N A:THR118 4.1 25.6 1.0 HA3 A:GLY270 4.1 30.1 1.0 HA2 A:GLY270 4.1 30.1 1.0 HG21 A:THR112 4.1 29.8 1.0 O A:HOH803 4.2 25.1 1.0 OD1 A:ASP12 4.2 23.4 1.0 CG2 A:THR118 4.2 24.4 1.0 O A:HOH781 4.2 33.7 1.0 CA A:THR118 4.3 25.0 1.0 CG A:GLU268 4.3 24.4 1.0 CB A:SER65 4.3 27.4 1.0 HG3 A:GLU268 4.4 29.3 1.0 O1 A:PO4612 4.4 25.8 1.0 HB3 A:HIS116 4.5 30.3 1.0 HE1 A:HIS116 4.5 30.4 1.0 CA A:GLY270 4.6 25.1 1.0 HD2 A:PRO119 4.6 31.8 1.0 O A:GLY270 4.6 25.7 1.0 HB3 A:ALA117 4.6 30.0 1.0 CE1 A:HIS116 4.6 25.3 1.0 HG23 A:THR118 4.6 29.4 1.0 HD3 A:PRO119 4.6 31.8 1.0 HG2 A:GLU268 4.6 29.3 1.0 HB2 A:SER65 4.7 32.9 1.0 HA A:THR118 4.7 30.0 1.0 ZN A:ZN602 4.8 25.8 1.0 OD2 A:ASP315 4.8 25.8 1.0 OG1 A:THR112 4.9 24.1 1.0 HG22 A:THR118 4.9 29.4 1.0 H A:ALA117 5.0 29.6 1.0 HG1 A:THR112 5.0 29.0 1.0 CG A:HIS116 5.0 25.2 1.0 CG2 A:THR112 5.0 24.8 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:31.3 occ:1.00 O A:GLY48 2.2 28.4 1.0 O B:HOH982 2.3 33.1 1.0 O B:SER485 2.3 25.5 1.0 O A:ALA45 2.5 30.4 1.0 O A:GLN46 2.5 31.6 0.4 O A:GLN46 2.5 31.6 0.6 O B:HOH970 3.0 41.6 1.0 C A:GLN46 3.1 31.8 0.4 C A:GLN46 3.1 31.9 0.6 HB3 B:LYS486 3.1 33.4 1.0 C A:GLY48 3.2 28.3 1.0 HA A:GLN46 3.2 38.9 0.6 HA A:GLN46 3.2 38.3 0.4 HA A:VAL49 3.4 32.1 1.0 C B:SER485 3.5 26.2 1.0 C A:ALA45 3.6 30.2 1.0 CA A:GLN46 3.6 32.4 0.6 CA A:GLN46 3.6 31.9 0.4 N A:GLY48 3.7 29.7 1.0 O A:HOH954 3.7 31.5 1.0 H A:GLY48 3.8 35.7 1.0 HB3 B:SER485 3.8 31.3 1.0 HA B:LYS486 3.8 32.5 1.0 CB B:LYS486 3.9 27.8 1.0 C A:GLU47 4.0 31.0 1.0 N A:VAL49 4.0 27.5 1.0 N A:GLU47 4.0 31.6 1.0 CA A:GLY48 4.0 29.0 1.0 N A:GLN46 4.1 30.8 0.6 N A:GLN46 4.1 30.6 0.4 HB2 B:LYS486 4.2 33.4 1.0 CA A:VAL49 4.2 26.7 1.0 CA B:LYS486 4.2 27.0 1.0 HG12 A:VAL49 4.2 32.9 1.0 N B:LYS486 4.3 26.5 1.0 O A:GLU47 4.4 30.9 1.0 CA A:GLU47 4.5 32.3 1.0 CB B:SER485 4.5 26.0 1.0 CA B:SER485 4.5 26.0 1.0 HA A:GLU47 4.5 38.8 1.0 HA2 A:GLY48 4.6 34.9 1.0 H A:GLU47 4.7 38.0 1.0 HA3 A:GLY48 4.7 34.9 1.0 O B:LEU482 4.8 27.1 1.0 H A:VAL49 4.8 33.0 1.0 HA A:ALA45 4.8 34.7 1.0 HD2 B:LYS486 4.8 36.0 1.0 HG2 A:GLN46 4.8 43.7 0.6 H B:SER485 4.8 31.7 1.0 CA A:ALA45 4.9 28.9 1.0 HG13 A:VAL49 4.9 32.9 1.0 CG1 A:VAL49 4.9 27.4 1.0 OG B:SER485 4.9 26.2 1.0 H A:GLN46 4.9 37.0 0.6 H A:GLN46 4.9 36.8 0.4 HG3 A:GLN46 5.0 41.5 0.4 HG13 A:ILE50 5.0 31.2 1.0 N B:SER485 5.0 26.4 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:69.1 occ:1.00 O A:HOH1048 2.0 70.1 1.0 O A:HOH717 2.1 45.5 1.0 O A:HOH997 2.2 46.3 1.0 O A:HOH805 2.2 53.8 1.0 O A:HOH999 2.3 44.8 1.0 HE22 A:GLN43 3.0 46.9 1.0 HE21 A:GLN296 3.4 50.6 1.0 NE2 A:GLN43 3.9 39.1 1.0 OE1 A:GLN43 4.1 40.5 1.0 NE2 A:GLN296 4.2 42.1 1.0 O A:HOH850 4.3 37.1 1.0 HE22 A:GLN296 4.3 50.6 1.0 OE2 A:GLU300 4.4 39.3 1.0 CD A:GLN43 4.4 39.1 1.0 HE21 A:GLN43 4.5 46.9 1.0 HB3 A:ASN37 4.8 47.7 1.0 HG3 A:GLN296 4.8 44.5 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:24.6 occ:1.00 OE2 B:GLU268 1.9 24.1 1.0 O B:HOH894 2.0 24.0 1.0 OD2 B:ASP12 2.0 23.7 1.0 OG1 B:THR118 2.1 24.5 1.0 O B:HOH884 2.1 25.4 1.0 O B:HOH791 2.2 25.6 1.0 CD B:GLU268 3.0 25.0 1.0 CG B:ASP12 3.0 22.1 1.0 HB B:THR118 3.1 29.9 1.0 CB B:THR118 3.2 24.9 1.0 HB2 B:ASP12 3.2 27.5 1.0 OE1 B:GLU268 3.5 25.7 1.0 H B:THR118 3.5 31.1 1.0 CB B:ASP12 3.6 22.9 1.0 OG B:SER65 3.8 32.1 1.0 HG21 B:THR118 3.8 29.9 1.0 HB3 B:ASP12 3.9 27.5 1.0 HB3 B:SER65 3.9 36.2 1.0 O B:HOH790 4.0 23.4 1.0 ND1 B:HIS116 4.0 28.0 1.0 HA2 B:GLY270 4.1 29.7 1.0 OD1 B:ASP12 4.1 21.8 1.0 CG2 B:THR118 4.1 24.9 1.0 HA3 B:GLY270 4.1 29.7 1.0 N B:THR118 4.1 25.9 1.0 HG21 B:THR112 4.2 32.8 1.0 CA B:THR118 4.3 25.4 1.0 CG B:GLU268 4.3 25.1 1.0 O B:HOH882 4.3 32.4 1.0 HG3 B:GLU268 4.3 30.1 1.0 CB B:SER65 4.4 30.1 1.0 O4 B:PO4609 4.5 29.6 1.0 HG23 B:THR118 4.5 29.9 1.0 HB3 B:HIS116 4.5 33.5 1.0 HE1 B:HIS116 4.5 33.3 1.0 CA B:GLY270 4.5 24.7 1.0 O B:GLY270 4.6 24.6 1.0 HG2 B:GLU268 4.6 30.1 1.0 CE1 B:HIS116 4.6 27.7 1.0 HA B:THR118 4.6 30.6 1.0 OD2 B:ASP315 4.7 23.5 1.0 ZN B:ZN601 4.7 28.1 1.0 HD2 B:PRO119 4.7 31.6 1.0 HD3 B:PRO119 4.7 31.6 1.0 HB2 B:SER65 4.7 36.2 1.0 HB3 B:ALA117 4.8 31.5 1.0 HG22 B:THR118 4.9 29.9 1.0 HG B:SER110 5.0 33.2 1.0 CA B:ASP12 5.0 23.0 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


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 with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:32.9 occ:1.00 O B:HOH868 2.0 27.6 1.0 O B:HOH808 2.1 29.8 1.0 O B:HOH754 2.2 25.2 1.0 O B:HOH825 2.2 28.1 1.0 HA B:ASP304 3.5 34.9 1.0 O B:ASP304 4.2 30.1 1.0 OD1 B:ASP304 4.3 30.4 1.0 O B:HOH1077 4.3 45.1 1.0 CA B:ASP304 4.4 29.0 1.0 O B:HOH1071 4.4 54.5 1.0 O B:LYS303 4.5 29.8 0.5 OE2 B:GLU306 4.5 33.3 1.0 O B:LYS303 4.5 29.5 0.5 O B:HOH788 4.5 32.5 1.0 C B:ASP304 4.6 29.6 1.0 HG2 B:GLU306 4.7 38.2 1.0 HB3 B:ASP304 4.8 35.4 1.0 HG3 B:GLU306 4.9 38.2 1.0 CB B:ASP304 5.0 29.5 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Vibrio Alkaline Phosphatase with Bound Hepes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:30.1 occ:1.00 O A:SER485 2.2 26.7 1.0 O B:GLY48 2.2 26.6 1.0 O A:HOH923 2.3 31.0 1.0 O B:ALA45 2.5 28.7 1.0 O B:GLN46 2.5 29.4 1.0 HA B:GLN46 3.1 36.8 1.0 C B:GLN46 3.1 29.7 1.0 HB3 A:LYS486 3.2 34.8 1.0 C B:GLY48 3.2 26.8 1.0 O A:HOH995 3.3 47.5 1.0 C A:SER485 3.4 27.1 1.0 HA B:VAL49 3.4 31.0 1.0 CA B:GLN46 3.5 30.6 1.0 C B:ALA45 3.6 28.8 1.0 HA A:LYS486 3.7 32.9 1.0 H B:GLY48 3.7 33.2 1.0 N B:GLY48 3.8 27.6 1.0 HB3 A:SER485 3.8 32.9 1.0 O B:HOH934 3.8 27.6 1.0 CB A:LYS486 3.9 29.0 1.0 N B:GLN46 4.0 29.1 1.0 HB2 A:LYS486 4.1 34.8 1.0 N B:VAL49 4.1 26.3 1.0 CA A:LYS486 4.1 27.4 1.0 CA B:GLY48 4.1 27.9 1.0 N B:GLU47 4.1 29.0 1.0 N A:LYS486 4.1 27.2 1.0 C B:GLU47 4.2 27.9 1.0 CA B:VAL49 4.2 25.8 1.0 HG12 B:VAL49 4.3 32.3 1.0 CA A:SER485 4.4 27.1 1.0 CB A:SER485 4.5 27.4 1.0 CA B:GLU47 4.6 28.7 1.0 HA2 B:GLY48 4.7 33.5 1.0 HA B:GLU47 4.7 34.5 1.0 O A:LEU482 4.7 28.0 1.0 O B:GLU47 4.7 26.7 1.0 H B:GLU47 4.7 34.9 1.0 HA3 B:GLY48 4.8 33.5 1.0 H A:SER485 4.8 32.7 1.0 OG A:SER485 4.8 27.3 1.0 HA B:ALA45 4.8 34.2 1.0 H B:VAL49 4.9 31.6 1.0 CA B:ALA45 4.9 28.4 1.0 HG13 B:ILE50 4.9 30.3 1.0 HG13 B:VAL49 4.9 32.3 1.0 H B:GLN46 4.9 35.0 1.0 N A:SER485 4.9 27.2 1.0 CB B:GLN46 4.9 33.4 1.0 HG2 B:GLN46 5.0 44.0 1.0 HD2 A:LYS486 5.0 39.3 1.0 HG3 B:GLN46 5.0 44.0 1.0 CG1 B:VAL49 5.0 26.8 1.0 H A:LYS486 5.0 32.6 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