Magnesium in PDB 6t26: X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine

The structure of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine, PDB code: 6t26 was solved by B.Asgeirsson, J.G.Hjorleifsson, S.Markusson, R.Helland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.72 / 2.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	76.916, 85.270, 84.785, 90.00, 113.55, 90.00
R / Rfree (%)	16 / 20.6

The structure of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine (pdb code 6t26). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine, PDB code: 6t26:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:33.2 occ:1.00 OD2 A:ASP12 2.0 31.7 1.0 OG1 A:THR118 2.1 35.5 1.0 OE2 A:GLU268 2.1 35.7 1.0 O A:HOH714 2.1 34.1 1.0 O A:HOH797 2.1 32.4 1.0 O A:HOH768 2.1 36.6 1.0 CB A:THR118 3.1 32.8 1.0 CD A:GLU268 3.1 36.2 1.0 CG A:ASP12 3.1 35.1 1.0 OG A:SER65 3.5 42.3 1.0 OE1 A:GLU268 3.5 32.4 1.0 CB A:ASP12 3.8 32.3 1.0 N A:THR118 4.0 31.8 1.0 ND1 A:HIS116 4.0 32.5 1.0 O A:HOH731 4.0 32.2 1.0 CG2 A:THR118 4.1 27.4 1.0 OD1 A:ASP12 4.1 37.3 1.0 CA A:THR118 4.1 32.8 1.0 O2 A:PO4607 4.3 34.7 1.0 CB A:SER65 4.3 37.4 1.0 CG A:GLU268 4.4 34.4 1.0 CA A:GLY270 4.6 35.4 1.0 CE1 A:HIS116 4.6 35.0 1.0 O A:GLY270 4.7 35.4 1.0 ZN A:ZN602 4.7 35.7 1.0 O4 A:PO4607 4.9 32.3 1.0 OD2 A:ASP315 4.9 37.0 1.0 CG A:HIS116 4.9 35.4 1.0 OG1 A:THR112 5.0 35.6 1.0

Magnesium binding site 2 out of 6 in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg610 b:40.5 occ:1.00 OD2 A:ASP261 2.4 47.7 1.0 O A:GLY103 2.5 39.8 1.0 OD1 A:ASP259 2.6 46.7 1.0 OD2 A:ASP259 2.6 41.8 1.0 CG A:ASP259 2.9 45.3 1.0 CG A:ASP261 3.5 54.0 1.0 C A:GLY103 3.7 43.7 1.0 CB A:ASP261 3.9 46.8 1.0 CA A:GLY103 4.4 40.5 1.0 CB A:ASP259 4.4 43.5 1.0 N A:ASP261 4.5 41.9 1.0 OD1 A:ASP261 4.5 47.5 1.0 N A:LYS104 4.7 40.7 1.0 CA A:LYS104 4.9 39.3 1.0 CA A:ASP261 4.9 44.1 1.0 N A:GLU260 4.9 47.9 1.0

Magnesium binding site 3 out of 6 in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg611 b:34.6 occ:1.00 O B:SER485 2.2 37.4 1.0 O A:GLY48 2.2 34.0 1.0 O A:ALA45 2.4 30.9 1.0 O B:HOH764 2.5 39.5 1.0 O A:GLN46 2.5 35.6 1.0 C A:GLN46 3.2 35.2 1.0 C A:GLY48 3.2 34.0 1.0 C B:SER485 3.3 37.1 1.0 C A:ALA45 3.6 36.5 1.0 CA A:GLN46 3.6 35.4 1.0 O A:HOH841 3.8 35.1 1.0 O B:HOH766 3.9 43.6 1.0 N A:GLY48 3.9 34.6 1.0 O A:HOH744 3.9 39.8 1.0 CB B:LYS486 3.9 35.1 1.0 N A:GLN46 4.0 36.0 1.0 N A:VAL49 4.1 36.5 1.0 CA B:LYS486 4.1 33.7 1.0 N B:LYS486 4.1 35.8 1.0 CA A:GLY48 4.2 34.9 1.0 N A:GLU47 4.2 35.1 1.0 CA A:VAL49 4.2 35.4 1.0 C A:GLU47 4.2 32.3 1.0 CA B:SER485 4.4 35.9 1.0 CB B:SER485 4.4 35.0 1.0 O A:HOH887 4.6 42.0 1.0 O B:LEU482 4.6 38.3 1.0 CA A:GLU47 4.7 36.8 1.0 O A:GLU47 4.7 34.3 1.0 CA A:ALA45 4.8 36.5 1.0 OG B:SER485 4.8 34.1 1.0 N B:SER485 4.9 35.5 1.0 CG1 A:VAL49 4.9 34.9 1.0 CB A:GLN46 5.0 34.0 1.0

Magnesium binding site 4 out of 6 in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:35.5 occ:1.00 OE2 B:GLU268 1.9 33.0 1.0 OD2 B:ASP12 1.9 33.4 1.0 O B:HOH814 2.0 35.4 1.0 O B:HOH748 2.2 29.9 1.0 O B:HOH773 2.2 31.9 1.0 OG1 B:THR118 2.3 31.4 1.0 CG B:ASP12 3.0 35.9 1.0 CD B:GLU268 3.0 33.2 1.0 CB B:THR118 3.3 32.4 1.0 OG B:SER65 3.5 44.8 1.0 OE1 B:GLU268 3.5 30.9 1.0 CB B:ASP12 3.6 30.6 1.0 O B:HOH729 4.0 31.5 1.0 OD1 B:ASP12 4.0 34.3 1.0 N B:THR118 4.2 32.4 1.0 ND1 B:HIS116 4.2 36.4 1.0 CG2 B:THR118 4.3 30.5 1.0 CG B:GLU268 4.3 30.6 1.0 O4 B:PO4607 4.3 30.3 1.0 CB B:SER65 4.3 37.0 1.0 CA B:THR118 4.4 32.8 1.0 CA B:GLY270 4.4 33.9 1.0 O B:GLY270 4.4 29.9 1.0 ZN B:ZN602 4.5 36.9 1.0 OD2 B:ASP315 4.7 37.1 1.0 CE1 B:HIS116 4.8 35.2 1.0 O2 B:PO4607 4.9 34.8 1.0 CG2 B:THR112 4.9 32.0 1.0 CA B:ASP12 4.9 32.0 1.0 C B:GLY270 5.0 32.0 1.0

Magnesium binding site 5 out of 6 in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg610 b:52.7 occ:1.00 OD1 B:ASP259 2.3 48.7 1.0 O B:GLY103 2.3 47.3 1.0 OD2 B:ASP261 2.4 56.4 1.0 OD2 B:ASP259 2.4 46.8 1.0 CG B:ASP259 2.7 43.1 1.0 CG B:ASP261 3.4 54.6 1.0 C B:GLY103 3.5 42.2 1.0 CB B:ASP261 3.8 48.5 1.0 N B:ASP261 4.2 53.5 1.0 CB B:ASP259 4.2 44.0 1.0 CA B:GLY103 4.3 42.6 1.0 OD1 B:ASP261 4.4 58.9 1.0 N B:LYS104 4.5 38.6 1.0 CA B:ASP261 4.6 53.4 1.0 N B:GLU260 4.6 53.6 1.0 CA B:LYS104 4.7 40.5 1.0 CA B:ASP259 4.9 47.2 1.0 C B:LYS104 5.0 39.8 1.0

Magnesium binding site 6 out of 6 in the X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non- Competitive Inhibitor Cyclohexylamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg611 b:35.8 occ:1.00 O B:GLY48 2.2 37.5 1.0 O A:SER485 2.3 33.0 1.0 O B:ALA45 2.3 36.7 1.0 O A:HOH856 2.4 36.9 1.0 O B:GLN46 2.4 37.6 1.0 C B:GLN46 3.0 38.3 1.0 C B:GLY48 3.2 34.4 1.0 C B:ALA45 3.4 35.2 1.0 CA B:GLN46 3.4 38.0 1.0 C A:SER485 3.4 32.7 1.0 N B:GLY48 3.7 37.6 1.0 O B:HOH840 3.8 41.6 1.0 CB A:LYS486 3.8 32.5 1.0 N B:GLN46 3.9 34.6 1.0 N B:GLU47 3.9 34.1 1.0 C B:GLU47 4.0 38.5 1.0 CA A:LYS486 4.1 32.0 1.0 CA B:GLY48 4.1 32.8 1.0 N B:VAL49 4.1 33.6 1.0 N A:LYS486 4.2 31.3 1.0 CA B:VAL49 4.2 34.5 1.0 CA B:GLU47 4.4 39.4 1.0 O B:GLU47 4.4 36.4 1.0 CA A:SER485 4.5 36.8 1.0 CB A:SER485 4.6 34.8 1.0 CA B:ALA45 4.7 34.9 1.0 CB B:GLN46 4.8 37.2 1.0 O A:LEU482 4.9 35.5 1.0 OG A:SER485 5.0 35.6 1.0

B.Asgeirsson, S.Markusson, S.S.Hlynsdottir, R.Helland, J.G.Hjorleifsson. X-Ray Crystal Structure of Vibrio Alkaline Phosphatase with the Non-Competitive Inhibitor Cyclohexylamine. Biochem Biophys Rep V. 24 00830 2020.
ISSN: ESSN 2405-5808
PubMed: 33102813
DOI: 10.1016/J.BBREP.2020.100830