Magnesium in PDB 5gza: Protein O-Mannose Kinase

All present enzymatic activity of Protein O-Mannose Kinase:
2.7.1.183;

The structure of Protein O-Mannose Kinase, PDB code: 5gza was solved by J.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.28 / 2.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	70.550, 70.550, 66.935, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 21.8

The structure of Protein O-Mannose Kinase also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Aluminium	(Al)	1 atom

The binding sites of Magnesium atom in the Protein O-Mannose Kinase (pdb code 5gza). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Protein O-Mannose Kinase, PDB code: 5gza:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Protein O-Mannose Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Protein O-Mannose Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:43.7 occ:1.00 O2B A:ADP401 1.9 42.9 1.0 F2 A:AF3404 1.9 45.7 1.0 OD1 A:ASP225 2.0 42.9 1.0 OD2 A:ASP227 2.1 38.2 1.0 OD2 A:ASP225 2.3 45.3 1.0 CG A:ASP225 2.5 43.0 1.0 AL A:AF3404 3.0 48.1 1.0 PB A:ADP401 3.1 45.8 1.0 CG A:ASP227 3.1 38.2 1.0 O1B A:ADP401 3.2 45.8 1.0 CB A:ASP227 3.7 38.8 1.0 F1 A:AF3404 3.7 45.5 1.0 CG2 A:VAL90 3.7 44.4 1.0 CE A:LYS91 3.7 40.1 1.0 MG A:MG403 3.8 43.3 1.0 NZ A:LYS91 3.9 38.6 1.0 CB A:VAL90 3.9 44.6 1.0 CB A:ASP225 4.0 41.8 1.0 OD1 A:ASP227 4.0 37.9 1.0 O3B A:ADP401 4.1 46.0 1.0 F3 A:AF3404 4.1 47.6 1.0 O3A A:ADP401 4.2 43.3 1.0 O6 A:MAN406 4.3 48.8 1.0 OD2 A:ASP202 4.3 43.4 1.0 O1A A:ADP401 4.3 40.8 1.0 OE1 A:GLN212 4.5 42.3 1.0 PA A:ADP401 4.6 43.0 1.0 O2A A:ADP401 4.6 40.5 1.0 CG1 A:VAL90 4.6 44.6 1.0 CA A:ASP225 4.7 40.6 1.0 N A:ASP227 4.7 39.2 1.0 CA A:ASP227 4.8 38.9 1.0 C A:ASP225 4.9 38.7 1.0 C6 A:MAN406 5.0 51.6 1.0

Magnesium binding site 2 out of 2 in the Protein O-Mannose Kinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Protein O-Mannose Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:43.3 occ:1.00 F1 A:AF3404 2.0 45.5 1.0 O1A A:ADP401 2.0 40.8 1.0 OD2 A:ASP225 2.0 45.3 1.0 NE2 A:GLN212 2.2 42.7 1.0 O1B A:ADP401 2.3 45.8 1.0 AL A:AF3404 2.9 48.1 1.0 CG A:ASP225 3.0 43.0 1.0 CD A:GLN212 3.2 42.5 1.0 PB A:ADP401 3.4 45.8 1.0 PA A:ADP401 3.4 43.0 1.0 OE1 A:GLN212 3.4 42.3 1.0 CB A:ASP225 3.5 41.8 1.0 O3A A:ADP401 3.6 43.3 1.0 O2B A:ADP401 3.8 42.9 1.0 MG A:MG402 3.8 43.7 1.0 F2 A:AF3404 3.9 45.7 1.0 OD1 A:ASP225 4.0 42.9 1.0 O2A A:ADP401 4.1 40.5 1.0 F3 A:AF3404 4.1 47.6 1.0 OG A:SER211 4.2 51.3 1.0 O5' A:ADP401 4.3 41.5 1.0 O A:SER211 4.3 45.9 1.0 NZ A:LYS208 4.3 53.3 1.0 O6 A:MAN406 4.4 48.8 1.0 C5' A:ADP401 4.4 42.9 1.0 CG A:GLN212 4.5 42.4 1.0 O3B A:ADP401 4.6 46.0 1.0 C A:SER211 4.6 44.6 1.0 OD2 A:ASP202 4.6 43.4 1.0 CD A:LYS208 4.7 50.8 1.0 CA A:GLN212 4.7 40.2 1.0 CB A:SER211 4.8 49.1 1.0 N A:GLN212 4.8 41.7 1.0 CB A:GLN212 5.0 41.1 1.0

Q.Zhu, D.Venzke, A.S.Walimbe, M.E.Anderson, Q.Fu, L.N.Kinch, W.Wang, X.Chen, N.V.Grishin, N.Huang, L.Yu, J.E.Dixon, K.P.Campbell, J.Xiao. Structure of Protein O-Mannose Kinase Reveals A Unique Active Site Architecture Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27879205
DOI: 10.7554/ELIFE.22238