Atomistry » Magnesium » PDB 5gre-5h1y » 5gza
Atomistry »
  Magnesium »
    PDB 5gre-5h1y »
      5gza »

Magnesium in PDB 5gza: Protein O-Mannose Kinase

Enzymatic activity of Protein O-Mannose Kinase

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

Protein crystallography data

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

Other elements in 5gza:

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

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

Magnesium Binding Sites:

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 5gza

Go back to Magnesium Binding Sites List in 5gza
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 5gza

Go back to Magnesium Binding Sites List in 5gza
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

Reference:

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
Page generated: Sun Sep 29 15:31:42 2024

Last articles

Sr in 2GB9
Sr in 2BOX
Sr in 1Y1H
Sr in 1YRM
Sr in 2BTF
Sr in 1Z7F
Sr in 2AWE
Sr in 1YBC
Sr in 1VQK
Sr in 1VQM
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy