Fluorine 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:

Magnesium	(Mg)	2 atoms
Aluminium	(Al)	1 atom

The binding sites of Fluorine atom in the Protein O-Mannose Kinase (pdb code 5gza). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Protein O-Mannose Kinase, PDB code: 5gza:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Protein O-Mannose Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Protein O-Mannose Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:45.5 occ:1.00 F1 A:AF3404 0.0 45.5 1.0 AL A:AF3404 1.8 48.1 1.0 MG A:MG403 2.0 43.3 1.0 OD2 A:ASP225 2.5 45.3 1.0 O6 A:MAN406 2.5 48.8 1.0 O1B A:ADP401 2.6 45.8 1.0 NE2 A:GLN212 2.7 42.7 1.0 F2 A:AF3404 2.9 45.7 1.0 OD2 A:ASP202 2.9 43.4 1.0 OE1 A:GLN212 3.1 42.3 1.0 F3 A:AF3404 3.2 47.6 1.0 CD A:GLN212 3.2 42.5 1.0 NZ A:LYS208 3.3 53.3 1.0 CD A:LYS208 3.5 50.8 1.0 MG A:MG402 3.7 43.7 1.0 CG A:ASP225 3.8 43.0 1.0 CG A:ASP202 3.8 43.5 1.0 C6 A:MAN406 3.9 51.6 1.0 CE A:LYS208 3.9 52.6 1.0 O1A A:ADP401 3.9 40.8 1.0 PB A:ADP401 4.0 45.8 1.0 O2B A:ADP401 4.2 42.9 1.0 OD1 A:ASP202 4.3 43.8 1.0 OG A:SER211 4.4 51.3 1.0 OD1 A:ASP225 4.6 42.9 1.0 CB A:ASP225 4.6 41.8 1.0 O5 A:MAN406 4.7 55.8 1.0 CG A:GLN212 4.7 42.4 1.0 CG A:LYS208 4.8 50.2 1.0 CB A:ASP202 4.8 43.3 1.0 O3A A:ADP401 4.9 43.3 1.0 C5 A:MAN406 4.9 54.2 1.0 O3B A:ADP401 4.9 46.0 1.0

Fluorine binding site 2 out of 3 in the Protein O-Mannose Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Protein O-Mannose Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:45.7 occ:1.00 F2 A:AF3404 0.0 45.7 1.0 AL A:AF3404 1.8 48.1 1.0 MG A:MG402 1.9 43.7 1.0 O6 A:MAN406 2.5 48.8 1.0 F1 A:AF3404 2.9 45.5 1.0 O2B A:ADP401 2.9 42.9 1.0 F3 A:AF3404 2.9 47.6 1.0 OD2 A:ASP225 3.0 45.3 1.0 O1B A:ADP401 3.0 45.8 1.0 OD2 A:ASP202 3.1 43.4 1.0 C6 A:MAN406 3.1 51.6 1.0 CG2 A:VAL90 3.2 44.4 1.0 OD2 A:ASP227 3.5 38.2 1.0 PB A:ADP401 3.5 45.8 1.0 OD1 A:ASP225 3.7 42.9 1.0 CG A:ASP225 3.8 43.0 1.0 MG A:MG403 3.9 43.3 1.0 CB A:VAL90 4.0 44.6 1.0 O3B A:ADP401 4.1 46.0 1.0 CG A:ASP202 4.3 43.5 1.0 CG A:ASP227 4.4 38.2 1.0 OE1 A:GLN212 4.5 42.3 1.0 N A:VAL90 4.6 46.0 1.0 CB A:ASP227 4.6 38.8 1.0 C5 A:MAN406 4.6 54.2 1.0 C8 A:NAG407 4.9 54.3 1.0 CA A:VAL90 5.0 46.8 1.0

Fluorine binding site 3 out of 3 in the Protein O-Mannose Kinase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Protein O-Mannose Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:47.6 occ:1.00 F3 A:AF3404 0.0 47.6 1.0 AL A:AF3404 1.7 48.1 1.0 O1B A:ADP401 2.2 45.8 1.0 O6 A:MAN406 2.7 48.8 1.0 N A:ALA89 2.7 50.8 1.0 O3B A:ADP401 2.9 46.0 1.0 F2 A:AF3404 2.9 45.7 1.0 PB A:ADP401 3.1 45.8 1.0 C6 A:MAN406 3.1 51.6 1.0 F1 A:AF3404 3.2 45.5 1.0 C A:GLY88 3.5 52.8 1.0 CB A:ALA89 3.5 49.4 1.0 CA A:ALA89 3.6 49.8 1.0 CA A:GLY88 3.6 52.4 1.0 N A:VAL90 3.6 46.0 1.0 O2B A:ADP401 3.8 42.9 1.0 O5 A:MAN406 4.0 55.8 1.0 NZ A:LYS208 4.0 53.3 1.0 C A:ALA89 4.1 48.9 1.0 MG A:MG403 4.1 43.3 1.0 MG A:MG402 4.1 43.7 1.0 C5 A:MAN406 4.1 54.2 1.0 CG2 A:VAL90 4.3 44.4 1.0 O3A A:ADP401 4.5 43.3 1.0 OD2 A:ASP225 4.6 45.3 1.0 O A:GLY88 4.6 53.8 1.0 CB A:VAL90 4.6 44.6 1.0 CA A:VAL90 4.7 46.8 1.0 O1 A:ZZ1405 4.8 62.8 1.0 OD2 A:ASP202 4.8 43.4 1.0 N A:GLY88 5.0 52.9 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