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Fluorine in PDB 3g3d: Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump

Enzymatic activity of Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump

All present enzymatic activity of Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump, PDB code: 3g3d was solved by Y.Liu, H.L.Tang, A.Bello, E.Poduch, L.Kotra, E.Pai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.72 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.682, 61.850, 70.320, 90.00, 112.73, 90.00
R / Rfree (%) 17.5 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump (pdb code 3g3d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump, PDB code: 3g3d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3g3d

Go back to Fluorine Binding Sites List in 3g3d
Fluorine binding site 1 out of 2 in the Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3000

b:20.6
occ:1.00
F5 A:5FU3000 0.0 20.6 1.0
C5 A:5FU3000 1.3 19.0 1.0
C6 A:5FU3000 2.4 18.2 1.0
C4 A:5FU3000 2.4 18.5 1.0
CE A:LYS125 2.5 17.8 1.0
NZ A:LYS125 2.8 20.5 1.0
O4 A:5FU3000 2.8 17.4 1.0
CD A:LYS125 3.5 18.5 1.0
CE A:MET182 3.5 22.1 1.0
N1 A:5FU3000 3.6 17.7 1.0
N3 A:5FU3000 3.6 16.6 1.0
C2 A:5FU3000 4.0 17.9 1.0
CG2 A:ILE212 4.0 18.6 1.0
CG A:MET182 4.1 19.5 1.0
CG2 A:ILE179 4.2 17.8 1.0
CD1 A:ILE179 4.2 18.8 1.0
O A:HOH381 4.3 30.3 1.0
CG A:LYS125 4.5 14.4 1.0
SD A:MET182 4.5 22.0 1.0
CG1 A:ILE179 4.6 18.4 1.0
CB A:MET182 4.7 19.3 1.0
CG A:PRO228 4.8 20.4 1.0
C1' A:5FU3000 4.8 18.4 1.0
O A:HOH295 4.8 22.7 1.0
OD1 B:ASP128 5.0 16.3 1.0

Fluorine binding site 2 out of 2 in 3g3d

Go back to Fluorine Binding Sites List in 3g3d
Fluorine binding site 2 out of 2 in the Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Orotidine 5'-Monophosphate Decarboxylase Covalently Modified By 5-Fluoro-6-Azido-Ump within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3000

b:19.9
occ:1.00
F5 B:5FU3000 0.0 19.9 1.0
C5 B:5FU3000 1.3 18.2 1.0
C6 B:5FU3000 2.4 17.9 1.0
C4 B:5FU3000 2.4 18.6 1.0
CE B:LYS125 2.6 15.3 1.0
O4 B:5FU3000 2.7 17.8 1.0
NZ B:LYS125 2.8 20.6 1.0
CD B:LYS125 3.5 15.9 1.0
CE B:MET182 3.6 17.2 1.0
N1 B:5FU3000 3.6 17.1 1.0
N3 B:5FU3000 3.6 15.6 1.0
CG2 B:ILE212 4.0 17.9 1.0
C2 B:5FU3000 4.0 17.1 1.0
CG B:MET182 4.1 20.5 1.0
CG2 B:ILE179 4.2 15.1 1.0
O B:HOH370 4.3 32.2 1.0
CD1 B:ILE179 4.4 14.9 1.0
CG B:LYS125 4.4 12.3 1.0
SD B:MET182 4.5 20.6 1.0
CG1 B:ILE179 4.6 11.9 1.0
CG B:PRO228 4.8 19.5 1.0
C1' B:5FU3000 4.8 16.9 1.0
CB B:MET182 4.9 19.1 1.0
OD1 A:ASP128 5.0 18.4 1.0
O B:HOH307 5.0 19.5 1.0

Reference:

A.M.Bello, D.Konforte, E.Poduch, C.Furlonger, L.Wei, Y.Liu, M.Lewis, E.F.Pai, C.J.Paige, L.P.Kotra. Structure-Activity Relationships of Orotidine-5'-Monophosphate Decarboxylase Inhibitors As Anticancer Agents. J.Med.Chem. V. 52 1648 2009.
ISSN: ISSN 0022-2623
PubMed: 19260677
DOI: 10.1021/JM801224T
Page generated: Sun Dec 13 11:46:32 2020

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