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Chlorine in PDB 3g1v: Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate

Enzymatic activity of Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate

All present enzymatic activity of Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate, PDB code: 3g1v was solved by A.A.Fedorov, E.V.Fedorov, K.K.Chan, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.93 / 1.30
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 56.620, 56.620, 127.443, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.1

Other elements in 3g1v:

The structure of Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate (pdb code 3g1v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate, PDB code: 3g1v:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 3g1v

Go back to Chlorine Binding Sites List in 3g1v
Chlorine binding site 1 out of 2 in the Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:12.1
occ:1.00
 NZ A:LYS72 3.1 13.9 1.0
NZ A:LYS42 3.2 10.2 1.0
O A:HOH574 3.5 21.3 1.0
C6 A:5FU501 3.5 12.4 1.0
CE A:LYS42 3.6 10.3 1.0
CA A:GLY70 3.6 8.8 1.0
O A:GLY70 3.6 11.8 1.0
CD1 A:ILE96 3.7 9.6 1.0
CD A:LYS42 3.7 9.5 1.0
CD A:LYS72 3.8 14.0 1.0
CG A:LYS72 3.9 12.7 1.0
C1' A:5FU501 3.9 10.0 1.0
C A:GLY70 3.9 9.5 1.0
CE A:LYS72 4.0 13.6 1.0
N1 A:5FU501 4.2 9.5 1.0
F5 A:5FU501 4.4 14.6 1.0
C5 A:5FU501 4.5 12.1 1.0
O4' A:5FU501 4.6 9.4 1.0
CG2 A:ILE96 4.7 10.1 1.0
CG A:LYS42 4.7 8.6 1.0
CG1 A:ILE96 4.7 8.9 1.0
CB A:ILE96 4.8 8.9 1.0
O2' A:5FU501 4.8 11.4 1.0
C2' A:5FU501 4.9 9.9 1.0
N A:GLY70 5.0 8.1 1.0
O3' A:5FU501 5.0 9.7 1.0

Chlorine binding site 2 out of 2 in 3g1v

Go back to Chlorine Binding Sites List in 3g1v
Chlorine binding site 2 out of 2 in the Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Mutant D70G of Orotidine 5'- Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 5-Fluorouridine 5'- Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl229

b:12.2
occ:1.00
 NZ B:LYS72 3.1 14.2 1.0
NZ B:LYS42 3.2 10.1 1.0
O B:HOH324 3.5 22.4 1.0
C6 B:5FU502 3.5 12.3 1.0
CE B:LYS42 3.6 10.3 1.0
CA B:GLY70 3.6 8.5 1.0
O B:GLY70 3.6 11.0 1.0
CD1 B:ILE96 3.7 10.0 1.0
CD B:LYS42 3.7 9.2 1.0
CD B:LYS72 3.8 13.8 1.0
CG B:LYS72 3.9 13.0 1.0
C1' B:5FU502 3.9 10.7 1.0
C B:GLY70 4.0 8.8 1.0
CE B:LYS72 4.0 13.6 1.0
N1 B:5FU502 4.2 10.0 1.0
F5 B:5FU502 4.4 14.4 1.0
C5 B:5FU502 4.4 12.2 1.0
O4' B:5FU502 4.6 9.3 1.0
CG2 B:ILE96 4.7 10.4 1.0
CG B:LYS42 4.7 7.5 1.0
O2' B:5FU502 4.7 11.4 1.0
CB B:ILE96 4.8 8.6 1.0
CG1 B:ILE96 4.8 9.0 1.0
C2' B:5FU502 4.9 10.1 1.0
N B:GLY70 5.0 7.9 1.0
O B:HOH544 5.0 14.7 1.0
O3' B:5FU502 5.0 9.5 1.0

Reference:

K.K.Chan, B.M.Wood, A.A.Fedorov, E.V.Fedorov, H.J.Imker, T.L.Amyes, J.P.Richard, S.C.Almo, J.A.Gerlt. Mechanism of the Orotidine 5'-Monophosphate Decarboxylase-Catalyzed Reaction: Evidence For Substrate Destabilization. Biochemistry V. 48 5518 2009.
ISSN: ISSN 0006-2960
PubMed: 19435314
DOI: 10.1021/BI900623R
Page generated: Sat Jul 20 19:55:23 2024

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