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Calcium in PDB 4nt0: Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate

Enzymatic activity of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate

All present enzymatic activity of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate:
4.1.1.23;

Protein crystallography data

The structure of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate, PDB code: 4nt0 was solved by A.A.Fedorov, E.V.Fedorov, V.Iiams, 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) 42.10 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.886, 56.896, 125.179, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate (pdb code 4nt0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate, PDB code: 4nt0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 4nt0

Go back to Calcium Binding Sites List in 4nt0
Calcium binding site 1 out of 2 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:14.6
occ:0.42
 OD2 A:ASP10 2.3 39.4 1.0
O A:VAL8 2.3 18.0 1.0
O A:ARG5 2.3 25.4 1.0
O A:HOH431 2.5 32.6 1.0
O A:HOH465 2.7 19.7 1.0
CG A:ASP10 3.4 43.2 1.0
C A:VAL8 3.4 19.2 1.0
C A:ARG5 3.4 25.7 1.0
O A:VAL6 3.8 22.1 1.0
C A:MET9 3.9 22.0 1.0
O A:MET9 3.9 22.5 1.0
C A:VAL6 3.9 26.1 1.0
CA A:VAL6 4.0 23.7 1.0
OD1 A:ASP10 4.0 49.2 1.0
N A:VAL8 4.0 22.5 1.0
N A:ASP10 4.1 24.6 1.0
N A:VAL6 4.2 25.0 1.0
CA A:VAL8 4.3 22.0 1.0
N A:MET9 4.3 16.9 1.0
N A:ARG5 4.3 27.5 1.0
CG2 A:VAL8 4.4 21.6 1.0
CB A:ARG4 4.4 38.1 1.0
CA A:ASP10 4.4 25.7 1.0
CA A:MET9 4.5 18.6 1.0
CB A:ASP10 4.5 33.1 1.0
CA A:ARG5 4.5 28.6 1.0
N A:ASP7 4.7 20.6 1.0
C A:ARG4 4.8 30.9 1.0
O A:HOH458 4.8 24.6 1.0
CB A:VAL8 5.0 22.8 1.0

Calcium binding site 2 out of 2 in 4nt0

Go back to Calcium Binding Sites List in 4nt0
Calcium binding site 2 out of 2 in the Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:13.7
occ:0.43
 O B:VAL8 2.2 21.4 1.0
OD1 B:ASP10 2.3 42.7 1.0
O B:ARG5 2.3 25.1 1.0
O B:HOH465 2.5 33.4 1.0
O B:HOH463 2.8 20.1 1.0
CG B:ASP10 3.3 44.5 1.0
C B:VAL8 3.4 19.2 1.0
C B:ARG5 3.4 24.5 1.0
O B:VAL6 3.8 22.8 1.0
OD2 B:ASP10 3.9 50.8 1.0
C B:MET9 3.9 21.7 1.0
O B:MET9 3.9 22.1 1.0
C B:VAL6 4.0 24.6 1.0
CA B:VAL6 4.0 22.8 1.0
N B:VAL8 4.0 21.7 1.0
N B:ASP10 4.1 25.1 1.0
N B:VAL6 4.2 24.5 1.0
CA B:VAL8 4.3 22.1 1.0
N B:ARG5 4.3 27.4 1.0
N B:MET9 4.3 18.3 1.0
CA B:ASP10 4.4 23.4 1.0
CB B:ARG4 4.4 42.5 1.0
CG2 B:VAL8 4.4 23.5 1.0
CA B:MET9 4.4 19.0 1.0
CB B:ASP10 4.5 33.7 1.0
CA B:ARG5 4.5 28.5 1.0
N B:ASP7 4.7 20.7 1.0
C B:ARG4 4.8 32.8 1.0
O B:HOH454 4.9 27.5 1.0
CB B:VAL8 5.0 26.9 1.0
CG B:ARG4 5.0 50.9 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, V.Iiams, J.A.Gerlt, S.C.Almo. Crystal Structure of Orotidine 5'-Monophosphate Decarboxylase From Methanobacterium Thermoautotrophicum Complexed with 3-Deazauridine 5'-Monophosphate To Be Published.
Page generated: Wed Jul 9 00:54:19 2025

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