Atomistry » Calcium » PDB 4niv-4o4h » 4nt0
Atomistry »
  Calcium »
    PDB 4niv-4o4h »
      4nt0 »

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: Sun Jul 14 11:09:05 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy