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Calcium in PDB 2xt6: Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form)

Enzymatic activity of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form)

All present enzymatic activity of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form):
4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form), PDB code: 2xt6 was solved by T.Wagner, M.Bellinzoni, A.M.Wehenkel, H.M.O'hare, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.12 / 2.74
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 151.990, 247.720, 79.980, 90.00, 90.00, 90.00
R / Rfree (%) 18.54 / 22.36

Other elements in 2xt6:

The structure of Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) (pdb code 2xt6). 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 Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form), PDB code: 2xt6:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2xt6

Go back to Calcium Binding Sites List in 2xt6
Calcium binding site 1 out of 2 in the Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form)


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 Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:73.0
occ:1.00
 O A:HOH3043 2.1 40.6 1.0
OD1 A:ASP1004 2.3 71.0 1.0
O A:ILE1060 2.5 63.5 1.0
OD2 A:ASP1058 2.6 66.4 1.0
O A:HIS1055 2.7 63.3 1.0
OD1 A:ASP1058 3.1 69.0 1.0
CG A:ASP1004 3.1 71.9 1.0
CG A:ASP1058 3.2 68.2 1.0
OD2 A:ASP1004 3.2 82.8 1.0
ND1 A:HIS1055 3.5 58.7 1.0
C A:ILE1060 3.6 62.6 1.0
CE1 A:HIS1055 3.6 57.4 1.0
C A:HIS1055 3.7 62.1 1.0
CA A:HIS1055 4.0 54.8 1.0
CG A:HIS1055 4.0 56.7 1.0
NE2 A:HIS1055 4.2 57.3 1.0
O A:ARG1062 4.3 59.1 1.0
N A:ARG1062 4.3 53.8 1.0
CA A:ILE1060 4.3 59.5 1.0
CB A:ILE1060 4.4 61.0 1.0
N A:ILE1060 4.4 62.3 1.0
CD2 A:HIS1055 4.4 57.5 1.0
N A:GLN1061 4.5 57.2 1.0
CB A:ASP1004 4.5 58.4 1.0
CA A:GLN1061 4.6 54.5 1.0
O A:HOH3042 4.6 41.3 1.0
CB A:HIS1055 4.7 54.1 1.0
CB A:ASP1058 4.7 62.9 1.0
CG2 A:ILE1060 4.7 56.8 1.0
N A:GLY1056 4.9 58.7 1.0
C A:GLN1061 5.0 56.9 1.0

Calcium binding site 2 out of 2 in 2xt6

Go back to Calcium Binding Sites List in 2xt6
Calcium binding site 2 out of 2 in the Crystal Structure of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form)


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 Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase Homodimer (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:67.8
occ:1.00
 O B:ILE1060 2.3 70.8 1.0
O B:HIS1055 2.3 58.5 1.0
OD2 B:ASP1058 2.5 79.2 1.0
OD1 B:ASP1004 2.5 69.4 1.0
O B:HOH3051 2.5 58.9 1.0
OD2 B:ASP1004 2.6 77.5 1.0
CG B:ASP1004 2.8 68.6 1.0
CG B:ASP1058 3.5 76.0 1.0
C B:HIS1055 3.5 59.7 1.0
C B:ILE1060 3.5 69.0 1.0
OD1 B:ASP1058 3.8 78.0 1.0
N B:ILE1060 4.1 66.1 1.0
CB B:ASP1004 4.2 53.1 1.0
CA B:HIS1055 4.3 54.0 1.0
ND1 B:HIS1055 4.3 57.7 1.0
CA B:ILE1060 4.4 65.7 1.0
NE2 B:GLN1061 4.4 94.0 1.0
CE1 B:HIS1055 4.4 56.6 1.0
N B:GLY1056 4.5 57.5 1.0
N B:GLN1061 4.5 61.5 1.0
CG B:HIS1055 4.5 55.7 1.0
CA B:GLN1061 4.6 58.9 1.0
NE2 B:HIS1055 4.6 56.9 1.0
CA B:GLY1056 4.6 57.4 1.0
N B:ASP1058 4.7 62.1 1.0
CD2 B:HIS1055 4.7 57.5 1.0
C B:GLY1056 4.7 61.4 1.0
N B:GLY1059 4.7 64.0 1.0
O B:GLY1056 4.8 62.2 1.0
CB B:ASP1058 4.8 63.4 1.0
CB B:ILE1060 4.8 69.3 1.0
N B:ARG1062 5.0 57.3 1.0

Reference:

T.Wagner, M.Bellinzoni, A.M.Wehenkel, H.M.O'hare, P.M.Alzari. Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism. Chem.Biol. V. 18 1011 2011.
ISSN: ISSN 1074-5521
PubMed: 21867916
DOI: 10.1016/J.CHEMBIOL.2011.06.004
Page generated: Tue Jul 8 09:28:37 2025

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