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Calcium in PDB 2yid: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate:
4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate, PDB code: 2yid 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) 32.94 / 2.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.843, 82.287, 163.478, 99.23, 99.03, 100.63
R / Rfree (%) 19.2 / 22.34

Other elements in 2yid:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate (pdb code 2yid). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate, PDB code: 2yid:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2yid

Go back to Calcium Binding Sites List in 2yid
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate


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 the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:33.2
occ:1.00
 O A:ILE1060 2.3 33.9 1.0
O A:HIS1055 2.4 28.9 1.0
O A:HOH3154 2.4 20.4 1.0
OD1 A:ASP1058 2.4 33.0 1.0
OD2 A:ASP1004 2.5 36.0 1.0
OD1 A:ASP1004 2.5 37.7 1.0
O A:HOH3153 2.6 33.3 1.0
CG A:ASP1004 2.8 36.5 1.0
CG A:ASP1058 3.4 36.7 1.0
C A:ILE1060 3.5 36.5 1.0
C A:HIS1055 3.5 28.3 1.0
OD2 A:ASP1058 3.6 43.0 1.0
CE1 A:HIS1055 4.0 24.8 1.0
ND1 A:HIS1055 4.0 25.7 1.0
N A:ILE1060 4.0 38.3 1.0
NE2 A:HIS1055 4.2 25.1 1.0
CA A:HIS1055 4.2 23.7 1.0
CG A:HIS1055 4.2 25.0 1.0
CA A:ILE1060 4.2 37.2 1.0
CD2 A:HIS1055 4.3 25.9 1.0
CB A:ASP1004 4.3 27.8 1.0
N A:GLN1061 4.5 31.2 1.0
CB A:ILE1060 4.6 40.9 1.0
N A:GLY1056 4.6 24.6 1.0
NE2 A:GLN1061 4.6 42.0 1.0
O A:HOH3135 4.6 38.9 1.0
CA A:GLN1061 4.7 29.4 1.0
N A:GLY1059 4.7 37.0 1.0
N A:ARG1062 4.7 25.9 1.0
O A:HOH3177 4.7 38.9 1.0
CB A:ASP1058 4.8 34.9 1.0
O A:ARG1062 4.8 23.7 1.0
CA A:GLY1056 4.8 24.7 1.0
CB A:HIS1055 4.8 22.7 1.0
C A:GLY1059 4.9 43.1 1.0
O A:HOH3106 4.9 44.3 1.0
N A:ASP1058 5.0 33.4 1.0
O A:ARG1054 5.0 30.9 1.0

Calcium binding site 2 out of 4 in 2yid

Go back to Calcium Binding Sites List in 2yid
Calcium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate


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 the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:30.3
occ:1.00
 O B:ILE1060 2.3 28.5 1.0
O B:HOH3127 2.3 19.0 1.0
O B:HIS1055 2.4 26.5 1.0
O B:HOH3128 2.4 17.2 1.0
OD2 B:ASP1004 2.4 37.9 1.0
OD1 B:ASP1058 2.4 31.9 1.0
OD1 B:ASP1004 2.6 32.0 1.0
CG B:ASP1004 2.8 32.8 1.0
CG B:ASP1058 3.4 34.0 1.0
C B:ILE1060 3.5 29.2 1.0
C B:HIS1055 3.6 24.3 1.0
OD2 B:ASP1058 3.6 38.3 1.0
N B:ILE1060 4.0 31.6 1.0
CE1 B:HIS1055 4.1 22.0 1.0
ND1 B:HIS1055 4.1 23.1 1.0
CA B:ILE1060 4.2 29.6 1.0
NE2 B:HIS1055 4.2 22.1 1.0
CA B:HIS1055 4.3 21.0 1.0
CG B:HIS1055 4.3 22.6 1.0
CB B:ASP1004 4.3 23.9 1.0
O B:HOH3145 4.4 37.5 1.0
CD2 B:HIS1055 4.4 23.3 1.0
N B:GLN1061 4.5 23.4 1.0
NE2 B:GLN1061 4.5 44.2 1.0
CB B:ILE1060 4.6 33.1 1.0
N B:GLY1056 4.6 18.9 1.0
CA B:GLN1061 4.6 21.4 1.0
N B:GLY1059 4.6 31.2 1.0
N B:ARG1062 4.8 21.9 1.0
CB B:ASP1058 4.8 29.6 1.0
CA B:GLY1056 4.8 19.4 1.0
C B:GLY1059 4.9 35.1 1.0
O B:ARG1062 4.9 22.6 1.0
N B:ASP1058 4.9 28.7 1.0
CB B:HIS1055 4.9 20.3 1.0
O B:HOH3095 5.0 32.8 1.0

Calcium binding site 3 out of 4 in 2yid

Go back to Calcium Binding Sites List in 2yid
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:27.7
occ:1.00
 O C:ILE1060 2.3 30.3 1.0
OD2 C:ASP1004 2.4 41.0 1.0
O C:HIS1055 2.4 23.6 1.0
O C:HOH3178 2.4 23.2 1.0
OD1 C:ASP1058 2.5 27.3 1.0
O C:HOH3177 2.5 27.2 1.0
OD1 C:ASP1004 2.5 37.3 1.0
CG C:ASP1004 2.8 35.2 1.0
CG C:ASP1058 3.4 30.8 1.0
C C:ILE1060 3.5 32.1 1.0
C C:HIS1055 3.6 22.3 1.0
OD2 C:ASP1058 3.6 38.9 1.0
N C:ILE1060 4.0 32.6 1.0
CE1 C:HIS1055 4.0 19.6 1.0
ND1 C:HIS1055 4.1 20.7 1.0
NE2 C:HIS1055 4.2 20.1 1.0
CA C:ILE1060 4.2 32.1 1.0
CA C:HIS1055 4.3 18.7 1.0
CB C:ASP1004 4.3 25.7 1.0
CG C:HIS1055 4.3 20.5 1.0
CD2 C:HIS1055 4.3 21.6 1.0
N C:GLN1061 4.5 27.0 1.0
NE2 C:GLN1061 4.5 49.4 1.0
O C:HOH3161 4.6 27.9 1.0
CB C:ILE1060 4.6 36.6 1.0
N C:GLY1056 4.6 18.2 1.0
CA C:GLN1061 4.6 25.6 1.0
N C:GLY1059 4.7 29.7 1.0
N C:ARG1062 4.7 24.3 1.0
O C:HOH3128 4.8 36.9 1.0
O C:HOH3203 4.8 38.1 1.0
CB C:ASP1058 4.8 27.6 1.0
CA C:GLY1056 4.8 19.0 1.0
O C:ARG1062 4.9 24.3 1.0
C C:GLY1059 4.9 35.8 1.0
CB C:HIS1055 4.9 18.3 1.0
N C:ASP1058 5.0 26.3 1.0

Calcium binding site 4 out of 4 in 2yid

Go back to Calcium Binding Sites List in 2yid
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with the Enamine-Thdp Intermediate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:29.0
occ:1.00
 O D:ILE1060 2.3 27.7 1.0
O D:HIS1055 2.3 29.8 1.0
OD1 D:ASP1058 2.4 23.2 1.0
O D:HOH3100 2.4 26.2 1.0
O D:HOH3101 2.5 31.7 1.0
OD2 D:ASP1004 2.5 48.7 1.0
OD1 D:ASP1004 2.7 38.5 1.0
CG D:ASP1004 2.9 38.1 1.0
CG D:ASP1058 3.3 26.7 1.0
C D:ILE1060 3.5 31.1 1.0
OD2 D:ASP1058 3.5 31.6 1.0
C D:HIS1055 3.5 29.2 1.0
N D:ILE1060 3.9 33.7 1.0
ND1 D:HIS1055 4.1 28.4 1.0
CE1 D:HIS1055 4.1 27.8 1.0
CA D:HIS1055 4.2 25.1 1.0
CA D:ILE1060 4.2 32.3 1.0
NE2 D:HIS1055 4.3 28.1 1.0
CG D:HIS1055 4.3 27.2 1.0
CD2 D:HIS1055 4.3 28.9 1.0
CB D:ASP1004 4.4 25.7 1.0
CB D:ILE1060 4.5 36.4 1.0
N D:GLN1061 4.5 27.5 1.0
N D:GLY1056 4.6 25.8 1.0
N D:GLY1059 4.6 32.2 1.0
NE2 D:GLN1061 4.6 44.0 1.0
CB D:ASP1058 4.7 29.5 1.0
CA D:GLN1061 4.7 25.8 1.0
N D:ARG1062 4.8 23.6 1.0
CA D:GLY1056 4.8 25.4 1.0
C D:GLY1059 4.8 37.6 1.0
CB D:HIS1055 4.9 24.5 1.0
N D:ASP1058 4.9 30.2 1.0
O D:ARG1054 4.9 33.0 1.0
O D:ARG1062 4.9 26.1 1.0
CG2 D:ILE1060 5.0 36.9 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 09:40:28 2025

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