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Calcium in PDB 2yic: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form):
4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form), PDB code: 2yic 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) 39.20 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.539, 83.244, 158.610, 99.48, 99.06, 101.25
R / Rfree (%) 18.84 / 21.08

Other elements in 2yic:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) 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 (Triclinic Form) (pdb code 2yic). 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 (Triclinic Form), PDB code: 2yic:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2yic

Go back to Calcium Binding Sites List in 2yic
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic 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 the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:20.7
occ:1.00
 O A:HOH3252 2.2 17.8 1.0
O A:ILE1060 2.2 23.3 1.0
O A:HIS1055 2.3 17.6 1.0
OD1 A:ASP1058 2.4 23.7 1.0
O A:HOH3253 2.4 21.7 1.0
OD2 A:ASP1004 2.5 27.6 1.0
OD1 A:ASP1004 2.5 21.0 1.0
CG A:ASP1004 2.8 21.8 1.0
CG A:ASP1058 3.4 22.3 1.0
C A:ILE1060 3.4 25.7 1.0
C A:HIS1055 3.5 20.1 1.0
OD2 A:ASP1058 3.7 23.2 1.0
N A:ILE1060 4.1 26.2 1.0
ND1 A:HIS1055 4.1 22.1 1.0
CE1 A:HIS1055 4.2 21.7 1.0
CA A:HIS1055 4.2 17.0 1.0
CA A:ILE1060 4.3 24.7 1.0
CB A:ASP1004 4.3 20.2 1.0
CG A:HIS1055 4.4 20.2 1.0
N A:GLN1061 4.4 20.3 1.0
NE2 A:HIS1055 4.4 22.1 1.0
N A:GLY1056 4.5 17.9 1.0
CD2 A:HIS1055 4.5 22.4 1.0
CA A:GLN1061 4.6 18.4 1.0
O A:HOH3222 4.6 23.9 1.0
N A:ARG1062 4.7 14.5 1.0
CB A:ILE1060 4.7 28.1 1.0
NE2 A:GLN1061 4.7 51.9 1.0
CA A:GLY1056 4.7 18.6 1.0
CB A:ASP1058 4.7 19.1 1.0
N A:GLY1059 4.8 27.9 1.0
O A:HOH3181 4.8 37.1 1.0
O A:HOH3293 4.8 35.1 1.0
N A:ASP1058 4.8 19.8 1.0
C A:GLY1056 4.9 22.2 1.0
CB A:HIS1055 4.9 17.1 1.0
O A:ARG1054 5.0 18.5 1.0
O A:ARG1062 5.0 19.9 1.0

Calcium binding site 2 out of 4 in 2yic

Go back to Calcium Binding Sites List in 2yic
Calcium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic 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 the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:23.9
occ:1.00
 O B:ILE1060 2.2 29.4 1.0
O B:HIS1055 2.3 20.8 1.0
O B:HOH3198 2.4 23.5 1.0
OD1 B:ASP1058 2.4 24.5 1.0
OD2 B:ASP1004 2.5 26.0 1.0
OD1 B:ASP1004 2.6 25.5 1.0
O B:HOH3199 2.6 18.9 1.0
CG B:ASP1004 2.8 25.6 1.0
CG B:ASP1058 3.4 24.5 1.0
C B:ILE1060 3.5 31.5 1.0
C B:HIS1055 3.5 22.5 1.0
OD2 B:ASP1058 3.6 25.2 1.0
N B:ILE1060 4.1 29.4 1.0
ND1 B:HIS1055 4.2 23.3 1.0
CE1 B:HIS1055 4.2 22.4 1.0
CA B:HIS1055 4.2 18.9 1.0
CA B:ILE1060 4.3 28.6 1.0
CB B:ASP1004 4.3 19.0 1.0
CG B:HIS1055 4.4 21.7 1.0
N B:GLN1061 4.4 26.6 1.0
NE2 B:HIS1055 4.5 22.6 1.0
N B:GLY1056 4.5 21.3 1.0
CA B:GLN1061 4.6 24.9 1.0
CD2 B:HIS1055 4.6 23.5 1.0
O B:HOH3177 4.6 25.5 1.0
CB B:ILE1060 4.7 32.1 1.0
CA B:GLY1056 4.7 21.0 1.0
N B:ARG1062 4.7 21.5 1.0
CB B:ASP1058 4.7 20.2 1.0
O B:HOH3145 4.7 34.9 1.0
NE2 B:GLN1061 4.8 32.4 1.0
N B:GLY1059 4.8 28.4 1.0
N B:ASP1058 4.8 21.0 1.0
C B:GLY1056 4.9 24.3 1.0
O B:HOH3227 4.9 31.4 1.0
CB B:HIS1055 5.0 18.8 1.0
O B:ARG1054 5.0 23.6 1.0

Calcium binding site 3 out of 4 in 2yic

Go back to Calcium Binding Sites List in 2yic
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)


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 (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:20.3
occ:1.00
 O C:ILE1060 2.2 25.5 1.0
O C:HOH3236 2.3 20.4 1.0
O C:HOH3237 2.3 18.3 1.0
O C:HIS1055 2.3 18.7 1.0
OD1 C:ASP1058 2.4 24.5 1.0
OD2 C:ASP1004 2.5 25.5 1.0
OD1 C:ASP1004 2.6 18.2 1.0
CG C:ASP1004 2.8 21.6 1.0
CG C:ASP1058 3.4 23.9 1.0
C C:ILE1060 3.4 28.0 1.0
C C:HIS1055 3.5 19.1 1.0
OD2 C:ASP1058 3.6 24.8 1.0
N C:ILE1060 4.0 27.6 1.0
ND1 C:HIS1055 4.1 20.9 1.0
CE1 C:HIS1055 4.2 19.8 1.0
CA C:HIS1055 4.2 16.4 1.0
CA C:ILE1060 4.2 26.1 1.0
CB C:ASP1004 4.3 17.7 1.0
CG C:HIS1055 4.4 19.6 1.0
NE2 C:HIS1055 4.4 20.6 1.0
O C:HOH3207 4.4 23.0 1.0
N C:GLN1061 4.4 23.4 1.0
N C:GLY1056 4.5 16.7 1.0
CD2 C:HIS1055 4.5 21.1 1.0
CA C:GLN1061 4.6 21.0 1.0
O C:HOH3274 4.6 34.2 1.0
CB C:ILE1060 4.7 28.7 1.0
N C:ARG1062 4.7 14.5 1.0
CA C:GLY1056 4.7 17.1 1.0
CB C:ASP1058 4.8 22.8 1.0
N C:GLY1059 4.8 27.1 1.0
NE2 C:GLN1061 4.8 48.7 1.0
N C:ASP1058 4.9 21.9 1.0
O C:HOH3167 4.9 28.8 1.0
C C:GLY1056 4.9 21.9 1.0
OE1 C:GLN1061 4.9 40.3 1.0
CB C:HIS1055 4.9 16.2 1.0
O C:ARG1054 5.0 20.9 1.0
O C:ARG1062 5.0 18.1 1.0

Calcium binding site 4 out of 4 in 2yic

Go back to Calcium Binding Sites List in 2yic
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase (Triclinic Form)


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 (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:25.0
occ:1.00
 O D:HIS1055 2.3 26.7 1.0
O D:ILE1060 2.3 27.5 1.0
O D:HOH3175 2.4 31.3 1.0
O D:HOH3174 2.4 23.5 1.0
OD1 D:ASP1058 2.4 25.0 1.0
OD2 D:ASP1004 2.5 32.2 1.0
OD1 D:ASP1004 2.5 29.2 1.0
CG D:ASP1004 2.8 28.5 1.0
CG D:ASP1058 3.4 24.1 1.0
C D:HIS1055 3.5 25.7 1.0
C D:ILE1060 3.5 28.0 1.0
OD2 D:ASP1058 3.6 24.6 1.0
N D:ILE1060 4.1 28.3 1.0
ND1 D:HIS1055 4.2 25.8 1.0
CA D:HIS1055 4.2 21.4 1.0
CE1 D:HIS1055 4.3 25.0 1.0
CB D:ASP1004 4.3 22.8 1.0
CA D:ILE1060 4.4 27.0 1.0
CG D:HIS1055 4.4 24.1 1.0
NE2 D:HIS1055 4.5 25.2 1.0
N D:GLN1061 4.5 21.9 1.0
N D:GLY1056 4.5 22.2 1.0
O D:HOH3152 4.6 22.8 1.0
CD2 D:HIS1055 4.6 26.1 1.0
CA D:GLN1061 4.6 21.1 1.0
CA D:GLY1056 4.6 22.4 1.0
NE2 D:GLN1061 4.7 40.9 1.0
CB D:ASP1058 4.8 22.1 1.0
N D:ARG1062 4.8 22.4 1.0
O D:HOH3201 4.8 38.5 1.0
N D:ASP1058 4.8 23.2 1.0
N D:GLY1059 4.9 30.4 1.0
C D:GLY1056 4.9 26.5 1.0
CB D:ILE1060 4.9 29.9 1.0
CB D:HIS1055 5.0 21.4 1.0
O D:ARG1054 5.0 23.5 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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