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Calcium in PDB 2xta: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (Triclinic Form):
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 Acetyl-Coa (Triclinic Form), PDB code: 2xta 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) 78.11 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.550, 83.580, 160.070, 99.59, 98.94, 100.68
R / Rfree (%) 18.8 / 21.36

Other elements in 2xta:

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

Calcium binding site 1 out of 4 in 2xta

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

b:75.6
occ:1.00
 OD1 A:ASP1004 2.4 60.4 1.0
O A:ILE1060 2.5 42.2 1.0
O A:HIS1055 2.6 34.8 1.0
OD1 A:ASP1058 2.7 52.1 1.0
OD2 A:ASP1004 2.9 76.2 1.0
O A:HOH3144 2.9 49.8 1.0
CG A:ASP1004 3.0 59.6 1.0
C A:ILE1060 3.5 43.2 1.0
ND1 A:HIS1055 3.5 34.6 1.0
C A:HIS1055 3.6 34.4 1.0
CE1 A:HIS1055 3.6 32.6 1.0
O A:HOH3143 3.7 45.7 1.0
CG A:ASP1058 3.8 52.4 1.0
N A:ILE1060 3.9 44.4 1.0
CG A:HIS1055 4.0 33.3 1.0
OD2 A:ASP1058 4.1 61.9 1.0
CA A:HIS1055 4.1 32.5 1.0
NE2 A:HIS1055 4.1 32.5 1.0
CA A:ILE1060 4.2 42.3 1.0
CD2 A:HIS1055 4.3 33.9 1.0
N A:GLN1061 4.5 37.9 1.0
CB A:ASP1004 4.5 37.0 1.0
O A:HOH3145 4.5 43.7 1.0
NE2 A:GLN1061 4.5 76.0 1.0
N A:GLY1059 4.6 45.9 1.0
CB A:ILE1060 4.6 44.9 1.0
CB A:HIS1055 4.6 30.9 1.0
CA A:GLN1061 4.7 35.5 1.0
C A:GLY1059 4.7 51.1 1.0
N A:GLY1056 4.8 29.4 1.0
N A:ARG1062 4.8 32.9 1.0
O A:ARG1062 4.8 31.8 1.0
CA A:GLY1059 5.0 46.3 1.0

Calcium binding site 2 out of 4 in 2xta

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

b:74.5
occ:1.00
 OD1 B:ASP1004 2.2 57.3 1.0
O B:ILE1060 2.5 54.0 1.0
O B:HIS1055 2.6 40.2 1.0
OD2 B:ASP1004 2.7 63.6 1.0
O B:HOH3153 2.7 56.5 1.0
CG B:ASP1004 2.8 55.7 1.0
OD1 B:ASP1058 2.9 51.2 1.0
O B:HOH3152 3.3 43.8 1.0
C B:ILE1060 3.5 53.0 1.0
ND1 B:HIS1055 3.7 34.0 1.0
CE1 B:HIS1055 3.7 32.5 1.0
C B:HIS1055 3.7 39.1 1.0
N B:ILE1060 3.9 49.5 1.0
CG B:ASP1058 4.0 53.5 1.0
NE2 B:HIS1055 4.0 32.6 1.0
CG B:HIS1055 4.1 33.2 1.0
CA B:ILE1060 4.2 49.0 1.0
CA B:HIS1055 4.2 32.2 1.0
CB B:ASP1004 4.3 38.4 1.0
NE2 B:GLN1061 4.3 63.7 1.0
CD2 B:HIS1055 4.3 33.6 1.0
OD2 B:ASP1058 4.3 58.2 1.0
N B:GLN1061 4.3 46.8 1.0
CA B:GLN1061 4.5 43.8 1.0
N B:GLY1059 4.7 49.8 1.0
N B:ARG1062 4.7 36.8 1.0
C B:GLY1059 4.7 54.9 1.0
CB B:ILE1060 4.7 52.8 1.0
O B:ARG1062 4.8 37.1 1.0
CB B:HIS1055 4.8 31.0 1.0
N B:GLY1056 4.9 36.8 1.0

Calcium binding site 3 out of 4 in 2xta

Go back to Calcium Binding Sites List in 2xta
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Alpha-Ketoglutarate Decarboxylase in Complex with Acetyl-Coa (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 in Complex with Acetyl-Coa (Triclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:55.0
occ:1.00
 OD1 C:ASP1004 2.4 63.4 1.0
O C:ILE1060 2.5 39.9 1.0
O C:HIS1055 2.5 36.1 1.0
OD1 C:ASP1058 2.7 49.8 1.0
OD2 C:ASP1004 2.9 71.9 1.0
O C:HOH3147 2.9 47.6 1.0
O C:HOH3146 3.0 45.8 1.0
CG C:ASP1004 3.0 60.4 1.0
C C:ILE1060 3.5 41.0 1.0
ND1 C:HIS1055 3.6 33.4 1.0
C C:HIS1055 3.6 36.0 1.0
CE1 C:HIS1055 3.7 31.5 1.0
CG C:ASP1058 3.8 50.2 1.0
N C:ILE1060 3.9 38.4 1.0
CG C:HIS1055 4.0 32.2 1.0
CA C:HIS1055 4.1 30.9 1.0
OD2 C:ASP1058 4.1 56.6 1.0
NE2 C:HIS1055 4.1 31.3 1.0
CA C:ILE1060 4.2 38.0 1.0
CD2 C:HIS1055 4.3 32.3 1.0
O C:HOH3124 4.4 30.3 1.0
N C:GLN1061 4.4 36.3 1.0
CB C:ASP1004 4.5 35.7 1.0
O C:HOH3123 4.5 51.7 1.0
N C:GLY1059 4.5 38.0 1.0
NE2 C:GLN1061 4.6 78.1 1.0
C C:GLY1059 4.6 43.9 1.0
CB C:ILE1060 4.6 41.1 1.0
CA C:GLN1061 4.6 35.1 1.0
CB C:HIS1055 4.7 30.2 1.0
N C:GLY1056 4.8 34.8 1.0
N C:ARG1062 4.8 32.4 1.0
O C:ARG1062 4.9 30.6 1.0
CA C:GLY1059 4.9 38.4 1.0

Calcium binding site 4 out of 4 in 2xta

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

b:57.8
occ:1.00
 OD1 D:ASP1004 2.3 51.8 1.0
O D:HIS1055 2.4 38.1 1.0
OD2 D:ASP1004 2.5 62.2 1.0
CG D:ASP1004 2.8 51.6 1.0
O D:ILE1060 2.8 49.1 1.0
OD1 D:ASP1058 3.0 50.1 1.0
C D:HIS1055 3.5 39.3 1.0
ND1 D:HIS1055 3.7 37.8 1.0
CE1 D:HIS1055 3.7 35.7 1.0
C D:ILE1060 3.7 48.5 1.0
O D:HOH3130 3.8 41.9 1.0
CG D:HIS1055 4.0 36.2 1.0
NE2 D:HIS1055 4.0 35.7 1.0
CG D:ASP1058 4.1 52.8 1.0
N D:ILE1060 4.1 47.4 1.0
CA D:HIS1055 4.2 34.1 1.0
CD2 D:HIS1055 4.2 36.4 1.0
CB D:ASP1004 4.2 36.7 1.0
NE2 D:GLN1061 4.3 68.9 1.0
OD2 D:ASP1058 4.4 61.4 1.0
CA D:ILE1060 4.5 47.0 1.0
N D:GLN1061 4.6 40.5 1.0
N D:GLY1056 4.6 37.8 1.0
N D:GLY1059 4.6 44.0 1.0
CB D:HIS1055 4.7 33.4 1.0
CA D:GLN1061 4.7 37.7 1.0
C D:GLY1059 4.8 50.6 1.0
CA D:GLY1056 4.9 37.4 1.0
CA D:GLY1059 5.0 44.4 1.0
N D:ARG1062 5.0 34.6 1.0
O D:ARG1062 5.0 32.5 1.0
CB D:ILE1060 5.0 50.2 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: Fri Jul 12 19:15:30 2024

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