Calcium in PDB 6i2r: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara:
1.2.4.2; 2.2.1.5; 2.3.1.61; 4.1.1.71;

Protein crystallography data

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara, PDB code: 6i2r was solved by T.Wagner, M.Bellinzoni, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.15 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 95.745, 143.145, 167.106, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.9

Other elements in 6i2r:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara (pdb code 6i2r). 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 the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara, PDB code: 6i2r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6i2r

Go back to Calcium Binding Sites List in 6i2r
Calcium binding site 1 out of 2 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara


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 Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:23.3
occ:1.00
 O A:ILE1060 2.2 36.2 1.0
O A:HOH2102 2.3 20.9 1.0
O A:HIS1055 2.3 24.7 1.0
OD2 A:ASP1058 2.4 21.3 1.0
OD2 A:ASP1004 2.4 24.3 1.0
O A:HOH2301 2.4 23.0 1.0
OD1 A:ASP1004 2.6 23.3 1.0
CG A:ASP1004 2.8 25.7 1.0
CG A:ASP1058 3.3 28.1 1.0
OD1 A:ASP1058 3.4 26.1 1.0
C A:ILE1060 3.4 34.8 1.0
C A:HIS1055 3.5 25.3 1.0
N A:ILE1060 4.0 32.4 1.0
ND1 A:HIS1055 4.0 24.5 1.0
CE1 A:HIS1055 4.1 23.9 1.0
CA A:HIS1055 4.2 20.3 1.0
CA A:ILE1060 4.2 33.0 1.0
CB A:ASP1004 4.3 20.9 1.0
CG A:HIS1055 4.3 23.1 1.0
NE2 A:HIS1055 4.4 23.9 1.0
N A:GLN1061 4.5 28.6 1.0
CB A:ILE1060 4.6 36.9 1.0
CD2 A:HIS1055 4.6 24.4 1.0
N A:GLY1056 4.6 21.1 1.0
O A:HOH2176 4.6 27.8 1.0
CA A:GLN1061 4.7 27.6 1.0
CB A:ASP1058 4.7 23.2 1.0
N A:GLY1059 4.7 27.0 1.0
N A:ARG1062 4.8 25.3 1.0
O A:HOH2238 4.8 40.1 1.0
CA A:GLY1056 4.8 20.8 1.0
N A:ASP1058 4.8 22.9 1.0
CB A:HIS1055 4.9 19.6 1.0
O A:HOH2265 4.9 35.8 1.0
C A:GLY1056 5.0 25.4 1.0
O A:ARG1054 5.0 27.7 1.0
CG2 A:ILE1060 5.0 36.0 1.0

Calcium binding site 2 out of 2 in 6i2r

Go back to Calcium Binding Sites List in 6i2r
Calcium binding site 2 out of 2 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara


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 Kgd (Alpha-Ketoglutarate Decarboxylase), Mutant R802A, in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:27.6
occ:1.00
 O C:ILE1060 2.2 35.3 1.0
OD2 C:ASP1004 2.3 36.2 1.0
O C:HOH2271 2.3 22.3 1.0
O C:HIS1055 2.3 28.5 1.0
O C:HOH2145 2.4 28.7 1.0
OD2 C:ASP1058 2.5 34.4 1.0
OD1 C:ASP1004 2.6 25.4 1.0
CG C:ASP1004 2.7 30.7 1.0
CG C:ASP1058 3.4 30.9 1.0
C C:ILE1060 3.4 36.6 1.0
C C:HIS1055 3.5 29.6 1.0
OD1 C:ASP1058 3.6 30.6 1.0
N C:ILE1060 4.0 34.6 1.0
ND1 C:HIS1055 4.1 29.7 1.0
CE1 C:HIS1055 4.2 28.9 1.0
CB C:ASP1004 4.2 24.8 1.0
CA C:ILE1060 4.2 33.6 1.0
CA C:HIS1055 4.3 26.3 1.0
CG C:HIS1055 4.4 28.6 1.0
NE2 C:HIS1055 4.4 29.4 1.0
N C:GLN1061 4.4 31.9 1.0
O C:HOH2184 4.5 25.2 1.0
CD2 C:HIS1055 4.6 30.0 1.0
N C:GLY1056 4.6 27.2 1.0
CA C:GLN1061 4.6 30.5 1.0
CB C:ILE1060 4.6 36.7 1.0
O C:HOH2232 4.7 35.4 1.0
N C:GLY1059 4.8 33.6 1.0
CA C:GLY1056 4.8 27.7 1.0
N C:ARG1062 4.8 28.2 1.0
CB C:ASP1058 4.8 28.1 1.0
N C:ASP1058 4.9 28.8 1.0
C C:GLY1056 4.9 33.6 1.0
NE2 C:GLN1061 4.9 51.4 1.0
CB C:HIS1055 5.0 25.9 1.0

Reference:

T.Wagner, G.Andre-Leroux, V.Hindie, N.Barilone, M.N.Lisa, S.Hoos, B.Raynal, B.Vulliez-Le Normand, H.M.O'hare, M.Bellinzoni, P.M.Alzari. Structural Insights Into the Functional Versatility of An Fha Domain Protein in Mycobacterial Signaling. Sci.Signal. V. 12 2019.
ISSN: ESSN 1937-9145
PubMed: 31064884
DOI: 10.1126/SCISIGNAL.AAV9504
Page generated: Sat Dec 12 06:10:44 2020

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