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Calcium in PDB 3zhu: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate:
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, Second Post-Decarboxylation Intermediate From 2-Oxoadipate, PDB code: 3zhu was solved by T.Wagner, N.Barilone, M.Bellinzoni, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.36 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.783, 82.286, 163.039, 99.19, 99.10, 100.71
R / Rfree (%) 19.99 / 23.49

Other elements in 3zhu:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate 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 Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate (pdb code 3zhu). 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 Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate, PDB code: 3zhu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3zhu

Go back to Calcium Binding Sites List in 3zhu
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate


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, Second Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:41.9
occ:1.00
 O A:ILE1060 2.3 39.7 1.0
O A:HOH3183 2.3 31.8 1.0
O A:HIS1055 2.3 40.8 1.0
O A:HOH3184 2.4 34.8 1.0
OD1 A:ASP1058 2.5 40.5 1.0
OD2 A:ASP1004 2.5 43.5 1.0
OD1 A:ASP1004 2.6 42.3 1.0
CG A:ASP1004 2.9 41.1 1.0
C A:ILE1060 3.5 41.4 1.0
C A:HIS1055 3.5 38.9 1.0
CG A:ASP1058 3.5 42.2 1.0
OD2 A:ASP1058 3.7 45.1 1.0
ND1 A:HIS1055 3.9 38.8 1.0
CE1 A:HIS1055 4.0 37.8 1.0
N A:ILE1060 4.1 43.3 1.0
CA A:HIS1055 4.1 34.8 1.0
CG A:HIS1055 4.2 37.4 1.0
CA A:ILE1060 4.2 41.7 1.0
NE2 A:HIS1055 4.2 37.9 1.0
CD2 A:HIS1055 4.3 38.5 1.0
CB A:ASP1004 4.3 35.3 1.0
O A:HOH3162 4.4 30.4 1.0
N A:GLN1061 4.4 35.7 1.0
N A:GLY1056 4.5 33.1 1.0
CB A:ILE1060 4.5 45.1 1.0
CA A:GLN1061 4.6 33.5 1.0
O A:HOH3130 4.7 41.8 1.0
N A:GLY1059 4.7 45.4 1.0
CB A:HIS1055 4.8 34.6 1.0
CA A:GLY1056 4.8 33.1 1.0
N A:ARG1062 4.8 31.2 1.0
CB A:ASP1058 4.8 40.8 1.0
NE2 A:GLN1061 4.9 50.7 1.0
C A:GLY1059 4.9 48.7 1.0
N A:ASP1058 4.9 39.0 1.0
O A:ARG1062 4.9 32.9 1.0
O A:ARG1054 5.0 41.3 1.0

Calcium binding site 2 out of 4 in 3zhu

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Calcium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate


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, Second Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:29.5
occ:1.00
 O B:HOH3149 2.2 19.2 1.0
O B:ILE1060 2.3 34.9 1.0
O B:HIS1055 2.3 29.9 1.0
OD2 B:ASP1004 2.4 38.7 1.0
O B:HOH3150 2.5 28.7 1.0
OD1 B:ASP1058 2.5 33.7 1.0
OD1 B:ASP1004 2.6 36.4 1.0
CG B:ASP1004 2.8 35.7 1.0
C B:ILE1060 3.5 33.9 1.0
C B:HIS1055 3.5 28.9 1.0
CG B:ASP1058 3.5 37.5 1.0
OD2 B:ASP1058 3.8 47.2 1.0
ND1 B:HIS1055 4.1 32.9 1.0
N B:ILE1060 4.1 34.3 1.0
CE1 B:HIS1055 4.1 31.6 1.0
CA B:HIS1055 4.2 27.0 1.0
CA B:ILE1060 4.3 32.4 1.0
O B:HOH3131 4.3 33.5 1.0
CG B:HIS1055 4.3 30.7 1.0
CB B:ASP1004 4.3 28.0 1.0
NE2 B:HIS1055 4.3 31.4 1.0
CD2 B:HIS1055 4.4 31.3 1.0
N B:GLN1061 4.5 28.3 1.0
N B:GLY1056 4.5 24.1 1.0
O B:HOH3173 4.6 44.6 1.0
CB B:ILE1060 4.6 35.4 1.0
CA B:GLN1061 4.6 27.2 1.0
N B:GLY1059 4.7 34.4 1.0
CA B:GLY1056 4.7 24.0 1.0
NE2 B:GLN1061 4.8 46.5 1.0
O B:HOH3167 4.8 38.7 1.0
CB B:ASP1058 4.8 30.0 1.0
N B:ASP1058 4.8 29.3 1.0
CB B:HIS1055 4.9 27.1 1.0
C B:GLY1059 4.9 38.7 1.0
N B:ARG1062 4.9 31.4 1.0
C B:GLY1056 4.9 31.5 1.0
O B:HOH3105 4.9 29.7 1.0
O B:ARG1054 5.0 34.8 1.0

Calcium binding site 3 out of 4 in 3zhu

Go back to Calcium Binding Sites List in 3zhu
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate


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 Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:28.8
occ:1.00
 O C:HOH3220 2.1 23.1 1.0
O C:ILE1060 2.2 35.3 1.0
O C:HIS1055 2.3 32.5 1.0
OD1 C:ASP1058 2.4 31.5 1.0
O C:HOH3221 2.5 25.5 1.0
OD2 C:ASP1004 2.5 43.1 1.0
OD1 C:ASP1004 2.6 38.5 1.0
CG C:ASP1004 2.9 38.0 1.0
C C:ILE1060 3.4 36.8 1.0
CG C:ASP1058 3.4 35.2 1.0
C C:HIS1055 3.5 33.0 1.0
OD2 C:ASP1058 3.8 38.5 1.0
N C:ILE1060 4.0 33.8 1.0
ND1 C:HIS1055 4.0 37.2 1.0
CE1 C:HIS1055 4.1 36.4 1.0
CA C:HIS1055 4.2 31.4 1.0
CA C:ILE1060 4.2 32.3 1.0
CG C:HIS1055 4.3 35.3 1.0
NE2 C:HIS1055 4.4 36.7 1.0
CB C:ASP1004 4.4 28.2 1.0
N C:GLN1061 4.4 32.9 1.0
CD2 C:HIS1055 4.5 37.0 1.0
O C:HOH3199 4.5 34.3 1.0
CB C:ILE1060 4.5 35.2 1.0
N C:GLY1056 4.5 29.6 1.0
CA C:GLN1061 4.6 31.5 1.0
N C:GLY1059 4.6 35.4 1.0
O C:HOH3255 4.6 33.0 1.0
CA C:GLY1056 4.8 30.5 1.0
CB C:ASP1058 4.8 33.0 1.0
O C:HOH3158 4.8 41.1 1.0
C C:GLY1059 4.8 39.2 1.0
NE2 C:GLN1061 4.8 53.2 1.0
N C:ASP1058 4.8 32.0 1.0
N C:ARG1062 4.9 30.8 1.0
CB C:HIS1055 4.9 31.8 1.0
O C:HOH3247 4.9 27.1 1.0
C C:GLY1056 5.0 35.7 1.0
O C:ARG1054 5.0 33.7 1.0

Calcium binding site 4 out of 4 in 3zhu

Go back to Calcium Binding Sites List in 3zhu
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate


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 Kgd, Second Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:41.1
occ:1.00
 O D:ILE1060 2.2 41.8 1.0
O D:HOH3155 2.4 37.0 1.0
O D:HIS1055 2.4 42.5 1.0
OD2 D:ASP1004 2.4 45.0 1.0
OD1 D:ASP1058 2.5 43.6 1.0
OD1 D:ASP1004 2.6 35.9 1.0
O D:HOH3156 2.6 45.9 1.0
CG D:ASP1004 2.8 37.5 1.0
C D:ILE1060 3.3 43.1 1.0
C D:HIS1055 3.6 40.0 1.0
CG D:ASP1058 3.6 44.1 1.0
OD2 D:ASP1058 3.9 47.9 1.0
N D:ILE1060 4.0 42.6 1.0
ND1 D:HIS1055 4.1 39.2 1.0
CE1 D:HIS1055 4.1 38.4 1.0
CA D:ILE1060 4.2 41.5 1.0
CB D:ASP1004 4.3 31.1 1.0
CA D:HIS1055 4.3 35.5 1.0
N D:GLN1061 4.3 39.0 1.0
CG D:HIS1055 4.3 37.5 1.0
NE2 D:HIS1055 4.4 38.8 1.0
O D:HOH3143 4.4 32.5 1.0
CD2 D:HIS1055 4.5 39.4 1.0
CA D:GLN1061 4.5 36.5 1.0
CB D:ILE1060 4.5 44.9 1.0
N D:GLY1056 4.6 33.9 1.0
N D:GLY1059 4.7 41.5 1.0
NE2 D:GLN1061 4.7 69.9 1.0
CA D:GLY1056 4.8 34.2 1.0
N D:ARG1062 4.8 31.0 1.0
C D:GLY1059 4.8 45.2 1.0
CB D:ASP1058 4.9 38.8 1.0
N D:ASP1058 5.0 38.2 1.0
CB D:HIS1055 5.0 35.2 1.0
C D:GLY1056 5.0 39.2 1.0
CD D:GLN1061 5.0 76.1 1.0

Reference:

T.Wagner, N.Barilone, P.M.Alzari, M.Bellinzoni. A Dual Conformation of the Post-Decarboxylation Intermediate Is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd). Biochem.J. V. 457 425 2014.
ISSN: ISSN 0264-6021
PubMed: 24171907
DOI: 10.1042/BJ20131142
Page generated: Tue Jul 8 18:15:11 2025

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