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Calcium in PDB 3zhs: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate:
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, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate, PDB code: 3zhs 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) 30.75 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.846, 83.713, 159.940, 99.89, 99.03, 100.20
R / Rfree (%) 20.04 / 22.83

Other elements in 3zhs:

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

Calcium binding site 1 out of 4 in 3zhs

Go back to Calcium Binding Sites List in 3zhs
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate


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, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:29.8
occ:1.00
 O A:ILE1060 2.3 37.5 1.0
O A:HOH3226 2.3 29.6 1.0
O A:HIS1055 2.4 29.3 1.0
OD1 A:ASP1058 2.4 34.1 1.0
O A:HOH3227 2.5 36.7 1.0
OD1 A:ASP1004 2.5 30.1 1.0
OD2 A:ASP1004 2.6 32.8 1.0
CG A:ASP1004 2.9 29.6 1.0
CG A:ASP1058 3.3 33.5 1.0
C A:ILE1060 3.5 36.1 1.0
OD2 A:ASP1058 3.5 39.3 1.0
C A:HIS1055 3.5 30.1 1.0
ND1 A:HIS1055 4.0 27.5 1.0
N A:ILE1060 4.1 35.1 1.0
CE1 A:HIS1055 4.1 25.6 1.0
CA A:HIS1055 4.1 25.7 1.0
CA A:ILE1060 4.2 32.7 1.0
CG A:HIS1055 4.3 26.9 1.0
CB A:ASP1004 4.3 22.6 1.0
NE2 A:HIS1055 4.4 26.0 1.0
N A:GLN1061 4.5 31.0 1.0
CD2 A:HIS1055 4.5 27.2 1.0
CB A:ILE1060 4.6 34.8 1.0
N A:GLY1056 4.6 28.5 1.0
CA A:GLN1061 4.6 30.1 1.0
O A:HOH3258 4.7 35.5 1.0
N A:ARG1062 4.7 29.4 1.0
CB A:ASP1058 4.7 28.9 1.0
NE2 A:GLN1061 4.8 55.0 1.0
O A:HOH3200 4.8 33.1 1.0
CB A:HIS1055 4.9 24.7 1.0
N A:ASP1058 4.9 29.9 1.0
N A:GLY1059 4.9 35.4 1.0
CA A:GLY1056 4.9 28.9 1.0
CG2 A:ILE1060 4.9 30.1 1.0
O A:ARG1062 5.0 31.0 1.0
O A:ARG1054 5.0 33.9 1.0

Calcium binding site 2 out of 4 in 3zhs

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


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, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:29.1
occ:1.00
 O B:ILE1060 2.2 39.0 1.0
O B:HIS1055 2.4 32.0 1.0
OD1 B:ASP1004 2.4 25.5 1.0
OD2 B:ASP1004 2.4 29.2 1.0
O B:HOH3174 2.4 37.4 1.0
OD1 B:ASP1058 2.5 26.5 1.0
O B:HOH3175 2.6 33.8 1.0
CG B:ASP1004 2.7 26.6 1.0
C B:ILE1060 3.5 38.6 1.0
CG B:ASP1058 3.5 31.0 1.0
C B:HIS1055 3.6 32.7 1.0
OD2 B:ASP1058 3.7 31.7 1.0
ND1 B:HIS1055 4.0 27.0 1.0
N B:ILE1060 4.1 35.2 1.0
CE1 B:HIS1055 4.1 25.3 1.0
CB B:ASP1004 4.2 27.3 1.0
CA B:HIS1055 4.2 25.4 1.0
CA B:ILE1060 4.3 35.1 1.0
CG B:HIS1055 4.3 26.1 1.0
NE2 B:HIS1055 4.4 25.3 1.0
N B:GLN1061 4.4 33.3 1.0
CD2 B:HIS1055 4.5 26.3 1.0
O B:HOH3201 4.5 31.6 1.0
CA B:GLN1061 4.6 32.1 1.0
O B:HOH3152 4.6 21.3 1.0
N B:GLY1056 4.6 32.4 1.0
NE2 B:GLN1061 4.6 65.7 1.0
N B:ARG1062 4.7 29.3 1.0
CB B:ILE1060 4.7 38.6 1.0
O B:HOH3124 4.8 33.9 1.0
CA B:GLY1056 4.9 32.8 1.0
CB B:ASP1058 4.9 32.8 1.0
CB B:HIS1055 4.9 24.4 1.0
N B:GLY1059 5.0 33.8 1.0
N B:ASP1058 5.0 32.9 1.0
O B:ARG1062 5.0 29.8 1.0

Calcium binding site 3 out of 4 in 3zhs

Go back to Calcium Binding Sites List in 3zhs
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate


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, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:34.0
occ:1.00
 O C:HOH3203 2.0 23.7 1.0
O C:ILE1060 2.4 41.9 1.0
O C:HOH3204 2.4 39.3 1.0
O C:HIS1055 2.4 34.4 1.0
OD1 C:ASP1058 2.4 34.0 1.0
OD2 C:ASP1004 2.5 42.2 1.0
OD1 C:ASP1004 2.5 32.7 1.0
CG C:ASP1004 2.8 34.2 1.0
CG C:ASP1058 3.4 34.9 1.0
C C:ILE1060 3.5 41.9 1.0
C C:HIS1055 3.6 35.3 1.0
OD2 C:ASP1058 3.6 42.0 1.0
N C:ILE1060 4.0 39.8 1.0
ND1 C:HIS1055 4.1 32.6 1.0
CE1 C:HIS1055 4.2 31.5 1.0
CA C:HIS1055 4.2 31.1 1.0
CA C:ILE1060 4.2 37.8 1.0
CB C:ASP1004 4.3 29.9 1.0
CG C:HIS1055 4.4 31.5 1.0
NE2 C:HIS1055 4.5 31.4 1.0
CB C:ILE1060 4.5 39.8 1.0
N C:GLN1061 4.5 38.1 1.0
CD2 C:HIS1055 4.6 32.6 1.0
N C:GLY1056 4.6 32.4 1.0
CA C:GLN1061 4.7 37.5 1.0
N C:ARG1062 4.8 37.2 1.0
CB C:ASP1058 4.8 34.4 1.0
N C:GLY1059 4.8 37.5 1.0
N C:ASP1058 4.9 36.2 1.0
CA C:GLY1056 4.9 32.7 1.0
O C:HOH3236 4.9 45.9 1.0
CB C:HIS1055 4.9 29.7 1.0

Calcium binding site 4 out of 4 in 3zhs

Go back to Calcium Binding Sites List in 3zhs
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate


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, First Post-Decarboxylation Intermediate From Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:31.7
occ:1.00
 O D:HIS1055 2.3 36.6 1.0
O D:ILE1060 2.3 35.5 1.0
O D:HOH3164 2.3 38.0 1.0
OD1 D:ASP1058 2.4 39.8 1.0
OD2 D:ASP1004 2.5 34.5 1.0
O D:HOH3163 2.5 32.1 1.0
OD1 D:ASP1004 2.6 31.2 1.0
CG D:ASP1004 2.8 32.7 1.0
CG D:ASP1058 3.4 37.7 1.0
C D:HIS1055 3.5 35.0 1.0
C D:ILE1060 3.5 36.0 1.0
OD2 D:ASP1058 3.6 34.3 1.0
ND1 D:HIS1055 4.1 32.7 1.0
N D:ILE1060 4.1 34.5 1.0
CA D:HIS1055 4.1 30.2 1.0
CE1 D:HIS1055 4.2 30.6 1.0
CA D:ILE1060 4.3 34.0 1.0
CG D:HIS1055 4.3 31.0 1.0
CB D:ASP1004 4.3 31.1 1.0
NE2 D:HIS1055 4.4 30.1 1.0
CD2 D:HIS1055 4.5 30.9 1.0
N D:GLN1061 4.5 32.6 1.0
N D:GLY1056 4.5 31.0 1.0
O D:HOH3144 4.6 31.5 1.0
CB D:ILE1060 4.7 38.0 1.0
CA D:GLN1061 4.7 31.7 1.0
NE2 D:GLN1061 4.7 65.2 1.0
CA D:GLY1056 4.8 29.3 1.0
CB D:ASP1058 4.8 34.7 1.0
N D:ARG1062 4.8 27.6 1.0
O D:HOH3185 4.8 43.0 1.0
N D:ASP1058 4.8 33.8 1.0
N D:GLY1059 4.9 34.6 1.0
CB D:HIS1055 4.9 29.5 1.0
C D:GLY1056 4.9 33.5 1.0
O D:ARG1054 5.0 33.6 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: Sat Jul 13 21:37:45 2024

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