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Calcium in PDB 3zhq: Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd

Enzymatic activity of Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd

All present enzymatic activity of Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd:
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 H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd, PDB code: 3zhq 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) 48.97 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.675, 83.737, 159.577, 99.86, 98.95, 100.44
R / Rfree (%) 19.37 / 22.34

Other elements in 3zhq:

The structure of Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd 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 H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd (pdb code 3zhq). 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 H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd, PDB code: 3zhq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 3zhq

Go back to Calcium Binding Sites List in 3zhq
Calcium binding site 1 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd


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 H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:32.3
occ:1.00
 O A:ILE1060 2.3 39.4 1.0
O A:HIS1055 2.3 36.9 1.0
OD1 A:ASP1004 2.4 35.7 1.0
OD1 A:ASP1058 2.5 36.6 1.0
O A:HOH3140 2.5 23.0 1.0
OD2 A:ASP1004 2.6 45.2 1.0
O A:HOH3141 2.8 35.9 1.0
CG A:ASP1004 2.8 37.5 1.0
CG A:ASP1058 3.4 39.8 1.0
C A:HIS1055 3.5 35.4 1.0
C A:ILE1060 3.5 38.1 1.0
OD2 A:ASP1058 3.7 50.4 1.0
ND1 A:HIS1055 4.1 35.1 1.0
N A:ILE1060 4.1 36.1 1.0
CE1 A:HIS1055 4.1 33.3 1.0
CA A:HIS1055 4.2 31.2 1.0
CB A:ASP1004 4.3 32.2 1.0
CG A:HIS1055 4.3 32.9 1.0
CA A:ILE1060 4.3 34.2 1.0
NE2 A:HIS1055 4.4 33.1 1.0
CD2 A:HIS1055 4.5 33.7 1.0
N A:GLN1061 4.5 33.2 1.0
NE2 A:GLN1061 4.5 67.8 1.0
N A:GLY1056 4.5 32.3 1.0
CA A:GLN1061 4.6 32.0 1.0
N A:ARG1062 4.6 34.9 1.0
O A:HOH3121 4.7 36.8 1.0
O A:HOH3093 4.7 39.3 1.0
CB A:ILE1060 4.7 36.6 1.0
CA A:GLY1056 4.8 32.6 1.0
CB A:ASP1058 4.8 33.6 1.0
N A:GLY1059 4.8 36.7 1.0
O A:ARG1062 4.8 38.0 1.0
CB A:HIS1055 4.9 30.4 1.0
N A:ASP1058 5.0 34.5 1.0

Calcium binding site 2 out of 4 in 3zhq

Go back to Calcium Binding Sites List in 3zhq
Calcium binding site 2 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd


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 H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:38.2
occ:1.00
 O B:HIS1055 2.2 35.8 1.0
O B:HOH3106 2.3 33.8 1.0
O B:HOH3107 2.3 35.2 1.0
O B:ILE1060 2.4 40.3 1.0
OD1 B:ASP1004 2.4 33.5 1.0
OD2 B:ASP1004 2.5 30.7 1.0
OD1 B:ASP1058 2.6 38.9 1.0
CG B:ASP1004 2.8 29.7 1.0
C B:HIS1055 3.4 36.4 1.0
CG B:ASP1058 3.5 40.9 1.0
C B:ILE1060 3.6 41.7 1.0
OD2 B:ASP1058 3.8 39.8 1.0
ND1 B:HIS1055 4.0 35.8 1.0
CE1 B:HIS1055 4.1 34.5 1.0
CA B:HIS1055 4.2 31.3 1.0
N B:ILE1060 4.2 40.4 1.0
CB B:ASP1004 4.2 29.1 1.0
CG B:HIS1055 4.3 33.9 1.0
NE2 B:HIS1055 4.3 34.6 1.0
CA B:ILE1060 4.4 39.8 1.0
CD2 B:HIS1055 4.4 34.9 1.0
N B:GLY1056 4.4 34.9 1.0
NE2 B:GLN1061 4.5 40.2 1.0
N B:GLN1061 4.6 37.6 1.0
O B:HOH3091 4.6 30.2 1.0
O B:HOH3074 4.6 36.0 1.0
O B:HOH3131 4.6 37.0 1.0
CA B:GLN1061 4.6 36.0 1.0
CA B:GLY1056 4.7 35.8 1.0
N B:ARG1062 4.7 29.5 1.0
CB B:ILE1060 4.8 42.8 1.0
CB B:HIS1055 4.9 31.2 1.0
N B:GLY1059 4.9 41.5 1.0
O B:ARG1062 4.9 31.9 1.0
CB B:ASP1058 4.9 38.8 1.0
C B:GLY1056 4.9 41.4 1.0

Calcium binding site 3 out of 4 in 3zhq

Go back to Calcium Binding Sites List in 3zhq
Calcium binding site 3 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd


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 H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:42.8
occ:1.00
 O C:HIS1055 2.3 39.6 1.0
O C:ILE1060 2.3 50.8 1.0
O C:HOH3120 2.4 25.6 1.0
OD1 C:ASP1004 2.4 39.5 1.0
OD1 C:ASP1058 2.5 52.4 1.0
OD2 C:ASP1004 2.6 44.9 1.0
CG C:ASP1004 2.8 41.2 1.0
O C:HOH3121 3.0 43.6 1.0
C C:HIS1055 3.5 39.5 1.0
CG C:ASP1058 3.5 51.6 1.0
C C:ILE1060 3.5 49.4 1.0
OD2 C:ASP1058 3.7 55.4 1.0
ND1 C:HIS1055 4.1 36.5 1.0
N C:ILE1060 4.1 46.3 1.0
CE1 C:HIS1055 4.1 34.8 1.0
CA C:HIS1055 4.2 34.4 1.0
CB C:ASP1004 4.3 37.6 1.0
CG C:HIS1055 4.3 35.2 1.0
CA C:ILE1060 4.3 45.3 1.0
NE2 C:HIS1055 4.4 34.6 1.0
CD2 C:HIS1055 4.5 35.7 1.0
NE2 C:GLN1061 4.5 96.5 1.0
N C:GLY1056 4.5 35.6 1.0
N C:GLN1061 4.5 45.2 1.0
CA C:GLN1061 4.6 43.5 1.0
N C:ARG1062 4.7 38.7 1.0
CA C:GLY1056 4.7 35.3 1.0
CB C:ILE1060 4.8 47.9 1.0
CB C:ASP1058 4.8 43.7 1.0
N C:GLY1059 4.8 43.8 1.0
CB C:HIS1055 4.9 32.5 1.0
O C:ARG1062 4.9 37.5 1.0
O C:HOH3078 4.9 29.2 1.0
N C:ASP1058 4.9 42.9 1.0
C C:GLY1056 5.0 41.5 1.0

Calcium binding site 4 out of 4 in 3zhq

Go back to Calcium Binding Sites List in 3zhq
Calcium binding site 4 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd


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 H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:40.7
occ:1.00
 O D:HOH3093 2.2 36.5 1.0
O D:ILE1060 2.3 38.0 1.0
O D:HIS1055 2.3 36.0 1.0
O D:HOH3094 2.4 45.4 1.0
OD1 D:ASP1058 2.5 37.5 1.0
OD1 D:ASP1004 2.5 38.9 1.0
OD2 D:ASP1004 2.6 40.7 1.0
CG D:ASP1004 2.9 37.1 1.0
CG D:ASP1058 3.5 41.5 1.0
C D:ILE1060 3.5 40.3 1.0
C D:HIS1055 3.5 35.2 1.0
OD2 D:ASP1058 3.7 43.0 1.0
N D:ILE1060 4.0 40.0 1.0
CA D:ILE1060 4.3 39.2 1.0
CA D:HIS1055 4.3 30.2 1.0
ND1 D:HIS1055 4.3 32.6 1.0
CE1 D:HIS1055 4.3 31.1 1.0
CB D:ASP1004 4.3 28.1 1.0
NE2 D:GLN1061 4.4 71.6 1.0
CG D:HIS1055 4.5 31.4 1.0
N D:GLN1061 4.5 36.5 1.0
N D:GLY1056 4.5 32.2 1.0
NE2 D:HIS1055 4.5 31.4 1.0
CD2 D:HIS1055 4.6 32.0 1.0
CA D:GLN1061 4.6 34.5 1.0
O D:HOH3085 4.7 35.8 1.0
CA D:GLY1056 4.7 32.9 1.0
N D:GLY1059 4.7 40.5 1.0
CB D:ILE1060 4.7 42.5 1.0
O D:HOH3106 4.7 51.1 1.0
N D:ARG1062 4.8 31.3 1.0
CB D:ASP1058 4.8 40.6 1.0
N D:ASP1058 4.9 39.2 1.0
C D:GLY1056 4.9 37.6 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: Tue Jul 8 18:13:42 2025

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