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Calcium in PDB 3zhr: Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd Showing the Active Site Lid Closed

Enzymatic activity of Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd Showing the Active Site Lid Closed

All present enzymatic activity of Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd Showing the Active Site Lid Closed:
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 Showing the Active Site Lid Closed, PDB code: 3zhr 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 (°) 79.970, 83.450, 159.670, 99.64, 98.82, 100.98
R / Rfree (%) 18.01 / 20.2

Other elements in 3zhr:

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

Calcium binding site 1 out of 4 in 3zhr

Go back to Calcium Binding Sites List in 3zhr
Calcium binding site 1 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd Showing the Active Site Lid Closed


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 Showing the Active Site Lid Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:29.3
occ:1.00
 O A:HOH3238 2.2 29.7 1.0
O A:HIS1055 2.3 29.8 1.0
O A:ILE1060 2.3 34.4 1.0
OD2 A:ASP1004 2.3 34.1 1.0
O A:HOH3239 2.5 25.8 1.0
OD1 A:ASP1058 2.5 31.1 1.0
OD1 A:ASP1004 2.6 29.9 1.0
CG A:ASP1004 2.8 32.7 1.0
CG A:ASP1058 3.5 33.1 1.0
C A:HIS1055 3.5 30.0 1.0
C A:ILE1060 3.5 36.3 1.0
OD2 A:ASP1058 3.7 37.2 1.0
ND1 A:HIS1055 4.1 31.0 1.0
N A:ILE1060 4.1 34.7 1.0
CE1 A:HIS1055 4.2 29.3 1.0
CA A:HIS1055 4.2 28.2 1.0
CB A:ASP1004 4.2 32.0 1.0
CA A:ILE1060 4.3 34.9 1.0
CG A:HIS1055 4.3 29.4 1.0
NE2 A:HIS1055 4.4 29.5 1.0
CD2 A:HIS1055 4.5 30.6 1.0
N A:GLY1056 4.5 27.4 1.0
N A:GLN1061 4.5 31.4 1.0
NE2 A:GLN1061 4.6 76.8 1.0
O A:HOH3209 4.6 27.5 1.0
O A:HOH3171 4.6 37.8 1.0
O A:HOH3278 4.6 38.8 1.0
CB A:ILE1060 4.7 38.7 1.0
CA A:GLN1061 4.7 30.9 1.0
CA A:GLY1056 4.7 27.8 1.0
N A:ARG1062 4.7 29.5 1.0
N A:GLY1059 4.8 37.4 1.0
CB A:ASP1058 4.8 32.7 1.0
N A:ASP1058 4.9 32.8 1.0
C A:GLY1056 4.9 33.7 1.0
CB A:HIS1055 4.9 26.9 1.0

Calcium binding site 2 out of 4 in 3zhr

Go back to Calcium Binding Sites List in 3zhr
Calcium binding site 2 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd Showing the Active Site Lid Closed


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 Showing the Active Site Lid Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:32.3
occ:1.00
 O B:ILE1060 2.3 37.9 1.0
O B:HIS1055 2.3 32.3 1.0
O B:HOH3184 2.4 30.8 1.0
OD2 B:ASP1004 2.4 37.8 1.0
OD1 B:ASP1058 2.4 33.5 1.0
OD1 B:ASP1004 2.6 30.5 1.0
O B:HOH3185 2.6 21.9 1.0
CG B:ASP1004 2.8 32.6 1.0
CG B:ASP1058 3.4 34.5 1.0
C B:ILE1060 3.5 39.0 1.0
C B:HIS1055 3.5 32.5 1.0
OD2 B:ASP1058 3.6 35.2 1.0
N B:ILE1060 4.1 38.0 1.0
ND1 B:HIS1055 4.1 32.1 1.0
CE1 B:HIS1055 4.2 31.0 1.0
CA B:HIS1055 4.2 27.7 1.0
CB B:ASP1004 4.3 27.2 1.0
CA B:ILE1060 4.3 37.2 1.0
CG B:HIS1055 4.4 30.6 1.0
NE2 B:HIS1055 4.5 31.4 1.0
N B:GLN1061 4.5 34.5 1.0
N B:GLY1056 4.5 30.9 1.0
CD2 B:HIS1055 4.6 32.2 1.0
NE2 B:GLN1061 4.6 47.6 1.0
O B:HOH3166 4.6 41.8 1.0
CA B:GLN1061 4.7 33.6 1.0
N B:ARG1062 4.7 28.8 1.0
CA B:GLY1056 4.7 31.0 1.0
CB B:ASP1058 4.8 31.7 1.0
N B:GLY1059 4.8 36.0 1.0
O B:HOH3213 4.8 43.5 1.0
CB B:ILE1060 4.8 41.4 1.0
N B:ASP1058 4.8 30.3 1.0
O B:HOH3134 4.9 47.5 1.0
C B:GLY1056 4.9 35.2 1.0
CB B:HIS1055 5.0 27.9 1.0
O B:ARG1054 5.0 29.5 1.0

Calcium binding site 3 out of 4 in 3zhr

Go back to Calcium Binding Sites List in 3zhr
Calcium binding site 3 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd Showing the Active Site Lid Closed


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 Showing the Active Site Lid Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:29.4
occ:1.00
 O C:HOH3240 2.3 28.6 1.0
O C:HIS1055 2.3 24.8 1.0
O C:ILE1060 2.3 33.4 1.0
OD2 C:ASP1004 2.4 38.3 1.0
O C:HOH3241 2.5 24.8 1.0
OD1 C:ASP1058 2.5 34.1 1.0
OD1 C:ASP1004 2.5 36.3 1.0
CG C:ASP1004 2.7 36.6 1.0
CG C:ASP1058 3.5 31.7 1.0
C C:HIS1055 3.5 27.4 1.0
C C:ILE1060 3.5 35.4 1.0
OD2 C:ASP1058 3.7 33.7 1.0
ND1 C:HIS1055 4.0 28.6 1.0
N C:ILE1060 4.1 34.5 1.0
CE1 C:HIS1055 4.1 28.2 1.0
CA C:HIS1055 4.2 24.8 1.0
CB C:ASP1004 4.2 30.8 1.0
CA C:ILE1060 4.3 33.8 1.0
CG C:HIS1055 4.3 27.5 1.0
NE2 C:HIS1055 4.4 28.5 1.0
OE1 C:GLN1061 4.4 76.5 1.0
O C:HOH3211 4.4 24.5 1.0
CD2 C:HIS1055 4.5 28.7 1.0
N C:GLN1061 4.5 30.4 1.0
N C:GLY1056 4.5 25.9 1.0
CA C:GLN1061 4.7 29.7 1.0
N C:ARG1062 4.7 24.9 1.0
CB C:ILE1060 4.7 37.3 1.0
CA C:GLY1056 4.7 26.7 1.0
O C:HOH3172 4.8 37.6 1.0
N C:GLY1059 4.8 36.4 1.0
CB C:ASP1058 4.8 31.7 1.0
O C:HOH3273 4.9 41.1 1.0
CB C:HIS1055 4.9 25.1 1.0
N C:ASP1058 4.9 32.7 1.0
C C:GLY1056 5.0 32.9 1.0
O C:ARG1062 5.0 26.9 1.0

Calcium binding site 4 out of 4 in 3zhr

Go back to Calcium Binding Sites List in 3zhr
Calcium binding site 4 out of 4 in the Crystal Structure of the H747A Mutant of the Suca Domain of Mycobacterium Smegmatis Kgd Showing the Active Site Lid Closed


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 Showing the Active Site Lid Closed within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:30.1
occ:1.00
 O D:HIS1055 2.3 33.8 1.0
O D:ILE1060 2.3 32.8 1.0
O D:HOH3183 2.3 34.8 1.0
OD2 D:ASP1004 2.4 37.4 1.0
O D:HOH3184 2.4 34.8 1.0
OD1 D:ASP1058 2.5 27.4 1.0
OD1 D:ASP1004 2.5 29.9 1.0
CG D:ASP1004 2.8 32.1 1.0
CG D:ASP1058 3.4 33.0 1.0
C D:HIS1055 3.5 33.8 1.0
C D:ILE1060 3.5 34.9 1.0
OD2 D:ASP1058 3.6 37.3 1.0
ND1 D:HIS1055 4.1 32.5 1.0
N D:ILE1060 4.1 34.3 1.0
CE1 D:HIS1055 4.1 31.6 1.0
CA D:HIS1055 4.2 29.3 1.0
CB D:ASP1004 4.3 31.0 1.0
CG D:HIS1055 4.3 31.1 1.0
CA D:ILE1060 4.4 33.7 1.0
NE2 D:HIS1055 4.4 31.2 1.0
N D:GLY1056 4.5 31.2 1.0
N D:GLN1061 4.5 30.9 1.0
CD2 D:HIS1055 4.5 31.6 1.0
O D:HOH3161 4.6 34.0 1.0
NE2 D:GLN1061 4.6 67.8 1.0
CA D:GLN1061 4.7 29.4 1.0
CA D:GLY1056 4.7 30.8 1.0
N D:ARG1062 4.7 25.9 1.0
O D:HOH3209 4.7 37.9 1.0
CB D:ASP1058 4.8 31.6 1.0
N D:GLY1059 4.8 36.4 1.0
CB D:ILE1060 4.8 37.0 1.0
N D:ASP1058 4.9 30.8 1.0
CB D:HIS1055 4.9 28.6 1.0
C D:GLY1056 4.9 33.8 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 21:37:37 2024

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