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

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

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First 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, First Post-Decarboxylation Intermediate From 2-Oxoadipate, PDB code: 3zht 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) 41.11 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.366, 83.800, 159.513, 99.76, 99.06, 100.61
R / Rfree (%) 22.3 / 24.57

Other elements in 3zht:

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

Calcium binding site 1 out of 4 in 3zht

Go back to Calcium Binding Sites List in 3zht
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First 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, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:38.1
occ:1.00
 O A:ILE1060 2.3 43.4 1.0
O A:HIS1055 2.4 35.0 1.0
OD2 A:ASP1004 2.4 43.9 1.0
OD1 A:ASP1058 2.5 35.4 1.0
O A:HOH3233 2.5 33.4 1.0
OD1 A:ASP1004 2.5 37.2 1.0
O A:HOH3234 2.6 41.1 1.0
CG A:ASP1004 2.8 38.3 1.0
CG A:ASP1058 3.4 37.8 1.0
C A:ILE1060 3.5 43.8 1.0
C A:HIS1055 3.5 35.0 1.0
OD2 A:ASP1058 3.6 42.7 1.0
ND1 A:HIS1055 4.0 34.4 1.0
N A:ILE1060 4.0 44.1 1.0
CE1 A:HIS1055 4.1 33.0 1.0
CA A:HIS1055 4.2 30.1 1.0
CG A:HIS1055 4.3 33.0 1.0
CB A:ASP1004 4.3 32.0 1.0
CA A:ILE1060 4.3 43.1 1.0
NE2 A:HIS1055 4.3 33.2 1.0
CD2 A:HIS1055 4.4 34.1 1.0
N A:GLN1061 4.5 37.0 1.0
O A:HOH3206 4.5 34.3 1.0
NE2 A:GLN1061 4.6 72.9 1.0
N A:GLY1056 4.6 33.1 1.0
CA A:GLN1061 4.6 36.2 1.0
O A:HOH3163 4.7 38.6 1.0
CB A:ILE1060 4.7 46.1 1.0
N A:ARG1062 4.7 32.7 1.0
O A:HOH3273 4.8 38.9 1.0
N A:GLY1059 4.8 44.9 1.0
CB A:ASP1058 4.8 37.9 1.0
CB A:HIS1055 4.9 30.2 1.0
CA A:GLY1056 4.9 33.3 1.0
N A:ASP1058 4.9 38.2 1.0
O A:ARG1062 5.0 33.0 1.0

Calcium binding site 2 out of 4 in 3zht

Go back to Calcium Binding Sites List in 3zht
Calcium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First 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, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:43.4
occ:1.00
 O B:ILE1060 2.2 50.2 1.0
OD2 B:ASP1004 2.4 49.9 1.0
OD1 B:ASP1004 2.4 40.8 1.0
O B:HOH3159 2.4 33.9 1.0
O B:HIS1055 2.4 37.5 1.0
OD1 B:ASP1058 2.6 42.7 1.0
CG B:ASP1004 2.7 40.8 1.0
O B:HOH3160 2.8 39.3 1.0
C B:ILE1060 3.4 49.0 1.0
CG B:ASP1058 3.5 43.3 1.0
C B:HIS1055 3.6 37.8 1.0
OD2 B:ASP1058 3.7 44.3 1.0
ND1 B:HIS1055 4.0 36.0 1.0
CE1 B:HIS1055 4.0 35.2 1.0
N B:ILE1060 4.1 46.9 1.0
CB B:ASP1004 4.1 36.0 1.0
CA B:HIS1055 4.3 32.0 1.0
CG B:HIS1055 4.3 34.5 1.0
CA B:ILE1060 4.3 47.2 1.0
NE2 B:HIS1055 4.3 35.7 1.0
NE2 B:GLN1061 4.3 37.1 1.0
N B:GLN1061 4.4 42.5 1.0
CD2 B:HIS1055 4.4 36.2 1.0
CA B:GLN1061 4.5 40.4 1.0
N B:ARG1062 4.5 34.2 1.0
O B:HOH3140 4.5 38.6 1.0
N B:GLY1056 4.7 36.4 1.0
CB B:ILE1060 4.7 51.0 1.0
N B:GLY1059 4.9 45.6 1.0
O B:HOH3113 4.9 56.2 1.0
O B:ARG1062 4.9 35.9 1.0
CB B:HIS1055 4.9 31.4 1.0
CB B:ASP1058 4.9 42.0 1.0
CA B:GLY1056 4.9 37.0 1.0
CD B:GLN1061 5.0 58.8 1.0

Calcium binding site 3 out of 4 in 3zht

Go back to Calcium Binding Sites List in 3zht
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First 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, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:38.5
occ:1.00
 O C:ILE1060 2.2 42.8 1.0
O C:HOH3212 2.3 32.5 1.0
OD2 C:ASP1004 2.4 39.3 1.0
O C:HIS1055 2.4 34.5 1.0
OD1 C:ASP1004 2.5 38.0 1.0
OD1 C:ASP1058 2.5 41.6 1.0
O C:HOH3213 2.6 42.1 1.0
CG C:ASP1004 2.7 37.5 1.0
C C:ILE1060 3.4 43.1 1.0
CG C:ASP1058 3.5 40.1 1.0
C C:HIS1055 3.6 34.5 1.0
OD2 C:ASP1058 3.7 38.8 1.0
N C:ILE1060 4.0 42.1 1.0
ND1 C:HIS1055 4.1 30.8 1.0
CE1 C:HIS1055 4.1 29.9 1.0
CB C:ASP1004 4.2 32.1 1.0
CA C:HIS1055 4.2 28.6 1.0
CA C:ILE1060 4.3 40.8 1.0
CG C:HIS1055 4.3 29.9 1.0
NE2 C:HIS1055 4.3 30.4 1.0
NE2 C:GLN1061 4.4 67.7 1.0
O C:HOH3184 4.4 29.7 1.0
N C:GLN1061 4.4 37.3 1.0
CD2 C:HIS1055 4.5 30.9 1.0
CA C:GLN1061 4.5 36.0 1.0
N C:GLY1056 4.6 33.9 1.0
N C:ARG1062 4.6 32.6 1.0
CB C:ILE1060 4.7 43.8 1.0
N C:GLY1059 4.8 43.1 1.0
O C:HOH3144 4.8 51.8 1.0
CB C:ASP1058 4.9 38.6 1.0
CA C:GLY1056 4.9 34.6 1.0
O C:HOH3250 4.9 49.7 1.0
CB C:HIS1055 4.9 27.4 1.0
N C:ASP1058 4.9 37.7 1.0
CD C:GLN1061 5.0 77.1 1.0

Calcium binding site 4 out of 4 in 3zht

Go back to Calcium Binding Sites List in 3zht
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, First 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, First Post-Decarboxylation Intermediate From 2-Oxoadipate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:41.6
occ:1.00
 O D:ILE1060 2.3 46.8 1.0
O D:HOH3159 2.3 42.0 1.0
OD2 D:ASP1004 2.3 40.0 1.0
O D:HIS1055 2.3 38.4 1.0
O D:HOH3158 2.4 39.2 1.0
OD1 D:ASP1058 2.5 40.8 1.0
OD1 D:ASP1004 2.6 34.7 1.0
CG D:ASP1004 2.8 36.3 1.0
CG D:ASP1058 3.5 42.5 1.0
C D:HIS1055 3.5 39.1 1.0
C D:ILE1060 3.5 47.1 1.0
OD2 D:ASP1058 3.7 39.2 1.0
N D:ILE1060 4.0 47.9 1.0
ND1 D:HIS1055 4.1 34.3 1.0
CE1 D:HIS1055 4.1 32.6 1.0
CA D:HIS1055 4.2 33.0 1.0
CB D:ASP1004 4.2 34.5 1.0
CG D:HIS1055 4.3 33.5 1.0
CA D:ILE1060 4.3 47.1 1.0
NE2 D:HIS1055 4.3 33.0 1.0
NE2 D:GLN1061 4.4 53.6 1.0
CD2 D:HIS1055 4.4 34.3 1.0
O D:HOH3138 4.5 37.5 1.0
N D:GLN1061 4.5 41.7 1.0
N D:GLY1056 4.6 38.4 1.0
CA D:GLN1061 4.6 39.7 1.0
N D:ARG1062 4.7 34.5 1.0
N D:GLY1059 4.8 46.6 1.0
O D:HOH3184 4.8 44.4 1.0
CB D:ILE1060 4.8 50.4 1.0
CA D:GLY1056 4.8 39.3 1.0
CB D:ASP1058 4.8 43.6 1.0
CB D:HIS1055 4.9 31.1 1.0
N D:ASP1058 4.9 43.7 1.0
C D:GLY1056 5.0 45.2 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 21:38:16 2024

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