Calcium in PDB 3zhv: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp):
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, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp), PDB code: 3zhv 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) 41.06 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.464, 83.702, 160.333, 99.68, 98.87, 100.63
R / Rfree (%) 20.34 / 23.54

Other elements in 3zhv:

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

Calcium binding site 1 out of 4 in 3zhv

Go back to Calcium Binding Sites List in 3zhv
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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

b:42.7
occ:1.00
 O A:HOH3206 2.2 35.0 1.0
O A:ILE1060 2.3 51.4 1.0
O A:HIS1055 2.4 43.7 1.0
OD2 A:ASP1004 2.4 54.8 1.0
OD1 A:ASP1058 2.4 53.7 1.0
O A:HOH3207 2.5 48.6 1.0
OD1 A:ASP1004 2.5 47.6 1.0
CG A:ASP1004 2.8 49.1 1.0
CG A:ASP1058 3.4 54.6 1.0
C A:ILE1060 3.5 52.4 1.0
C A:HIS1055 3.5 45.1 1.0
OD2 A:ASP1058 3.6 60.6 1.0
ND1 A:HIS1055 4.0 45.0 1.0
N A:ILE1060 4.1 53.4 1.0
CE1 A:HIS1055 4.1 43.1 1.0
CA A:HIS1055 4.2 41.4 1.0
CB A:ASP1004 4.2 39.8 1.0
CG A:HIS1055 4.3 43.4 1.0
CA A:ILE1060 4.3 51.8 1.0
NE2 A:HIS1055 4.4 42.9 1.0
CD2 A:HIS1055 4.5 44.0 1.0
N A:GLN1061 4.5 46.0 1.0
O A:HOH3179 4.5 33.9 1.0
N A:GLY1056 4.6 43.5 1.0
CA A:GLN1061 4.6 43.2 1.0
NE2 A:GLN1061 4.7 88.2 1.0
O A:HOH3145 4.7 45.4 1.0
O A:HOH3238 4.7 60.5 1.0
N A:ARG1062 4.7 40.2 1.0
CB A:ASP1058 4.8 51.9 1.0
CB A:ILE1060 4.8 54.7 1.0
N A:GLY1059 4.8 55.6 1.0
CA A:GLY1056 4.8 44.3 1.0
N A:ASP1058 4.9 52.0 1.0
CB A:HIS1055 4.9 40.5 1.0
CG2 A:ILE1060 4.9 52.5 1.0

Calcium binding site 2 out of 4 in 3zhv

Go back to Calcium Binding Sites List in 3zhv
Calcium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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

b:52.3
occ:1.00
 OD1 B:ASP1004 2.2 38.2 1.0
O B:ILE1060 2.3 51.8 1.0
OD1 B:ASP1058 2.4 48.9 1.0
O B:HIS1055 2.4 44.3 1.0
O B:HOH3160 2.6 45.4 1.0
CG B:ASP1004 2.9 42.3 1.0
OD2 B:ASP1004 2.9 48.3 1.0
O B:HOH3184 2.9 41.0 1.0
CG B:ASP1058 3.3 50.5 1.0
OD2 B:ASP1058 3.4 45.6 1.0
C B:ILE1060 3.4 51.7 1.0
C B:HIS1055 3.6 43.8 1.0
N B:ILE1060 4.1 48.7 1.0
ND1 B:HIS1055 4.1 40.9 1.0
CE1 B:HIS1055 4.1 39.2 1.0
CA B:HIS1055 4.3 36.7 1.0
CB B:ASP1004 4.3 40.3 1.0
CA B:ILE1060 4.3 49.0 1.0
N B:GLN1061 4.4 46.5 1.0
CG B:HIS1055 4.4 39.4 1.0
NE2 B:GLN1061 4.4 62.4 1.0
NE2 B:HIS1055 4.4 38.7 1.0
CA B:GLN1061 4.5 44.1 1.0
CD2 B:HIS1055 4.6 39.5 1.0
O B:HOH3141 4.6 34.2 1.0
N B:GLY1056 4.6 42.1 1.0
N B:ARG1062 4.7 39.3 1.0
CB B:ASP1058 4.7 45.9 1.0
N B:GLY1059 4.7 48.4 1.0
CA B:GLY1056 4.9 42.5 1.0
CB B:ILE1060 5.0 53.2 1.0
N B:ASP1058 5.0 44.8 1.0

Calcium binding site 3 out of 4 in 3zhv

Go back to Calcium Binding Sites List in 3zhv
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:48.0
occ:1.00
 O C:HOH3200 2.2 33.2 1.0
O C:ILE1060 2.3 57.3 1.0
O C:HIS1055 2.4 42.0 1.0
O C:HOH3201 2.5 44.3 1.0
OD1 C:ASP1004 2.5 49.9 1.0
OD2 C:ASP1004 2.5 62.9 1.0
OD1 C:ASP1058 2.6 52.5 1.0
CG C:ASP1004 2.8 50.8 1.0
C C:ILE1060 3.6 57.5 1.0
CG C:ASP1058 3.6 55.6 1.0
C C:HIS1055 3.6 44.6 1.0
OD2 C:ASP1058 3.9 62.6 1.0
N C:ILE1060 4.1 56.1 1.0
ND1 C:HIS1055 4.2 44.4 1.0
CE1 C:HIS1055 4.2 43.0 1.0
CB C:ASP1004 4.2 39.7 1.0
CA C:HIS1055 4.3 40.7 1.0
CA C:ILE1060 4.3 55.1 1.0
CG C:HIS1055 4.4 42.9 1.0
NE2 C:HIS1055 4.4 43.1 1.0
CD2 C:HIS1055 4.5 43.9 1.0
O C:HOH3136 4.5 63.1 1.0
N C:GLN1061 4.5 51.4 1.0
N C:GLY1056 4.6 45.2 1.0
NE2 C:GLN1061 4.7 95.9 1.0
CA C:GLN1061 4.7 49.0 1.0
N C:GLY1059 4.7 54.6 1.0
CA C:GLY1056 4.8 46.6 1.0
O C:HOH3231 4.8 61.7 1.0
N C:ARG1062 4.8 43.5 1.0
N C:ASP1058 4.8 52.9 1.0
CB C:ILE1060 4.8 58.4 1.0
CB C:ASP1058 4.9 53.4 1.0
C C:GLY1056 4.9 53.2 1.0
CB C:HIS1055 5.0 40.1 1.0

Calcium binding site 4 out of 4 in 3zhv

Go back to Calcium Binding Sites List in 3zhv
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp)


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, Post-Decarboxylation Intermediate From Pyruvate (2-Hydroxyethyl-Thdp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:44.5
occ:1.00
 OD1 D:ASP1058 2.3 42.8 1.0
O D:ILE1060 2.3 48.2 1.0
O D:HIS1055 2.4 46.2 1.0
OD2 D:ASP1004 2.4 44.5 1.0
O D:HOH3152 2.5 45.9 1.0
O D:HOH3151 2.5 40.2 1.0
OD1 D:ASP1004 2.6 37.4 1.0
CG D:ASP1004 2.8 39.4 1.0
CG D:ASP1058 3.1 47.2 1.0
OD2 D:ASP1058 3.3 44.6 1.0
C D:ILE1060 3.5 48.4 1.0
C D:HIS1055 3.5 45.3 1.0
ND1 D:HIS1055 4.0 41.6 1.0
CE1 D:HIS1055 4.1 40.1 1.0
N D:ILE1060 4.1 48.4 1.0
CA D:HIS1055 4.2 40.1 1.0
CB D:ASP1004 4.3 36.2 1.0
CG D:HIS1055 4.3 40.9 1.0
CA D:ILE1060 4.4 47.8 1.0
NE2 D:HIS1055 4.4 40.5 1.0
N D:GLN1061 4.4 42.0 1.0
O D:HOH3135 4.5 34.4 1.0
CD2 D:HIS1055 4.5 41.5 1.0
CB D:ASP1058 4.6 44.7 1.0
CA D:GLN1061 4.6 39.9 1.0
N D:GLY1056 4.6 43.4 1.0
N D:ARG1062 4.6 36.6 1.0
NE2 D:GLN1061 4.7 70.2 1.0
O D:HOH3173 4.8 55.1 1.0
N D:GLY1059 4.8 46.0 1.0
N D:ASP1058 4.8 43.8 1.0
CA D:GLY1056 4.8 43.1 1.0
CB D:HIS1055 4.9 39.0 1.0
CB D:ILE1060 4.9 52.1 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: Sat Dec 12 04:37:22 2020

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