Atomistry » Calcium » PDB 3wt3-3zq4 » 3zhr
Atomistry »
  Calcium »
    PDB 3wt3-3zq4 »
      3zhr »

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 Dec 12 04:37:08 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy