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Calcium in PDB 6r2b: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate:
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 After Soaking with Succinylphosphonate, PDB code: 6r2b was solved by T.Wagner, P.M.Alzari, M.Bellinzoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 158.87 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.120, 82.760, 162.970, 98.55, 97.52, 102.18
R / Rfree (%) 22.8 / 24.5

Other elements in 6r2b:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate 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 After Soaking with Succinylphosphonate (pdb code 6r2b). 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 After Soaking with Succinylphosphonate, PDB code: 6r2b:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6r2b

Go back to Calcium Binding Sites List in 6r2b
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate


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 After Soaking with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:28.5
occ:1.00
 O A:ILE1060 2.3 30.9 1.0
O A:HIS1055 2.4 26.1 1.0
O A:HOH2115 2.4 30.7 1.0
OD2 A:ASP1004 2.4 32.6 1.0
O A:HOH2394 2.5 30.8 1.0
OD1 A:ASP1058 2.5 30.6 1.0
OD1 A:ASP1004 2.6 27.6 1.0
CG A:ASP1004 2.8 29.0 1.0
C A:ILE1060 3.5 32.4 1.0
CG A:ASP1058 3.5 31.3 1.0
C A:HIS1055 3.5 27.1 1.0
OD2 A:ASP1058 3.8 30.3 1.0
ND1 A:HIS1055 4.0 27.7 1.0
CE1 A:HIS1055 4.0 26.8 1.0
N A:ILE1060 4.1 33.8 1.0
CA A:HIS1055 4.2 23.7 1.0
CA A:ILE1060 4.2 32.9 1.0
CB A:ASP1004 4.3 22.3 1.0
CG A:HIS1055 4.3 26.3 1.0
NE2 A:HIS1055 4.4 26.8 1.0
N A:GLN1061 4.5 25.6 1.0
O A:HOH2112 4.5 34.4 1.0
CB A:ILE1060 4.5 37.1 1.0
CD2 A:HIS1055 4.5 27.4 1.0
NE2 A:GLN1061 4.5 34.1 1.0
N A:GLY1056 4.6 23.2 1.0
CA A:GLN1061 4.6 24.1 1.0
N A:GLY1059 4.7 30.7 1.0
CA A:GLY1056 4.8 23.2 1.0
O A:HOH2303 4.8 36.6 1.0
CB A:ASP1058 4.8 28.8 1.0
N A:ARG1062 4.8 22.7 1.0
N A:ASP1058 4.9 27.6 1.0
CB A:HIS1055 4.9 23.4 1.0
C A:GLY1056 5.0 27.9 1.0
C A:GLY1059 5.0 36.5 1.0

Calcium binding site 2 out of 4 in 6r2b

Go back to Calcium Binding Sites List in 6r2b
Calcium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate


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 After Soaking with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:26.6
occ:1.00
 O B:HOH2312 2.2 24.5 1.0
O B:HOH2201 2.3 23.4 1.0
O B:HIS1055 2.3 25.2 1.0
O B:ILE1060 2.4 28.3 1.0
OD2 B:ASP1004 2.4 31.6 1.0
OD1 B:ASP1058 2.5 30.1 1.0
OD1 B:ASP1004 2.6 28.4 1.0
CG B:ASP1004 2.8 28.4 1.0
C B:HIS1055 3.5 25.2 1.0
CG B:ASP1058 3.5 29.2 1.0
C B:ILE1060 3.5 29.9 1.0
OD2 B:ASP1058 3.8 29.6 1.0
ND1 B:HIS1055 3.9 23.2 1.0
CE1 B:HIS1055 4.0 22.7 1.0
N B:ILE1060 4.1 30.2 1.0
CA B:HIS1055 4.2 20.4 1.0
CG B:HIS1055 4.2 21.8 1.0
CA B:ILE1060 4.3 28.7 1.0
NE2 B:HIS1055 4.3 22.5 1.0
CB B:ASP1004 4.3 21.7 1.0
CD2 B:HIS1055 4.4 22.4 1.0
O B:HOH2237 4.5 29.6 1.0
CB B:ILE1060 4.5 32.1 1.0
N B:GLN1061 4.6 25.5 1.0
N B:GLY1056 4.6 22.3 1.0
NE2 B:GLN1061 4.6 32.3 1.0
CA B:GLN1061 4.7 24.0 1.0
N B:GLY1059 4.7 29.9 1.0
O B:HOH2223 4.8 35.8 1.0
CA B:GLY1056 4.8 22.6 1.0
CB B:ASP1058 4.9 27.4 1.0
CB B:HIS1055 4.9 19.5 1.0
N B:ASP1058 4.9 25.7 1.0
N B:ARG1062 4.9 22.6 1.0
O B:HOH2265 4.9 34.1 1.0
C B:GLY1056 4.9 27.3 1.0

Calcium binding site 3 out of 4 in 6r2b

Go back to Calcium Binding Sites List in 6r2b
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate


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 After Soaking with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:26.6
occ:1.00
 O C:HOH2242 2.3 26.3 1.0
O C:ILE1060 2.3 27.7 1.0
O C:HOH2403 2.3 23.9 1.0
O C:HIS1055 2.4 24.9 1.0
OD2 C:ASP1004 2.4 33.1 1.0
OD1 C:ASP1058 2.5 28.9 1.0
OD1 C:ASP1004 2.6 23.2 1.0
CG C:ASP1004 2.8 27.1 1.0
C C:ILE1060 3.5 29.3 1.0
CG C:ASP1058 3.5 29.3 1.0
C C:HIS1055 3.5 25.5 1.0
OD2 C:ASP1058 3.8 34.8 1.0
ND1 C:HIS1055 4.0 24.4 1.0
N C:ILE1060 4.0 28.5 1.0
CE1 C:HIS1055 4.0 23.4 1.0
CA C:ILE1060 4.2 27.4 1.0
CA C:HIS1055 4.2 20.4 1.0
CB C:ASP1004 4.3 20.5 1.0
CG C:HIS1055 4.3 23.1 1.0
NE2 C:HIS1055 4.4 23.3 1.0
O C:HOH2188 4.4 30.9 1.0
N C:GLN1061 4.5 25.1 1.0
NE2 C:GLN1061 4.5 31.0 1.0
CD2 C:HIS1055 4.5 23.3 1.0
CB C:ILE1060 4.5 31.6 1.0
N C:GLY1056 4.6 24.1 1.0
CA C:GLN1061 4.7 23.2 1.0
N C:GLY1059 4.7 28.1 1.0
O C:HOH2318 4.7 29.2 1.0
O C:HOH2239 4.8 38.0 1.0
CA C:GLY1056 4.8 23.8 1.0
CB C:ASP1058 4.9 26.6 1.0
N C:ASP1058 4.9 25.2 1.0
N C:ARG1062 4.9 22.5 1.0
CB C:HIS1055 4.9 20.3 1.0
C C:GLY1056 4.9 27.9 1.0
C C:GLY1059 5.0 32.8 1.0
CD C:GLN1061 5.0 43.4 1.0

Calcium binding site 4 out of 4 in 6r2b

Go back to Calcium Binding Sites List in 6r2b
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate


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 After Soaking with Succinylphosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:27.7
occ:1.00
 O D:HOH2125 2.3 27.1 1.0
O D:ILE1060 2.3 31.3 1.0
O D:HOH2343 2.4 31.4 1.0
O D:HIS1055 2.4 29.6 1.0
OD2 D:ASP1004 2.4 35.1 1.0
OD1 D:ASP1058 2.5 29.8 1.0
OD1 D:ASP1004 2.6 25.0 1.0
CG D:ASP1004 2.8 28.7 1.0
CG D:ASP1058 3.5 32.0 1.0
C D:ILE1060 3.5 32.9 1.0
C D:HIS1055 3.5 29.4 1.0
OD2 D:ASP1058 3.8 35.7 1.0
ND1 D:HIS1055 4.0 27.5 1.0
CE1 D:HIS1055 4.0 26.1 1.0
N D:ILE1060 4.1 32.9 1.0
CA D:HIS1055 4.2 24.1 1.0
CA D:ILE1060 4.3 32.1 1.0
CG D:HIS1055 4.3 26.0 1.0
CB D:ASP1004 4.3 23.4 1.0
NE2 D:HIS1055 4.4 26.0 1.0
CD2 D:HIS1055 4.5 26.8 1.0
N D:GLN1061 4.5 27.8 1.0
CB D:ILE1060 4.5 35.6 1.0
O D:HOH2151 4.5 37.1 1.0
NE2 D:GLN1061 4.6 37.4 1.0
N D:GLY1056 4.6 25.6 1.0
CA D:GLN1061 4.7 26.2 1.0
N D:GLY1059 4.7 32.9 1.0
CA D:GLY1056 4.8 25.8 1.0
N D:ARG1062 4.8 23.3 1.0
CB D:ASP1058 4.8 27.2 1.0
O D:HOH2235 4.9 38.8 1.0
N D:ASP1058 4.9 26.7 1.0
CB D:HIS1055 4.9 23.3 1.0
C D:GLY1056 5.0 30.9 1.0
O D:HOH2251 5.0 38.8 1.0
C D:GLY1059 5.0 37.2 1.0

Reference:

T.Wagner, A.Boyko, P.M.Alzari, V.I.Bunik, M.Bellinzoni. Conformational Transitions in the Active Site of Mycobacterial 2-Oxoglutarate Dehydrogenase Upon Binding Phosphonate Analogues of 2-Oxoglutarate: From A Michaelis-Like Complex to Thdp Adducts. J.Struct.Biol. V. 208 182 2019.
ISSN: ESSN 1095-8657
PubMed: 31476368
DOI: 10.1016/J.JSB.2019.08.012
Page generated: Tue Jul 16 14:10:33 2024

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