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Calcium in PDB 6r2d: Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase

Enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase

All present enzymatic activity of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase:
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 Phosphonoethyl Ester, Followed By Temperature Increase, PDB code: 6r2d 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) 33.44 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 80.840, 83.730, 160.570, 99.52, 98.94, 100.81
R / Rfree (%) 21.7 / 24.2

Other elements in 6r2d:

The structure of Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase 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 Phosphonoethyl Ester, Followed By Temperature Increase (pdb code 6r2d). 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 Phosphonoethyl Ester, Followed By Temperature Increase, PDB code: 6r2d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6r2d

Go back to Calcium Binding Sites List in 6r2d
Calcium binding site 1 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2003

b:54.4
occ:1.00
 O A:ILE1060 2.3 58.1 1.0
O A:HIS1055 2.4 50.6 1.0
O A:HOH2120 2.4 58.1 1.0
OD1 A:ASP1058 2.5 62.9 1.0
OD1 A:ASP1004 2.5 53.0 1.0
OD2 A:ASP1004 2.5 60.8 1.0
O A:HOH2285 2.6 60.1 1.0
CG A:ASP1004 2.8 53.8 1.0
CG A:ASP1058 3.4 63.2 1.0
C A:ILE1060 3.5 59.1 1.0
C A:HIS1055 3.5 51.8 1.0
OD2 A:ASP1058 3.5 67.8 1.0
ND1 A:HIS1055 3.9 51.7 1.0
CE1 A:HIS1055 4.0 49.9 1.0
N A:ILE1060 4.0 60.4 1.0
CA A:HIS1055 4.2 47.7 1.0
CG A:HIS1055 4.2 50.4 1.0
CA A:ILE1060 4.2 59.5 1.0
NE2 A:HIS1055 4.3 49.9 1.0
CB A:ASP1004 4.3 43.8 1.0
CD2 A:HIS1055 4.4 50.7 1.0
N A:GLN1061 4.5 52.2 1.0
CB A:ILE1060 4.5 63.5 1.0
O A:HOH2143 4.5 48.5 1.0
N A:GLY1056 4.6 49.0 1.0
CA A:GLN1061 4.7 50.7 1.0
N A:ARG1062 4.7 46.2 1.0
CB A:ASP1058 4.8 58.0 1.0
O A:HOH2259 4.8 53.0 1.0
O A:HOH2288 4.8 58.2 1.0
N A:GLY1059 4.8 60.0 1.0
NE2 A:GLN1061 4.8 93.8 1.0
CB A:HIS1055 4.8 47.5 1.0
CA A:GLY1056 4.9 49.0 1.0
O A:ARG1062 4.9 45.0 1.0
N A:ASP1058 5.0 57.0 1.0

Calcium binding site 2 out of 4 in 6r2d

Go back to Calcium Binding Sites List in 6r2d
Calcium binding site 2 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2003

b:60.4
occ:1.00
 O B:HIS1055 2.3 49.4 1.0
O B:ILE1060 2.4 58.2 1.0
OD1 B:ASP1058 2.5 55.1 1.0
OD2 B:ASP1004 2.5 64.2 1.0
O B:HOH2319 2.6 50.9 1.0
O B:HOH2193 2.6 46.5 1.0
OD1 B:ASP1004 2.6 51.2 1.0
CG B:ASP1004 2.9 53.6 1.0
CG B:ASP1058 3.3 57.7 1.0
C B:HIS1055 3.4 51.1 1.0
OD2 B:ASP1058 3.5 59.8 1.0
C B:ILE1060 3.5 58.1 1.0
ND1 B:HIS1055 3.9 51.8 1.0
CE1 B:HIS1055 4.0 50.8 1.0
N B:ILE1060 4.1 56.9 1.0
CA B:HIS1055 4.1 46.3 1.0
CG B:HIS1055 4.2 49.9 1.0
CA B:ILE1060 4.3 56.6 1.0
CB B:ASP1004 4.4 46.4 1.0
NE2 B:HIS1055 4.4 51.0 1.0
N B:GLY1056 4.5 50.2 1.0
CD2 B:HIS1055 4.5 51.5 1.0
N B:GLN1061 4.6 53.0 1.0
O B:HOH2108 4.6 52.2 1.0
CB B:ILE1060 4.7 60.5 1.0
CA B:GLN1061 4.7 52.5 1.0
CA B:GLY1056 4.7 51.0 1.0
N B:ARG1062 4.8 49.3 1.0
CB B:ASP1058 4.8 53.4 1.0
O B:HOH2284 4.8 57.2 1.0
NE2 B:GLN1061 4.8 58.4 1.0
N B:GLY1059 4.8 56.8 1.0
CB B:HIS1055 4.8 46.3 1.0
N B:ASP1058 4.9 52.4 1.0
C B:GLY1056 5.0 55.9 1.0
O B:ARG1062 5.0 50.6 1.0
O B:ARG1054 5.0 50.2 1.0

Calcium binding site 3 out of 4 in 6r2d

Go back to Calcium Binding Sites List in 6r2d
Calcium binding site 3 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca2003

b:51.9
occ:1.00
 O C:HOH2155 2.2 51.6 1.0
O C:ILE1060 2.3 60.0 1.0
O C:HIS1055 2.3 53.6 1.0
OD2 C:ASP1004 2.5 66.0 1.0
OD1 C:ASP1058 2.5 67.6 1.0
OD1 C:ASP1004 2.5 60.4 1.0
O C:HOH2316 2.6 56.8 1.0
CG C:ASP1004 2.8 59.8 1.0
CG C:ASP1058 3.4 66.8 1.0
C C:ILE1060 3.5 61.7 1.0
C C:HIS1055 3.5 53.5 1.0
OD2 C:ASP1058 3.6 71.4 1.0
ND1 C:HIS1055 3.9 53.6 1.0
CE1 C:HIS1055 4.0 52.4 1.0
N C:ILE1060 4.0 62.6 1.0
CA C:HIS1055 4.2 50.2 1.0
CG C:HIS1055 4.2 52.2 1.0
CA C:ILE1060 4.2 61.6 1.0
NE2 C:HIS1055 4.3 52.5 1.0
CB C:ASP1004 4.3 48.4 1.0
CD2 C:HIS1055 4.4 53.0 1.0
N C:GLN1061 4.5 55.6 1.0
O C:HOH2187 4.5 54.9 1.0
O C:HOH2174 4.6 51.5 1.0
N C:GLY1056 4.6 51.3 1.0
CB C:ILE1060 4.6 64.9 1.0
CA C:GLN1061 4.7 54.0 1.0
N C:ARG1062 4.7 48.7 1.0
N C:GLY1059 4.8 61.6 1.0
CB C:ASP1058 4.8 59.2 1.0
CA C:GLY1056 4.8 52.3 1.0
CB C:HIS1055 4.8 49.6 1.0
O C:HOH2251 4.9 67.6 1.0
NE2 C:GLN1061 4.9 83.5 1.0
O C:ARG1062 5.0 49.3 1.0
N C:ASP1058 5.0 57.4 1.0

Calcium binding site 4 out of 4 in 6r2d

Go back to Calcium Binding Sites List in 6r2d
Calcium binding site 4 out of 4 in the Crystal Structure of the Suca Domain of Mycobacterium Smegmatis Kgd After Soaking with Succinylphosphonate Phosphonoethyl Ester, Followed By Temperature Increase


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 Phosphonoethyl Ester, Followed By Temperature Increase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:58.1
occ:1.00
 O D:ILE1060 2.3 61.3 1.0
O D:HOH2292 2.3 56.8 1.0
O D:HIS1055 2.3 52.6 1.0
OD1 D:ASP1058 2.4 58.1 1.0
OD2 D:ASP1004 2.5 62.5 1.0
OD1 D:ASP1004 2.6 54.1 1.0
CG D:ASP1004 2.9 55.6 1.0
CG D:ASP1058 3.4 59.7 1.0
C D:ILE1060 3.4 60.9 1.0
C D:HIS1055 3.5 52.8 1.0
OD2 D:ASP1058 3.6 61.3 1.0
N D:ILE1060 3.9 60.5 1.0
ND1 D:HIS1055 4.1 50.7 1.0
CE1 D:HIS1055 4.1 49.6 1.0
CA D:ILE1060 4.2 60.3 1.0
CA D:HIS1055 4.2 48.0 1.0
CG D:HIS1055 4.3 49.5 1.0
CB D:ASP1004 4.4 48.8 1.0
NE2 D:HIS1055 4.4 49.9 1.0
N D:GLN1061 4.5 55.0 1.0
CD2 D:HIS1055 4.5 50.5 1.0
N D:GLY1056 4.5 50.3 1.0
O D:HOH2118 4.5 52.4 1.0
CB D:ILE1060 4.6 64.2 1.0
CA D:GLN1061 4.7 54.2 1.0
O D:HOH2206 4.7 54.3 1.0
N D:GLY1059 4.7 58.3 1.0
NE2 D:GLN1061 4.7 77.1 1.0
CA D:GLY1056 4.8 50.4 1.0
CB D:ASP1058 4.8 57.4 1.0
N D:ARG1062 4.8 49.4 1.0
N D:ASP1058 4.9 55.4 1.0
CB D:HIS1055 4.9 47.2 1.0
C D:GLY1059 5.0 65.4 1.0
C D:GLY1056 5.0 55.5 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: Wed Jul 9 17:26:43 2025

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