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Calcium in PDB 8p5r: Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara

Enzymatic activity of Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara

All present enzymatic activity of Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara:
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 Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara, PDB code: 8p5r was solved by T.Wagner, A.M.Mechaly, P.M.Alzari, M.Bellinzoni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.99 / 4.56
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 325.75, 325.75, 396.944, 90, 90, 120
R / Rfree (%) 19.8 / 22.9

Other elements in 8p5r:

The structure of Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara (pdb code 8p5r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara, PDB code: 8p5r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 1 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


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 Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1302

b:300.0
occ:1.00
 O A:HIS1055 3.4 261.3 1.0
OD2 A:ASP1004 3.5 269.2 1.0
OD1 A:ASP1058 3.5 257.3 1.0
OD1 A:ASP1004 3.5 269.2 1.0
CG A:ASP1004 3.7 269.2 1.0
O A:GLY1056 3.7 296.8 1.0
N A:GLY1059 3.9 300.0 1.0
C A:GLY1056 4.0 296.8 1.0
CA A:GLY1059 4.2 300.0 1.0
C A:GLY1059 4.3 300.0 1.0
OE1 A:GLN1061 4.4 261.2 1.0
CA A:GLY1056 4.4 296.8 1.0
O A:GLY1059 4.4 300.0 1.0
C A:HIS1055 4.5 261.3 1.0
O A:ILE1060 4.6 274.3 1.0
N A:ASP1058 4.7 257.3 1.0
N A:LYS1057 4.7 260.5 1.0
CE A:LYS894 4.7 256.9 1.0
O A:PRO967 4.7 210.8 1.0
CG A:ASP1058 4.7 257.3 1.0
NZ A:LYS894 4.9 256.9 1.0
N A:GLY1056 4.9 296.8 1.0
N A:ILE1060 5.0 274.3 1.0
CB A:ASP1004 5.0 269.2 1.0

Calcium binding site 2 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 2 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


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 Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1304

b:176.4
occ:1.00
 OE2 C:GLU288 2.9 188.4 1.0
OE2 A:GLU288 3.0 160.2 1.0
OE2 E:GLU288 3.2 178.6 1.0
CD C:GLU288 3.8 188.4 1.0
CD A:GLU288 3.9 160.2 1.0
OE1 C:GLU288 4.0 188.4 1.0
OE1 A:GLU288 4.1 160.2 1.0
CD E:GLU288 4.1 178.6 1.0
CB A:PRO286 4.2 206.3 1.0
OE1 E:GLU288 4.3 178.6 1.0
CG A:PRO286 4.3 206.3 1.0
CB C:PRO286 4.4 224.9 1.0
CB E:PRO286 4.5 208.6 1.0
CG C:PRO286 4.6 224.9 1.0
CG E:PRO286 4.6 208.6 1.0

Calcium binding site 3 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 3 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


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 Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1302

b:220.9
occ:1.00
 O B:HIS1055 3.4 217.4 1.0
OD1 B:ASP1058 3.5 252.0 1.0
OD2 B:ASP1004 3.5 221.9 1.0
OD1 B:ASP1004 3.5 221.9 1.0
CG B:ASP1004 3.7 221.9 1.0
O B:GLY1056 3.8 226.3 1.0
N B:GLY1059 3.9 296.1 1.0
C B:GLY1056 4.0 226.3 1.0
CA B:GLY1059 4.2 296.1 1.0
C B:GLY1059 4.3 296.1 1.0
OE1 B:GLN1061 4.3 263.8 1.0
CA B:GLY1056 4.4 226.3 1.0
O B:GLY1059 4.4 296.1 1.0
C B:HIS1055 4.5 217.4 1.0
O B:ILE1060 4.6 258.7 1.0
N B:ASP1058 4.7 252.0 1.0
N B:LYS1057 4.7 243.6 1.0
CE B:LYS894 4.7 222.1 1.0
O B:PRO967 4.7 212.2 1.0
CG B:ASP1058 4.7 252.0 1.0
NZ B:LYS894 4.9 222.1 1.0
N B:GLY1056 4.9 226.3 1.0
N B:ILE1060 5.0 258.7 1.0
CB B:ASP1004 5.0 221.9 1.0

Calcium binding site 4 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 4 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


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 Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1304

b:170.2
occ:1.00
 OE2 D:GLU288 2.9 192.0 1.0
OE2 B:GLU288 3.0 189.1 1.0
OE2 F:GLU288 3.0 161.6 1.0
CD D:GLU288 3.8 192.0 1.0
CD B:GLU288 3.9 189.1 1.0
CD F:GLU288 3.9 161.6 1.0
OE1 D:GLU288 4.0 192.0 1.0
OE1 B:GLU288 4.1 189.1 1.0
OE1 F:GLU288 4.1 161.6 1.0
CB D:PRO286 4.3 228.4 1.0
CB F:PRO286 4.3 209.4 1.0
CG D:PRO286 4.4 228.4 1.0
CG F:PRO286 4.4 209.4 1.0
CB B:PRO286 4.4 215.4 1.0
CG B:PRO286 4.5 215.4 1.0

Calcium binding site 5 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 5 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1302

b:289.0
occ:1.00
 O C:HIS1055 3.4 231.7 1.0
OD1 C:ASP1058 3.5 251.4 1.0
OD2 C:ASP1004 3.5 238.4 1.0
OD1 C:ASP1004 3.5 238.4 1.0
CG C:ASP1004 3.7 238.4 1.0
O C:GLY1056 3.7 254.3 1.0
N C:GLY1059 3.9 291.6 1.0
C C:GLY1056 4.0 254.3 1.0
CA C:GLY1059 4.2 291.6 1.0
C C:GLY1059 4.3 291.6 1.0
OE1 C:GLN1061 4.4 263.8 1.0
CA C:GLY1056 4.4 254.3 1.0
O C:GLY1059 4.4 291.6 1.0
C C:HIS1055 4.5 231.7 1.0
O C:ILE1060 4.6 257.3 1.0
N C:ASP1058 4.6 251.4 1.0
N C:LYS1057 4.7 221.5 1.0
CE C:LYS894 4.7 247.8 1.0
CG C:ASP1058 4.7 251.4 1.0
O C:PRO967 4.7 199.2 1.0
NZ C:LYS894 4.8 247.8 1.0
N C:GLY1056 4.9 254.3 1.0
N C:ILE1060 5.0 257.3 1.0
CB C:ASP1004 5.0 238.4 1.0

Calcium binding site 6 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 6 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1302

b:298.5
occ:1.00
 O D:HIS1055 3.4 241.7 1.0
OD2 D:ASP1004 3.5 248.5 1.0
OD1 D:ASP1058 3.5 244.4 1.0
OD1 D:ASP1004 3.5 248.5 1.0
CG D:ASP1004 3.7 248.5 1.0
O D:GLY1056 3.7 265.5 1.0
N D:GLY1059 3.9 294.9 1.0
C D:GLY1056 4.0 265.5 1.0
CA D:GLY1059 4.2 294.9 1.0
C D:GLY1059 4.3 294.9 1.0
OE1 D:GLN1061 4.4 271.2 1.0
CA D:GLY1056 4.4 265.5 1.0
O D:GLY1059 4.4 294.9 1.0
C D:HIS1055 4.5 241.7 1.0
O D:ILE1060 4.6 259.2 1.0
N D:ASP1058 4.6 244.4 1.0
CE D:LYS894 4.7 239.7 1.0
N D:LYS1057 4.7 217.2 1.0
CG D:ASP1058 4.7 244.4 1.0
O D:PRO967 4.7 196.6 1.0
NZ D:LYS894 4.8 239.7 1.0
N D:GLY1056 4.9 265.5 1.0
N D:ILE1060 5.0 259.2 1.0
CB D:ASP1004 5.0 248.5 1.0

Calcium binding site 7 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 7 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1302

b:239.1
occ:1.00
 O E:HIS1055 3.4 218.7 1.0
OD1 E:ASP1058 3.5 238.2 1.0
OD2 E:ASP1004 3.5 223.2 1.0
OD1 E:ASP1004 3.5 223.2 1.0
O E:GLY1056 3.7 214.1 1.0
CG E:ASP1004 3.7 223.2 1.0
N E:GLY1059 3.9 281.8 1.0
C E:GLY1056 4.0 214.1 1.0
CA E:GLY1059 4.2 281.8 1.0
OE1 E:GLN1061 4.3 259.2 1.0
C E:GLY1059 4.3 281.8 1.0
CA E:GLY1056 4.4 214.1 1.0
O E:GLY1059 4.4 281.8 1.0
C E:HIS1055 4.5 218.7 1.0
O E:ILE1060 4.6 270.7 1.0
N E:ASP1058 4.6 238.2 1.0
N E:LYS1057 4.7 231.5 1.0
O E:PRO967 4.7 216.3 1.0
CE E:LYS894 4.7 220.1 1.0
CG E:ASP1058 4.7 238.2 1.0
NZ E:LYS894 4.8 220.1 1.0
N E:GLY1056 4.9 214.1 1.0
N E:ILE1060 5.0 270.7 1.0
CB E:ASP1004 5.0 223.2 1.0

Calcium binding site 8 out of 8 in 8p5r

Go back to Calcium Binding Sites List in 8p5r
Calcium binding site 8 out of 8 in the Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Full-Length, Homohexameric 2-Oxoglutarate Dehydrogenase Kgd From Mycobacterium Smegmatis in Complex with Gara within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1302

b:300.0
occ:1.00
 O F:HIS1055 3.4 273.2 1.0
OD2 F:ASP1004 3.5 275.8 1.0
OD1 F:ASP1058 3.5 273.6 1.0
OD1 F:ASP1004 3.5 275.8 1.0
CG F:ASP1004 3.7 275.8 1.0
O F:GLY1056 3.7 266.5 1.0
N F:GLY1059 3.9 286.2 1.0
C F:GLY1056 4.0 266.5 1.0
CA F:GLY1059 4.2 286.2 1.0
C F:GLY1059 4.3 286.2 1.0
OE1 F:GLN1061 4.4 279.5 1.0
CA F:GLY1056 4.4 266.5 1.0
O F:GLY1059 4.4 286.2 1.0
C F:HIS1055 4.5 273.2 1.0
O F:ILE1060 4.6 279.1 1.0
N F:ASP1058 4.6 273.6 1.0
N F:LYS1057 4.7 254.2 1.0
O F:PRO967 4.7 217.4 1.0
CE F:LYS894 4.7 241.9 1.0
CG F:ASP1058 4.7 273.6 1.0
NZ F:LYS894 4.9 241.9 1.0
N F:GLY1056 4.9 266.5 1.0
N F:ILE1060 5.0 279.1 1.0
CB F:ASP1004 5.0 275.8 1.0

Reference:

L.Yang, T.Wagner, A.Mechaly, A.Boyko, E.M.Bruch, D.Megrian, F.Gubellini, P.M.Alzari, M.Bellinzoni. High Resolution Cryo-Em and Crystallographic Snapshots of the Actinobacterial Two-in-One 2-Oxoglutarate Dehydrogenase Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-40253-6
Page generated: Fri Jul 19 11:08:34 2024

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