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Magnesium 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:

Calcium (Ca) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8p5r

Go back to Magnesium Binding Sites List in 8p5r
Magnesium binding site 1 out of 6 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 Magnesium with other atoms in the Mg 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:Mg1301

b:106.0
occ:1.00
O1B A:TPP1303 2.0 226.7 1.0
O3A A:TPP1303 2.7 226.7 1.0
PB A:TPP1303 2.8 226.7 1.0
CE1 A:HIS747 2.9 300.0 1.0
O A:ILE680 3.0 233.2 1.0
C7 A:TPP1303 3.1 226.7 1.0
CA A:GLY681 3.4 230.0 1.0
O7 A:TPP1303 3.4 226.7 1.0
ND2 A:ASN678 3.5 218.8 1.0
PA A:TPP1303 3.5 226.7 1.0
O3B A:TPP1303 3.5 226.7 1.0
O1A A:TPP1303 3.6 226.7 1.0
C A:ILE680 3.7 233.2 1.0
NE2 A:HIS747 3.7 300.0 1.0
ND1 A:HIS747 3.8 300.0 1.0
N A:PHE682 3.8 232.1 1.0
NH1 A:ARG743 3.8 278.6 1.0
N A:GLY681 3.9 230.0 1.0
OD1 A:ASN678 3.9 218.8 1.0
NH2 A:ARG540 4.0 222.0 1.0
C A:GLY681 4.1 230.0 1.0
O2B A:TPP1303 4.1 226.7 1.0
CG A:ASN678 4.2 218.8 1.0
C6 A:TPP1303 4.2 226.7 1.0
OD1 A:ASP645 4.2 216.9 1.0
NE A:ARG540 4.5 222.0 1.0
CZ A:ARG540 4.5 222.0 1.0
CG2 A:ILE680 4.7 233.2 1.0
CD A:ARG743 4.8 278.6 1.0
O2A A:TPP1303 4.9 226.7 1.0
CD2 A:HIS747 4.9 300.0 1.0
CG A:HIS747 4.9 300.0 1.0

Magnesium binding site 2 out of 6 in 8p5r

Go back to Magnesium Binding Sites List in 8p5r
Magnesium binding site 2 out of 6 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 Magnesium with other atoms in the Mg 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
B:Mg1301

b:216.4
occ:1.00
O2A B:TPP1303 1.9 216.4 1.0
OD1 B:ASN678 2.1 216.6 1.0
OD1 B:ASP645 2.1 227.7 1.0
O B:ILE680 2.3 229.9 1.0
CG B:ASP645 2.8 227.7 1.0
O1B B:TPP1303 3.0 216.4 1.0
O3B B:TPP1303 3.1 216.4 1.0
CG B:ASN678 3.1 216.6 1.0
N B:ASP645 3.1 227.7 1.0
CB B:ASP645 3.2 227.7 1.0
PA B:TPP1303 3.3 216.4 1.0
PB B:TPP1303 3.4 216.4 1.0
C B:ILE680 3.4 229.9 1.0
N B:ALA646 3.5 199.4 1.0
ND2 B:ASN678 3.5 216.6 1.0
CA B:ASP645 3.5 227.7 1.0
O3A B:TPP1303 3.6 216.4 1.0
OD2 B:ASP645 3.9 227.7 1.0
C B:ASP645 4.0 227.7 1.0
O7 B:TPP1303 4.1 216.4 1.0
CA B:GLY681 4.2 227.2 1.0
N B:GLY681 4.2 227.2 1.0
C B:GLY644 4.2 227.0 1.0
N B:ILE680 4.3 229.9 1.0
N B:ASN678 4.3 216.6 1.0
CB B:ASN678 4.4 216.6 1.0
O1A B:TPP1303 4.4 216.4 1.0
CA B:ILE680 4.5 229.9 1.0
CB B:ALA646 4.6 199.4 1.0
CA B:GLY644 4.6 227.0 1.0
CA B:ALA646 4.7 199.4 1.0
CA B:ASN678 4.7 216.6 1.0
O B:VAL676 4.8 185.7 1.0
N B:GLN679 4.8 235.5 1.0
O2B B:TPP1303 4.9 216.4 1.0
C7 B:TPP1303 5.0 216.4 1.0
C B:ASN678 5.0 216.6 1.0

Magnesium binding site 3 out of 6 in 8p5r

Go back to Magnesium Binding Sites List in 8p5r
Magnesium binding site 3 out of 6 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 Magnesium with other atoms in the Mg 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
C:Mg1301

b:160.9
occ:1.00
O1A C:TPP1303 1.9 225.0 1.0
O3A C:TPP1303 2.3 225.0 1.0
OD1 C:ASP645 2.4 208.8 1.0
PA C:TPP1303 2.4 225.0 1.0
N C:ASP645 2.7 208.8 1.0
PB C:TPP1303 2.9 225.0 1.0
O2B C:TPP1303 2.9 225.0 1.0
O1B C:TPP1303 2.9 225.0 1.0
O2A C:TPP1303 3.1 225.0 1.0
OD1 C:ASN678 3.1 225.7 1.0
CA C:GLY644 3.2 233.8 1.0
C C:GLY644 3.3 233.8 1.0
CG C:ASP645 3.4 208.8 1.0
O C:ILE680 3.7 240.2 1.0
CA C:ASP645 3.7 208.8 1.0
CB C:ASP645 3.8 208.8 1.0
CG C:ASN678 3.9 225.7 1.0
O7 C:TPP1303 3.9 225.0 1.0
ND2 C:ASN678 4.0 225.7 1.0
N C:ALA646 4.1 192.8 1.0
O C:VAL676 4.2 170.6 1.0
O3B C:TPP1303 4.3 225.0 1.0
C C:ASP645 4.4 208.8 1.0
OD2 C:ASP645 4.5 208.8 1.0
O C:GLY644 4.5 233.8 1.0
N C:GLY644 4.7 233.8 1.0
C C:ILE680 4.9 240.2 1.0
N C:ASN678 4.9 225.7 1.0
C7 C:TPP1303 4.9 225.0 1.0

Magnesium binding site 4 out of 6 in 8p5r

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Magnesium binding site 4 out of 6 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 Magnesium with other atoms in the Mg 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
D:Mg1301

b:149.9
occ:1.00
O2A D:TPP1303 1.9 223.1 1.0
OD1 D:ASP645 2.1 248.8 1.0
N D:ASP645 2.5 248.8 1.0
OD1 D:ASN678 2.6 227.8 1.0
O1B D:TPP1303 2.8 223.1 1.0
CG D:ASP645 2.9 248.8 1.0
O3B D:TPP1303 3.0 223.1 1.0
PA D:TPP1303 3.0 223.1 1.0
CB D:ASP645 3.1 248.8 1.0
O3A D:TPP1303 3.1 223.1 1.0
PB D:TPP1303 3.2 223.1 1.0
CA D:ASP645 3.3 248.8 1.0
O D:ILE680 3.3 253.4 1.0
C D:GLY644 3.5 211.1 1.0
CG D:ASN678 3.6 227.8 1.0
N D:ALA646 3.7 189.1 1.0
CA D:GLY644 3.8 211.1 1.0
O1A D:TPP1303 3.9 223.1 1.0
C D:ASP645 4.0 248.8 1.0
ND2 D:ASN678 4.0 227.8 1.0
O D:VAL676 4.0 166.4 1.0
OD2 D:ASP645 4.1 248.8 1.0
O7 D:TPP1303 4.3 223.1 1.0
N D:ASN678 4.4 227.8 1.0
C D:ILE680 4.5 253.4 1.0
O2B D:TPP1303 4.6 223.1 1.0
O D:GLY644 4.7 211.1 1.0
CB D:ASN678 4.8 227.8 1.0
CA D:ALA646 5.0 189.1 1.0

Magnesium binding site 5 out of 6 in 8p5r

Go back to Magnesium Binding Sites List in 8p5r
Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg 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
E:Mg1301

b:190.3
occ:1.00
O1A E:TPP1303 1.9 223.6 1.0
O E:ILE680 2.0 252.7 1.0
O3B E:TPP1303 2.1 223.6 1.0
OD1 E:ASN678 2.2 218.1 1.0
OD1 E:ASP645 2.8 223.7 1.0
PB E:TPP1303 3.0 223.6 1.0
CG E:ASN678 3.0 218.1 1.0
O2B E:TPP1303 3.1 223.6 1.0
PA E:TPP1303 3.1 223.6 1.0
ND2 E:ASN678 3.2 218.1 1.0
O3A E:TPP1303 3.2 223.6 1.0
C E:ILE680 3.3 252.7 1.0
CB E:ASP645 3.3 223.7 1.0
CG E:ASP645 3.4 223.7 1.0
N E:ASP645 3.5 223.7 1.0
O7 E:TPP1303 3.8 223.6 1.0
CA E:ASP645 3.9 223.7 1.0
CA E:GLY681 3.9 221.2 1.0
N E:ALA646 3.9 178.3 1.0
N E:GLY681 4.0 221.2 1.0
N E:ILE680 4.3 252.7 1.0
O2A E:TPP1303 4.3 223.6 1.0
O1B E:TPP1303 4.4 223.6 1.0
CA E:ILE680 4.4 252.7 1.0
C E:ASP645 4.4 223.7 1.0
CB E:ASN678 4.5 218.1 1.0
C E:GLY644 4.5 236.5 1.0
C7 E:TPP1303 4.6 223.6 1.0
OD2 E:ASP645 4.6 223.7 1.0
N E:ASN678 4.6 218.1 1.0
CA E:GLY644 4.9 236.5 1.0
CB E:ALA646 4.9 178.3 1.0
CG2 E:ILE680 4.9 252.7 1.0
CA E:ASN678 5.0 218.1 1.0

Magnesium binding site 6 out of 6 in 8p5r

Go back to Magnesium Binding Sites List in 8p5r
Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg 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
F:Mg1301

b:119.3
occ:1.00
O3A F:TPP1303 2.1 230.2 1.0
CA F:GLY644 2.3 246.9 1.0
O1A F:TPP1303 2.4 230.2 1.0
PA F:TPP1303 2.5 230.2 1.0
O3B F:TPP1303 2.8 230.2 1.0
PB F:TPP1303 2.9 230.2 1.0
O2A F:TPP1303 3.0 230.2 1.0
C F:GLY644 3.1 246.9 1.0
N F:ASP645 3.1 225.2 1.0
OD1 F:ASP645 3.6 225.2 1.0
O2B F:TPP1303 3.6 230.2 1.0
N F:GLY644 3.6 246.9 1.0
O7 F:TPP1303 4.1 230.2 1.0
O F:GLY644 4.2 246.9 1.0
O1B F:TPP1303 4.3 230.2 1.0
CA F:ASP645 4.5 225.2 1.0
OD1 F:ASN678 4.5 242.6 1.0
C F:HIS643 4.6 189.6 1.0
CG F:ASP645 4.6 225.2 1.0
O F:HIS643 4.7 189.6 1.0
N F:ALA646 4.7 194.8 1.0
O F:VAL676 4.8 166.3 1.0
CD2 F:LEU606 4.8 242.1 1.0
C7 F:TPP1303 4.8 230.2 1.0
CB F:ALA647 4.9 197.3 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 Oct 4 15:52:15 2024

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