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:
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
Go back to
Magnesium Binding Sites List in 8p5r
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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