Magnesium in PDB 8p5w: Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
Enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
All present enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate:
1.2.4.2;
2.3.1.61;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
(pdb code 8p5w). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate, PDB code: 8p5w:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8p5w
Go back to
Magnesium Binding Sites List in 8p5w
Magnesium binding site 1 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1301
b:22.1
occ:1.00
|
OD1
|
A:ASN678
|
2.1
|
35.1
|
1.0
|
O3B
|
A:QSP1303
|
2.1
|
25.8
|
1.0
|
O
|
A:ILE680
|
2.4
|
32.2
|
1.0
|
OD1
|
A:ASP645
|
2.5
|
48.8
|
1.0
|
O1A
|
A:QSP1303
|
2.5
|
28.0
|
1.0
|
CG
|
A:ASP645
|
3.2
|
43.8
|
1.0
|
CG
|
A:ASN678
|
3.2
|
27.1
|
1.0
|
PB
|
A:QSP1303
|
3.4
|
19.8
|
1.0
|
OD2
|
A:ASP645
|
3.5
|
47.4
|
1.0
|
O3A
|
A:QSP1303
|
3.6
|
24.5
|
1.0
|
C
|
A:ILE680
|
3.6
|
27.9
|
1.0
|
PA
|
A:QSP1303
|
3.6
|
22.9
|
1.0
|
ND2
|
A:ASN678
|
3.7
|
29.7
|
1.0
|
O1B
|
A:QSP1303
|
4.0
|
25.8
|
1.0
|
N
|
A:ILE680
|
4.1
|
27.8
|
1.0
|
N
|
A:ASP645
|
4.2
|
27.8
|
1.0
|
N
|
A:ASN678
|
4.3
|
26.4
|
1.0
|
O
|
A:VAL676
|
4.3
|
32.7
|
1.0
|
CB
|
A:ASP645
|
4.5
|
36.7
|
1.0
|
CA
|
A:ILE680
|
4.5
|
27.4
|
1.0
|
N
|
A:GLY681
|
4.5
|
30.3
|
1.0
|
CB
|
A:ASN678
|
4.5
|
26.3
|
1.0
|
O7
|
A:QSP1303
|
4.6
|
27.8
|
1.0
|
O2B
|
A:QSP1303
|
4.6
|
24.9
|
1.0
|
CA
|
A:GLY681
|
4.6
|
31.0
|
1.0
|
O2A
|
A:QSP1303
|
4.6
|
28.3
|
1.0
|
N
|
A:GLN679
|
4.7
|
25.6
|
1.0
|
CA
|
A:ASN678
|
4.7
|
24.6
|
1.0
|
N
|
A:ALA646
|
4.7
|
28.5
|
1.0
|
O
|
A:GLY681
|
4.7
|
46.9
|
1.0
|
C
|
A:ASN678
|
4.7
|
25.5
|
1.0
|
CG2
|
A:ILE680
|
4.8
|
33.4
|
1.0
|
CA
|
A:ASP645
|
4.8
|
29.6
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8p5w
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Magnesium Binding Sites List in 8p5w
Magnesium binding site 2 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1301
b:21.1
occ:1.00
|
O3B
|
B:QSP1303
|
2.1
|
25.6
|
1.0
|
OD1
|
B:ASN678
|
2.1
|
34.4
|
1.0
|
O
|
B:ILE680
|
2.4
|
32.6
|
1.0
|
O1A
|
B:QSP1303
|
2.4
|
28.4
|
1.0
|
OD1
|
B:ASP645
|
2.4
|
48.5
|
1.0
|
CG
|
B:ASP645
|
3.2
|
43.6
|
1.0
|
CG
|
B:ASN678
|
3.2
|
26.7
|
1.0
|
PB
|
B:QSP1303
|
3.4
|
19.8
|
1.0
|
OD2
|
B:ASP645
|
3.4
|
47.2
|
1.0
|
C
|
B:ILE680
|
3.5
|
28.3
|
1.0
|
PA
|
B:QSP1303
|
3.6
|
23.2
|
1.0
|
O3A
|
B:QSP1303
|
3.6
|
24.6
|
1.0
|
ND2
|
B:ASN678
|
3.7
|
29.2
|
1.0
|
N
|
B:ILE680
|
4.1
|
27.8
|
1.0
|
O1B
|
B:QSP1303
|
4.1
|
25.6
|
1.0
|
N
|
B:ASP645
|
4.2
|
27.7
|
1.0
|
N
|
B:ASN678
|
4.3
|
26.3
|
1.0
|
O
|
B:VAL676
|
4.3
|
32.7
|
1.0
|
CB
|
B:ASP645
|
4.5
|
36.6
|
1.0
|
CA
|
B:ILE680
|
4.5
|
27.5
|
1.0
|
N
|
B:GLY681
|
4.5
|
30.7
|
1.0
|
CB
|
B:ASN678
|
4.5
|
26.1
|
1.0
|
O2B
|
B:QSP1303
|
4.6
|
25.1
|
1.0
|
CA
|
B:GLY681
|
4.6
|
31.5
|
1.0
|
O7
|
B:QSP1303
|
4.6
|
28.2
|
1.0
|
O2A
|
B:QSP1303
|
4.6
|
28.7
|
1.0
|
N
|
B:GLN679
|
4.6
|
25.4
|
1.0
|
CA
|
B:ASN678
|
4.7
|
24.4
|
1.0
|
N
|
B:ALA646
|
4.7
|
28.7
|
1.0
|
O
|
B:GLY681
|
4.7
|
47.7
|
1.0
|
C
|
B:ASN678
|
4.7
|
25.4
|
1.0
|
CG2
|
B:ILE680
|
4.8
|
33.5
|
1.0
|
CA
|
B:ASP645
|
4.8
|
29.6
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8p5w
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Magnesium Binding Sites List in 8p5w
Magnesium binding site 3 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1301
b:22.5
occ:1.00
|
OD1
|
C:ASN678
|
2.1
|
34.7
|
1.0
|
O3B
|
C:QSP1303
|
2.1
|
26.1
|
1.0
|
O
|
C:ILE680
|
2.4
|
32.7
|
1.0
|
OD1
|
C:ASP645
|
2.5
|
49.6
|
1.0
|
O1A
|
C:QSP1303
|
2.5
|
28.6
|
1.0
|
CG
|
C:ASP645
|
3.2
|
44.5
|
1.0
|
CG
|
C:ASN678
|
3.2
|
27.0
|
1.0
|
PB
|
C:QSP1303
|
3.4
|
20.1
|
1.0
|
OD2
|
C:ASP645
|
3.5
|
48.0
|
1.0
|
C
|
C:ILE680
|
3.6
|
28.5
|
1.0
|
O3A
|
C:QSP1303
|
3.6
|
24.8
|
1.0
|
PA
|
C:QSP1303
|
3.6
|
23.3
|
1.0
|
ND2
|
C:ASN678
|
3.7
|
29.5
|
1.0
|
O1B
|
C:QSP1303
|
4.1
|
25.8
|
1.0
|
N
|
C:ILE680
|
4.1
|
27.9
|
1.0
|
N
|
C:ASP645
|
4.2
|
28.1
|
1.0
|
N
|
C:ASN678
|
4.3
|
26.6
|
1.0
|
O
|
C:VAL676
|
4.3
|
32.5
|
1.0
|
CA
|
C:ILE680
|
4.5
|
27.8
|
1.0
|
N
|
C:GLY681
|
4.5
|
30.9
|
1.0
|
CB
|
C:ASP645
|
4.5
|
37.3
|
1.0
|
CB
|
C:ASN678
|
4.5
|
26.3
|
1.0
|
O7
|
C:QSP1303
|
4.6
|
28.3
|
1.0
|
O2B
|
C:QSP1303
|
4.6
|
25.6
|
1.0
|
CA
|
C:GLY681
|
4.6
|
31.7
|
1.0
|
O2A
|
C:QSP1303
|
4.6
|
28.7
|
1.0
|
N
|
C:GLN679
|
4.7
|
25.5
|
1.0
|
CA
|
C:ASN678
|
4.7
|
24.6
|
1.0
|
N
|
C:ALA646
|
4.7
|
28.9
|
1.0
|
O
|
C:GLY681
|
4.7
|
47.4
|
1.0
|
C
|
C:ASN678
|
4.7
|
25.4
|
1.0
|
CG2
|
C:ILE680
|
4.8
|
33.6
|
1.0
|
CA
|
C:ASP645
|
4.8
|
30.1
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8p5w
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Magnesium Binding Sites List in 8p5w
Magnesium binding site 4 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1301
b:21.7
occ:1.00
|
O3B
|
D:QSP1303
|
2.1
|
25.8
|
1.0
|
OD1
|
D:ASN678
|
2.1
|
34.8
|
1.0
|
O
|
D:ILE680
|
2.4
|
32.7
|
1.0
|
OD1
|
D:ASP645
|
2.4
|
48.9
|
1.0
|
O1A
|
D:QSP1303
|
2.5
|
28.7
|
1.0
|
CG
|
D:ASP645
|
3.2
|
43.9
|
1.0
|
CG
|
D:ASN678
|
3.2
|
27.1
|
1.0
|
PB
|
D:QSP1303
|
3.4
|
19.8
|
1.0
|
OD2
|
D:ASP645
|
3.4
|
47.5
|
1.0
|
C
|
D:ILE680
|
3.6
|
28.4
|
1.0
|
PA
|
D:QSP1303
|
3.6
|
23.2
|
1.0
|
O3A
|
D:QSP1303
|
3.6
|
24.6
|
1.0
|
ND2
|
D:ASN678
|
3.7
|
29.6
|
1.0
|
O1B
|
D:QSP1303
|
4.1
|
25.5
|
1.0
|
N
|
D:ILE680
|
4.1
|
27.7
|
1.0
|
N
|
D:ASP645
|
4.2
|
27.9
|
1.0
|
N
|
D:ASN678
|
4.2
|
26.5
|
1.0
|
O
|
D:VAL676
|
4.3
|
32.8
|
1.0
|
CB
|
D:ASP645
|
4.4
|
37.0
|
1.0
|
CA
|
D:ILE680
|
4.5
|
27.5
|
1.0
|
N
|
D:GLY681
|
4.5
|
30.7
|
1.0
|
CB
|
D:ASN678
|
4.5
|
26.3
|
1.0
|
O2B
|
D:QSP1303
|
4.6
|
25.2
|
1.0
|
CA
|
D:GLY681
|
4.6
|
31.5
|
1.0
|
O7
|
D:QSP1303
|
4.6
|
28.2
|
1.0
|
N
|
D:GLN679
|
4.6
|
25.4
|
1.0
|
O2A
|
D:QSP1303
|
4.6
|
28.8
|
1.0
|
CA
|
D:ASN678
|
4.7
|
24.5
|
1.0
|
N
|
D:ALA646
|
4.7
|
28.9
|
1.0
|
O
|
D:GLY681
|
4.7
|
47.4
|
1.0
|
C
|
D:ASN678
|
4.7
|
25.4
|
1.0
|
CG2
|
D:ILE680
|
4.8
|
33.1
|
1.0
|
CA
|
D:ASP645
|
4.8
|
29.9
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8p5w
Go back to
Magnesium Binding Sites List in 8p5w
Magnesium binding site 5 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1301
b:21.8
occ:1.00
|
O3B
|
E:QSP1303
|
2.1
|
25.4
|
1.0
|
OD1
|
E:ASN678
|
2.1
|
34.6
|
1.0
|
O
|
E:ILE680
|
2.4
|
32.2
|
1.0
|
OD1
|
E:ASP645
|
2.4
|
48.7
|
1.0
|
O1A
|
E:QSP1303
|
2.5
|
28.1
|
1.0
|
CG
|
E:ASP645
|
3.2
|
43.6
|
1.0
|
CG
|
E:ASN678
|
3.2
|
26.7
|
1.0
|
PB
|
E:QSP1303
|
3.4
|
19.7
|
1.0
|
OD2
|
E:ASP645
|
3.4
|
47.2
|
1.0
|
C
|
E:ILE680
|
3.5
|
28.1
|
1.0
|
O3A
|
E:QSP1303
|
3.6
|
24.4
|
1.0
|
PA
|
E:QSP1303
|
3.6
|
23.0
|
1.0
|
ND2
|
E:ASN678
|
3.7
|
29.2
|
1.0
|
N
|
E:ILE680
|
4.1
|
27.6
|
1.0
|
O1B
|
E:QSP1303
|
4.1
|
25.4
|
1.0
|
N
|
E:ASP645
|
4.2
|
27.6
|
1.0
|
N
|
E:ASN678
|
4.3
|
26.1
|
1.0
|
O
|
E:VAL676
|
4.4
|
32.4
|
1.0
|
CA
|
E:ILE680
|
4.4
|
27.3
|
1.0
|
N
|
E:GLY681
|
4.4
|
30.5
|
1.0
|
CB
|
E:ASP645
|
4.5
|
36.5
|
1.0
|
CB
|
E:ASN678
|
4.5
|
26.0
|
1.0
|
O2B
|
E:QSP1303
|
4.6
|
24.9
|
1.0
|
CA
|
E:GLY681
|
4.6
|
31.3
|
1.0
|
O7
|
E:QSP1303
|
4.6
|
28.1
|
1.0
|
N
|
E:GLN679
|
4.6
|
25.2
|
1.0
|
O2A
|
E:QSP1303
|
4.7
|
28.4
|
1.0
|
N
|
E:ALA646
|
4.7
|
28.5
|
1.0
|
CA
|
E:ASN678
|
4.7
|
24.2
|
1.0
|
O
|
E:GLY681
|
4.7
|
47.4
|
1.0
|
C
|
E:ASN678
|
4.7
|
25.1
|
1.0
|
CG2
|
E:ILE680
|
4.8
|
33.4
|
1.0
|
CA
|
E:ASP645
|
4.8
|
29.4
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8p5w
Go back to
Magnesium Binding Sites List in 8p5w
Magnesium binding site 6 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum Following Reaction with the 2-Oxoglutarate Analogue Succinyl Phosphonate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1301
b:21.4
occ:1.00
|
OD1
|
F:ASN678
|
2.1
|
34.8
|
1.0
|
O3B
|
F:QSP1303
|
2.1
|
25.6
|
1.0
|
O
|
F:ILE680
|
2.4
|
32.5
|
1.0
|
O1A
|
F:QSP1303
|
2.4
|
28.2
|
1.0
|
OD1
|
F:ASP645
|
2.5
|
49.1
|
1.0
|
CG
|
F:ASP645
|
3.2
|
44.2
|
1.0
|
CG
|
F:ASN678
|
3.2
|
27.0
|
1.0
|
PB
|
F:QSP1303
|
3.4
|
19.6
|
1.0
|
OD2
|
F:ASP645
|
3.5
|
47.8
|
1.0
|
C
|
F:ILE680
|
3.6
|
28.3
|
1.0
|
PA
|
F:QSP1303
|
3.6
|
23.0
|
1.0
|
O3A
|
F:QSP1303
|
3.6
|
24.5
|
1.0
|
ND2
|
F:ASN678
|
3.7
|
29.6
|
1.0
|
O1B
|
F:QSP1303
|
4.0
|
25.4
|
1.0
|
N
|
F:ILE680
|
4.1
|
27.9
|
1.0
|
N
|
F:ASP645
|
4.2
|
28.0
|
1.0
|
N
|
F:ASN678
|
4.2
|
26.5
|
1.0
|
O
|
F:VAL676
|
4.3
|
32.7
|
1.0
|
CB
|
F:ASP645
|
4.5
|
37.1
|
1.0
|
CA
|
F:ILE680
|
4.5
|
27.6
|
1.0
|
N
|
F:GLY681
|
4.5
|
30.8
|
1.0
|
CB
|
F:ASN678
|
4.5
|
26.3
|
1.0
|
O7
|
F:QSP1303
|
4.6
|
28.0
|
1.0
|
CA
|
F:GLY681
|
4.6
|
31.5
|
1.0
|
O2B
|
F:QSP1303
|
4.6
|
24.8
|
1.0
|
O2A
|
F:QSP1303
|
4.6
|
28.6
|
1.0
|
N
|
F:GLN679
|
4.7
|
25.6
|
1.0
|
CA
|
F:ASN678
|
4.7
|
24.6
|
1.0
|
N
|
F:ALA646
|
4.7
|
28.8
|
1.0
|
O
|
F:GLY681
|
4.7
|
47.8
|
1.0
|
C
|
F:ASN678
|
4.7
|
25.6
|
1.0
|
CG2
|
F:ILE680
|
4.8
|
33.3
|
1.0
|
CA
|
F:ASP645
|
4.8
|
29.9
|
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 15:55:51 2024
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