Magnesium in PDB 8p5v: Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
Enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
All present enzymatic activity of Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa:
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 in Complex with the Product Succinyl-Coa
(pdb code 8p5v). 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 in Complex with the Product Succinyl-Coa, PDB code: 8p5v:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8p5v
Go back to
Magnesium Binding Sites List in 8p5v
Magnesium binding site 1 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
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 in Complex with the Product Succinyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1301
b:38.0
occ:1.00
|
OD1
|
A:ASN678
|
2.0
|
50.1
|
1.0
|
O
|
A:ILE680
|
2.0
|
54.3
|
1.0
|
O1B
|
A:TPP1303
|
2.1
|
49.7
|
1.0
|
OD1
|
A:ASP645
|
2.2
|
52.1
|
1.0
|
O1A
|
A:TPP1303
|
2.2
|
50.5
|
1.0
|
CG
|
A:ASN678
|
3.0
|
40.5
|
1.0
|
C
|
A:ILE680
|
3.2
|
51.4
|
1.0
|
CG
|
A:ASP645
|
3.2
|
48.5
|
1.0
|
PB
|
A:TPP1303
|
3.3
|
46.0
|
1.0
|
PA
|
A:TPP1303
|
3.3
|
48.8
|
1.0
|
ND2
|
A:ASN678
|
3.4
|
40.6
|
1.0
|
O3A
|
A:TPP1303
|
3.4
|
51.2
|
1.0
|
OD2
|
A:ASP645
|
3.7
|
57.1
|
1.0
|
O2B
|
A:TPP1303
|
3.9
|
51.0
|
1.0
|
N
|
A:ILE680
|
4.0
|
49.0
|
1.0
|
O7
|
A:TPP1303
|
4.1
|
55.4
|
1.0
|
N
|
A:GLY681
|
4.1
|
55.7
|
1.0
|
N
|
A:ASP645
|
4.1
|
39.9
|
1.0
|
CA
|
A:GLY681
|
4.2
|
58.9
|
1.0
|
CA
|
A:ILE680
|
4.2
|
51.3
|
1.0
|
N
|
A:ASN678
|
4.4
|
42.0
|
1.0
|
O
|
A:VAL676
|
4.4
|
44.1
|
1.0
|
CB
|
A:ASN678
|
4.4
|
41.7
|
1.0
|
N
|
A:ALA646
|
4.4
|
43.2
|
1.0
|
CB
|
A:ASP645
|
4.5
|
46.4
|
1.0
|
O2A
|
A:TPP1303
|
4.5
|
52.2
|
1.0
|
O3B
|
A:TPP1303
|
4.6
|
50.8
|
1.0
|
N
|
A:GLN679
|
4.6
|
45.3
|
1.0
|
CG2
|
A:ILE680
|
4.6
|
52.9
|
1.0
|
CA
|
A:ASN678
|
4.7
|
42.4
|
1.0
|
C
|
A:ASN678
|
4.7
|
44.0
|
1.0
|
O
|
A:GLY681
|
4.8
|
83.1
|
1.0
|
CA
|
A:ASP645
|
4.8
|
42.7
|
1.0
|
CB
|
A:ALA646
|
4.9
|
46.1
|
1.0
|
CA
|
A:GLY644
|
4.9
|
37.5
|
1.0
|
C
|
A:GLY644
|
4.9
|
38.4
|
1.0
|
C
|
A:GLY681
|
5.0
|
69.5
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8p5v
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Magnesium Binding Sites List in 8p5v
Magnesium binding site 2 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
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 in Complex with the Product Succinyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1301
b:41.4
occ:1.00
|
OD1
|
B:ASN678
|
2.0
|
52.3
|
1.0
|
O
|
B:ILE680
|
2.0
|
60.2
|
1.0
|
O2A
|
B:TPP1303
|
2.1
|
54.7
|
1.0
|
OD1
|
B:ASP645
|
2.2
|
55.2
|
1.0
|
O2B
|
B:TPP1303
|
2.2
|
54.5
|
1.0
|
CG
|
B:ASN678
|
3.0
|
43.5
|
1.0
|
PA
|
B:TPP1303
|
3.2
|
51.7
|
1.0
|
C
|
B:ILE680
|
3.3
|
57.6
|
1.0
|
CG
|
B:ASP645
|
3.3
|
51.2
|
1.0
|
PB
|
B:TPP1303
|
3.3
|
49.2
|
1.0
|
O3A
|
B:TPP1303
|
3.4
|
53.3
|
1.0
|
ND2
|
B:ASN678
|
3.4
|
43.7
|
1.0
|
OD2
|
B:ASP645
|
3.7
|
60.9
|
1.0
|
O1B
|
B:TPP1303
|
3.9
|
54.9
|
1.0
|
N
|
B:ILE680
|
4.0
|
54.6
|
1.0
|
O7
|
B:TPP1303
|
4.1
|
59.7
|
1.0
|
N
|
B:GLY681
|
4.1
|
61.3
|
1.0
|
N
|
B:ASP645
|
4.1
|
44.4
|
1.0
|
CA
|
B:GLY681
|
4.2
|
64.0
|
1.0
|
CA
|
B:ILE680
|
4.2
|
56.1
|
1.0
|
N
|
B:ASN678
|
4.4
|
44.5
|
1.0
|
CB
|
B:ASN678
|
4.4
|
44.4
|
1.0
|
O
|
B:VAL676
|
4.4
|
48.8
|
1.0
|
N
|
B:ALA646
|
4.4
|
48.1
|
1.0
|
O1A
|
B:TPP1303
|
4.4
|
53.4
|
1.0
|
CB
|
B:ASP645
|
4.5
|
49.7
|
1.0
|
O3B
|
B:TPP1303
|
4.6
|
55.0
|
1.0
|
CG2
|
B:ILE680
|
4.6
|
57.7
|
1.0
|
N
|
B:GLN679
|
4.6
|
48.0
|
1.0
|
CA
|
B:ASN678
|
4.7
|
44.6
|
1.0
|
C
|
B:ASN678
|
4.7
|
46.4
|
1.0
|
O
|
B:GLY681
|
4.8
|
86.5
|
1.0
|
CA
|
B:ASP645
|
4.8
|
46.9
|
1.0
|
CB
|
B:ALA646
|
4.9
|
50.6
|
1.0
|
CA
|
B:GLY644
|
4.9
|
42.2
|
1.0
|
C
|
B:GLY644
|
4.9
|
42.4
|
1.0
|
C
|
B:GLY681
|
5.0
|
74.2
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8p5v
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Magnesium Binding Sites List in 8p5v
Magnesium binding site 3 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
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 in Complex with the Product Succinyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1301
b:39.2
occ:1.00
|
OD1
|
C:ASN678
|
2.0
|
50.4
|
1.0
|
O
|
C:ILE680
|
2.0
|
55.6
|
1.0
|
O1A
|
C:TPP1303
|
2.1
|
49.8
|
1.0
|
O1B
|
C:TPP1303
|
2.1
|
50.4
|
1.0
|
OD1
|
C:ASP645
|
2.2
|
51.5
|
1.0
|
CG
|
C:ASN678
|
3.0
|
40.9
|
1.0
|
C
|
C:ILE680
|
3.2
|
52.2
|
1.0
|
CG
|
C:ASP645
|
3.3
|
48.7
|
1.0
|
PB
|
C:TPP1303
|
3.3
|
46.2
|
1.0
|
PA
|
C:TPP1303
|
3.3
|
48.0
|
1.0
|
ND2
|
C:ASN678
|
3.4
|
40.8
|
1.0
|
O3A
|
C:TPP1303
|
3.4
|
50.9
|
1.0
|
OD2
|
C:ASP645
|
3.7
|
57.9
|
1.0
|
O2B
|
C:TPP1303
|
3.9
|
51.5
|
1.0
|
N
|
C:ILE680
|
4.0
|
49.5
|
1.0
|
O7
|
C:TPP1303
|
4.1
|
56.2
|
1.0
|
N
|
C:GLY681
|
4.1
|
56.0
|
1.0
|
N
|
C:ASP645
|
4.2
|
41.0
|
1.0
|
CA
|
C:GLY681
|
4.2
|
59.3
|
1.0
|
CA
|
C:ILE680
|
4.2
|
51.7
|
1.0
|
N
|
C:ASN678
|
4.4
|
41.9
|
1.0
|
CB
|
C:ASN678
|
4.4
|
41.8
|
1.0
|
O
|
C:VAL676
|
4.4
|
44.9
|
1.0
|
N
|
C:ALA646
|
4.5
|
44.0
|
1.0
|
O2A
|
C:TPP1303
|
4.5
|
51.3
|
1.0
|
O3B
|
C:TPP1303
|
4.6
|
51.5
|
1.0
|
CB
|
C:ASP645
|
4.6
|
46.4
|
1.0
|
CG2
|
C:ILE680
|
4.6
|
53.6
|
1.0
|
N
|
C:GLN679
|
4.6
|
45.3
|
1.0
|
CA
|
C:ASN678
|
4.7
|
42.6
|
1.0
|
C
|
C:ASN678
|
4.7
|
44.3
|
1.0
|
O
|
C:GLY681
|
4.7
|
83.2
|
1.0
|
CA
|
C:ASP645
|
4.8
|
43.3
|
1.0
|
CB
|
C:ALA646
|
4.9
|
46.6
|
1.0
|
CA
|
C:GLY644
|
4.9
|
39.6
|
1.0
|
C
|
C:GLY644
|
5.0
|
39.7
|
1.0
|
C
|
C:GLY681
|
5.0
|
69.9
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8p5v
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Magnesium Binding Sites List in 8p5v
Magnesium binding site 4 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
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 in Complex with the Product Succinyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1301
b:41.5
occ:1.00
|
OD1
|
D:ASN678
|
2.0
|
52.1
|
1.0
|
O
|
D:ILE680
|
2.0
|
60.7
|
1.0
|
O2A
|
D:TPP1303
|
2.1
|
55.5
|
1.0
|
O2B
|
D:TPP1303
|
2.2
|
54.8
|
1.0
|
OD1
|
D:ASP645
|
2.2
|
55.2
|
1.0
|
CG
|
D:ASN678
|
3.0
|
43.2
|
1.0
|
PA
|
D:TPP1303
|
3.2
|
52.2
|
1.0
|
C
|
D:ILE680
|
3.2
|
57.9
|
1.0
|
PB
|
D:TPP1303
|
3.3
|
49.3
|
1.0
|
CG
|
D:ASP645
|
3.3
|
51.6
|
1.0
|
O3A
|
D:TPP1303
|
3.4
|
53.5
|
1.0
|
ND2
|
D:ASN678
|
3.4
|
43.8
|
1.0
|
OD2
|
D:ASP645
|
3.7
|
61.1
|
1.0
|
O1B
|
D:TPP1303
|
3.9
|
55.0
|
1.0
|
N
|
D:ILE680
|
4.0
|
54.6
|
1.0
|
O7
|
D:TPP1303
|
4.1
|
60.0
|
1.0
|
N
|
D:GLY681
|
4.1
|
62.2
|
1.0
|
N
|
D:ASP645
|
4.1
|
44.2
|
1.0
|
CA
|
D:GLY681
|
4.2
|
64.9
|
1.0
|
CA
|
D:ILE680
|
4.2
|
56.5
|
1.0
|
N
|
D:ASN678
|
4.4
|
44.5
|
1.0
|
CB
|
D:ASN678
|
4.4
|
44.3
|
1.0
|
O
|
D:VAL676
|
4.4
|
48.7
|
1.0
|
N
|
D:ALA646
|
4.4
|
47.9
|
1.0
|
O1A
|
D:TPP1303
|
4.4
|
53.7
|
1.0
|
CB
|
D:ASP645
|
4.5
|
49.9
|
1.0
|
O3B
|
D:TPP1303
|
4.5
|
54.8
|
1.0
|
CG2
|
D:ILE680
|
4.6
|
57.9
|
1.0
|
N
|
D:GLN679
|
4.6
|
48.3
|
1.0
|
CA
|
D:ASN678
|
4.7
|
44.6
|
1.0
|
C
|
D:ASN678
|
4.7
|
46.4
|
1.0
|
O
|
D:GLY681
|
4.8
|
86.8
|
1.0
|
CA
|
D:ASP645
|
4.8
|
46.7
|
1.0
|
CB
|
D:ALA646
|
4.9
|
50.4
|
1.0
|
CA
|
D:GLY644
|
4.9
|
41.8
|
1.0
|
C
|
D:GLY644
|
4.9
|
42.0
|
1.0
|
C
|
D:GLY681
|
5.0
|
74.6
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8p5v
Go back to
Magnesium Binding Sites List in 8p5v
Magnesium binding site 5 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
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 in Complex with the Product Succinyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1301
b:38.7
occ:1.00
|
OD1
|
E:ASN678
|
2.0
|
50.3
|
1.0
|
O
|
E:ILE680
|
2.0
|
56.1
|
1.0
|
O1A
|
E:TPP1303
|
2.1
|
49.6
|
1.0
|
O1B
|
E:TPP1303
|
2.1
|
49.9
|
1.0
|
OD1
|
E:ASP645
|
2.2
|
52.7
|
1.0
|
CG
|
E:ASN678
|
3.0
|
40.2
|
1.0
|
C
|
E:ILE680
|
3.2
|
52.7
|
1.0
|
PB
|
E:TPP1303
|
3.2
|
45.5
|
1.0
|
PA
|
E:TPP1303
|
3.3
|
47.8
|
1.0
|
CG
|
E:ASP645
|
3.3
|
50.3
|
1.0
|
ND2
|
E:ASN678
|
3.4
|
40.2
|
1.0
|
O3A
|
E:TPP1303
|
3.4
|
50.2
|
1.0
|
OD2
|
E:ASP645
|
3.8
|
57.4
|
1.0
|
O2B
|
E:TPP1303
|
3.8
|
51.2
|
1.0
|
N
|
E:ILE680
|
4.0
|
49.9
|
1.0
|
O7
|
E:TPP1303
|
4.1
|
55.2
|
1.0
|
N
|
E:GLY681
|
4.1
|
56.6
|
1.0
|
N
|
E:ASP645
|
4.2
|
40.8
|
1.0
|
CA
|
E:GLY681
|
4.2
|
59.7
|
1.0
|
CA
|
E:ILE680
|
4.2
|
51.6
|
1.0
|
CB
|
E:ASN678
|
4.4
|
41.6
|
1.0
|
O
|
E:VAL676
|
4.4
|
44.4
|
1.0
|
N
|
E:ASN678
|
4.4
|
41.4
|
1.0
|
N
|
E:ALA646
|
4.5
|
44.4
|
1.0
|
O2A
|
E:TPP1303
|
4.5
|
51.2
|
1.0
|
O3B
|
E:TPP1303
|
4.5
|
51.7
|
1.0
|
CB
|
E:ASP645
|
4.6
|
46.9
|
1.0
|
CG2
|
E:ILE680
|
4.6
|
53.6
|
1.0
|
N
|
E:GLN679
|
4.6
|
45.1
|
1.0
|
O
|
E:GLY681
|
4.7
|
84.0
|
1.0
|
CA
|
E:ASN678
|
4.7
|
42.2
|
1.0
|
C
|
E:ASN678
|
4.7
|
44.3
|
1.0
|
CA
|
E:ASP645
|
4.8
|
43.3
|
1.0
|
CA
|
E:GLY644
|
4.9
|
38.1
|
1.0
|
C
|
E:GLY681
|
4.9
|
70.3
|
1.0
|
CB
|
E:ALA646
|
5.0
|
46.4
|
1.0
|
C
|
E:GLY644
|
5.0
|
38.7
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8p5v
Go back to
Magnesium Binding Sites List in 8p5v
Magnesium binding site 6 out
of 6 in the Single Particle Cryo-Em Structure of Homohexameric 2-Oxoglutarate Dehydrogenase Odha From Corynebacterium Glutamicum in Complex with the Product Succinyl-Coa
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 in Complex with the Product Succinyl-Coa within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1301
b:41.5
occ:1.00
|
OD1
|
F:ASN678
|
2.0
|
52.0
|
1.0
|
O
|
F:ILE680
|
2.0
|
60.6
|
1.0
|
O2A
|
F:TPP1303
|
2.1
|
56.0
|
1.0
|
O2B
|
F:TPP1303
|
2.1
|
55.1
|
1.0
|
OD1
|
F:ASP645
|
2.2
|
56.2
|
1.0
|
CG
|
F:ASN678
|
3.0
|
43.5
|
1.0
|
PB
|
F:TPP1303
|
3.3
|
50.0
|
1.0
|
PA
|
F:TPP1303
|
3.3
|
52.6
|
1.0
|
C
|
F:ILE680
|
3.3
|
58.0
|
1.0
|
CG
|
F:ASP645
|
3.3
|
52.0
|
1.0
|
O3A
|
F:TPP1303
|
3.4
|
54.4
|
1.0
|
ND2
|
F:ASN678
|
3.4
|
43.4
|
1.0
|
OD2
|
F:ASP645
|
3.7
|
61.5
|
1.0
|
O1B
|
F:TPP1303
|
3.9
|
55.2
|
1.0
|
N
|
F:ILE680
|
4.0
|
54.8
|
1.0
|
O7
|
F:TPP1303
|
4.1
|
60.7
|
1.0
|
N
|
F:ASP645
|
4.1
|
44.9
|
1.0
|
N
|
F:GLY681
|
4.1
|
62.0
|
1.0
|
CA
|
F:GLY681
|
4.2
|
64.6
|
1.0
|
CA
|
F:ILE680
|
4.2
|
56.4
|
1.0
|
N
|
F:ASN678
|
4.4
|
44.3
|
1.0
|
O
|
F:VAL676
|
4.4
|
48.9
|
1.0
|
CB
|
F:ASN678
|
4.4
|
44.5
|
1.0
|
N
|
F:ALA646
|
4.4
|
48.9
|
1.0
|
O1A
|
F:TPP1303
|
4.4
|
54.4
|
1.0
|
O3B
|
F:TPP1303
|
4.5
|
55.6
|
1.0
|
CB
|
F:ASP645
|
4.5
|
50.4
|
1.0
|
N
|
F:GLN679
|
4.6
|
47.9
|
1.0
|
CG2
|
F:ILE680
|
4.6
|
57.8
|
1.0
|
CA
|
F:ASN678
|
4.7
|
44.4
|
1.0
|
C
|
F:ASN678
|
4.7
|
46.5
|
1.0
|
O
|
F:GLY681
|
4.8
|
87.0
|
1.0
|
CA
|
F:ASP645
|
4.8
|
47.3
|
1.0
|
CB
|
F:ALA646
|
4.9
|
51.1
|
1.0
|
CA
|
F:GLY644
|
4.9
|
42.5
|
1.0
|
C
|
F:GLY644
|
4.9
|
42.5
|
1.0
|
C
|
F:GLY681
|
5.0
|
74.3
|
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 15:55:36 2024
|