Magnesium in PDB 8p5x: Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
Enzymatic activity of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
All present enzymatic activity of Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi:
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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
(pdb code 8p5x). 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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi, PDB code: 8p5x:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 8p5x
Go back to
Magnesium Binding Sites List in 8p5x
Magnesium binding site 1 out
of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1302
b:54.6
occ:1.00
|
OD1
|
A:ASN678
|
2.3
|
55.3
|
1.0
|
O2A
|
A:TPP1301
|
2.4
|
90.0
|
1.0
|
O
|
A:ILE680
|
2.5
|
96.6
|
1.0
|
O3B
|
A:TPP1301
|
2.9
|
81.9
|
1.0
|
OD2
|
A:ASP645
|
3.2
|
53.8
|
1.0
|
OD1
|
A:ASP645
|
3.2
|
57.4
|
1.0
|
O3A
|
A:TPP1301
|
3.2
|
87.0
|
1.0
|
CG
|
A:ASN678
|
3.3
|
46.3
|
1.0
|
CG
|
A:ASP645
|
3.3
|
50.6
|
1.0
|
PB
|
A:TPP1301
|
3.4
|
74.3
|
1.0
|
PA
|
A:TPP1301
|
3.4
|
85.1
|
1.0
|
C
|
A:ILE680
|
3.7
|
92.8
|
1.0
|
O1B
|
A:TPP1301
|
3.7
|
80.4
|
1.0
|
ND2
|
A:ASN678
|
3.8
|
53.6
|
1.0
|
N
|
A:ASP645
|
4.1
|
28.5
|
1.0
|
O
|
A:VAL676
|
4.4
|
37.7
|
1.0
|
N
|
A:ILE680
|
4.4
|
71.3
|
1.0
|
N
|
A:ASN678
|
4.4
|
36.3
|
1.0
|
O7
|
A:TPP1301
|
4.4
|
104.0
|
1.0
|
N
|
A:GLY681
|
4.4
|
103.8
|
1.0
|
CA
|
A:GLY681
|
4.5
|
112.6
|
1.0
|
CB
|
A:ASP645
|
4.5
|
40.0
|
1.0
|
O1A
|
A:TPP1301
|
4.5
|
89.4
|
1.0
|
CB
|
A:ASN678
|
4.6
|
43.2
|
1.0
|
O
|
A:GLY681
|
4.6
|
126.6
|
1.0
|
N
|
A:ALA646
|
4.6
|
30.3
|
1.0
|
CA
|
A:ILE680
|
4.7
|
81.9
|
1.0
|
CA
|
A:ASP645
|
4.8
|
30.5
|
1.0
|
N
|
A:GLN679
|
4.8
|
45.0
|
1.0
|
CA
|
A:ASN678
|
4.8
|
38.5
|
1.0
|
C
|
A:ASN678
|
4.9
|
40.1
|
1.0
|
O2B
|
A:TPP1301
|
4.9
|
81.9
|
1.0
|
C
|
A:GLY644
|
4.9
|
26.0
|
1.0
|
CA
|
A:GLY644
|
5.0
|
24.9
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 8p5x
Go back to
Magnesium Binding Sites List in 8p5x
Magnesium binding site 2 out
of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1302
b:51.2
occ:1.00
|
OD1
|
B:ASN678
|
2.3
|
57.4
|
1.0
|
O1A
|
B:TPP1301
|
2.4
|
85.4
|
1.0
|
O
|
B:ILE680
|
2.5
|
112.7
|
1.0
|
O1B
|
B:TPP1301
|
2.9
|
79.0
|
1.0
|
O3A
|
B:TPP1301
|
3.1
|
83.4
|
1.0
|
OD2
|
B:ASP645
|
3.2
|
56.0
|
1.0
|
CG
|
B:ASN678
|
3.3
|
48.4
|
1.0
|
OD1
|
B:ASP645
|
3.3
|
58.7
|
1.0
|
PB
|
B:TPP1301
|
3.3
|
70.8
|
1.0
|
CG
|
B:ASP645
|
3.4
|
52.3
|
1.0
|
PA
|
B:TPP1301
|
3.4
|
79.6
|
1.0
|
O3B
|
B:TPP1301
|
3.6
|
76.7
|
1.0
|
ND2
|
B:ASN678
|
3.7
|
55.8
|
1.0
|
C
|
B:ILE680
|
3.7
|
111.5
|
1.0
|
N
|
B:ASP645
|
4.1
|
29.4
|
1.0
|
O
|
B:VAL676
|
4.3
|
36.5
|
1.0
|
N
|
B:ASN678
|
4.4
|
36.6
|
1.0
|
O7
|
B:TPP1301
|
4.4
|
101.3
|
1.0
|
N
|
B:ILE680
|
4.4
|
84.3
|
1.0
|
N
|
B:GLY681
|
4.5
|
128.2
|
1.0
|
O2A
|
B:TPP1301
|
4.5
|
83.9
|
1.0
|
CA
|
B:GLY681
|
4.5
|
140.2
|
1.0
|
CB
|
B:ASP645
|
4.5
|
40.3
|
1.0
|
CB
|
B:ASN678
|
4.5
|
44.5
|
1.0
|
O
|
B:GLY681
|
4.6
|
152.9
|
1.0
|
N
|
B:ALA646
|
4.7
|
30.3
|
1.0
|
CA
|
B:ILE680
|
4.7
|
98.2
|
1.0
|
CA
|
B:ASN678
|
4.8
|
40.1
|
1.0
|
N
|
B:GLN679
|
4.8
|
50.1
|
1.0
|
CA
|
B:ASP645
|
4.8
|
30.7
|
1.0
|
O2B
|
B:TPP1301
|
4.8
|
78.7
|
1.0
|
C
|
B:ASN678
|
4.8
|
44.1
|
1.0
|
C
|
B:GLY644
|
4.9
|
26.5
|
1.0
|
CA
|
B:GLY644
|
5.0
|
24.8
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 8p5x
Go back to
Magnesium Binding Sites List in 8p5x
Magnesium binding site 3 out
of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1301
b:53.9
occ:1.00
|
OD1
|
C:ASN678
|
2.3
|
55.7
|
1.0
|
O2A
|
C:TPP1302
|
2.4
|
88.7
|
1.0
|
O
|
C:ILE680
|
2.5
|
98.5
|
1.0
|
O3B
|
C:TPP1302
|
2.9
|
81.2
|
1.0
|
OD2
|
C:ASP645
|
3.2
|
54.2
|
1.0
|
OD1
|
C:ASP645
|
3.2
|
57.8
|
1.0
|
O3A
|
C:TPP1302
|
3.3
|
85.7
|
1.0
|
CG
|
C:ASN678
|
3.3
|
47.0
|
1.0
|
CG
|
C:ASP645
|
3.3
|
51.1
|
1.0
|
PB
|
C:TPP1302
|
3.4
|
73.1
|
1.0
|
PA
|
C:TPP1302
|
3.4
|
83.8
|
1.0
|
C
|
C:ILE680
|
3.7
|
94.4
|
1.0
|
O1B
|
C:TPP1302
|
3.7
|
79.5
|
1.0
|
ND2
|
C:ASN678
|
3.8
|
54.4
|
1.0
|
N
|
C:ASP645
|
4.1
|
28.9
|
1.0
|
O
|
C:VAL676
|
4.3
|
38.1
|
1.0
|
N
|
C:ILE680
|
4.4
|
72.4
|
1.0
|
N
|
C:ASN678
|
4.4
|
36.7
|
1.0
|
O7
|
C:TPP1302
|
4.4
|
101.2
|
1.0
|
N
|
C:GLY681
|
4.5
|
105.5
|
1.0
|
CA
|
C:GLY681
|
4.5
|
114.3
|
1.0
|
CB
|
C:ASP645
|
4.5
|
40.4
|
1.0
|
O1A
|
C:TPP1302
|
4.5
|
88.5
|
1.0
|
CB
|
C:ASN678
|
4.6
|
43.9
|
1.0
|
N
|
C:ALA646
|
4.6
|
30.5
|
1.0
|
O
|
C:GLY681
|
4.6
|
128.1
|
1.0
|
CA
|
C:ILE680
|
4.7
|
83.0
|
1.0
|
CA
|
C:ASP645
|
4.8
|
30.7
|
1.0
|
N
|
C:GLN679
|
4.8
|
45.6
|
1.0
|
CA
|
C:ASN678
|
4.8
|
39.0
|
1.0
|
C
|
C:ASN678
|
4.9
|
40.6
|
1.0
|
O2B
|
C:TPP1302
|
4.9
|
81.1
|
1.0
|
C
|
C:GLY644
|
4.9
|
26.4
|
1.0
|
CA
|
C:GLY644
|
5.0
|
25.3
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 8p5x
Go back to
Magnesium Binding Sites List in 8p5x
Magnesium binding site 4 out
of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1302
b:50.5
occ:1.00
|
OD1
|
D:ASN678
|
2.3
|
57.7
|
1.0
|
O1A
|
D:TPP1301
|
2.4
|
85.8
|
1.0
|
O
|
D:ILE680
|
2.5
|
114.2
|
1.0
|
O1B
|
D:TPP1301
|
2.9
|
79.9
|
1.0
|
O3A
|
D:TPP1301
|
3.2
|
83.8
|
1.0
|
OD2
|
D:ASP645
|
3.2
|
55.7
|
1.0
|
CG
|
D:ASN678
|
3.3
|
48.7
|
1.0
|
OD1
|
D:ASP645
|
3.3
|
58.5
|
1.0
|
PB
|
D:TPP1301
|
3.3
|
71.2
|
1.0
|
CG
|
D:ASP645
|
3.4
|
52.1
|
1.0
|
PA
|
D:TPP1301
|
3.4
|
79.9
|
1.0
|
O3B
|
D:TPP1301
|
3.6
|
77.4
|
1.0
|
ND2
|
D:ASN678
|
3.7
|
56.2
|
1.0
|
C
|
D:ILE680
|
3.7
|
112.9
|
1.0
|
N
|
D:ASP645
|
4.1
|
29.3
|
1.0
|
O
|
D:VAL676
|
4.3
|
36.8
|
1.0
|
N
|
D:ASN678
|
4.3
|
36.7
|
1.0
|
O7
|
D:TPP1301
|
4.4
|
101.8
|
1.0
|
N
|
D:ILE680
|
4.4
|
85.5
|
1.0
|
O2A
|
D:TPP1301
|
4.5
|
84.8
|
1.0
|
N
|
D:GLY681
|
4.5
|
129.5
|
1.0
|
CB
|
D:ASP645
|
4.5
|
40.1
|
1.0
|
CA
|
D:GLY681
|
4.5
|
141.8
|
1.0
|
CB
|
D:ASN678
|
4.5
|
44.7
|
1.0
|
O
|
D:GLY681
|
4.6
|
154.6
|
1.0
|
N
|
D:ALA646
|
4.7
|
30.0
|
1.0
|
CA
|
D:ILE680
|
4.7
|
99.5
|
1.0
|
CA
|
D:ASN678
|
4.8
|
40.2
|
1.0
|
CA
|
D:ASP645
|
4.8
|
30.5
|
1.0
|
N
|
D:GLN679
|
4.8
|
50.5
|
1.0
|
O2B
|
D:TPP1301
|
4.8
|
78.9
|
1.0
|
C
|
D:ASN678
|
4.8
|
44.4
|
1.0
|
C
|
D:GLY644
|
4.9
|
26.4
|
1.0
|
CA
|
D:GLY644
|
4.9
|
24.7
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 8p5x
Go back to
Magnesium Binding Sites List in 8p5x
Magnesium binding site 5 out
of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg1302
b:53.5
occ:1.00
|
OD1
|
E:ASN678
|
2.3
|
55.4
|
1.0
|
O2A
|
E:TPP1301
|
2.4
|
89.2
|
1.0
|
O
|
E:ILE680
|
2.5
|
97.2
|
1.0
|
O3B
|
E:TPP1301
|
2.9
|
81.4
|
1.0
|
OD2
|
E:ASP645
|
3.2
|
53.8
|
1.0
|
O3A
|
E:TPP1301
|
3.2
|
85.3
|
1.0
|
OD1
|
E:ASP645
|
3.2
|
57.4
|
1.0
|
CG
|
E:ASN678
|
3.3
|
46.6
|
1.0
|
CG
|
E:ASP645
|
3.3
|
50.7
|
1.0
|
PA
|
E:TPP1301
|
3.4
|
83.9
|
1.0
|
PB
|
E:TPP1301
|
3.4
|
73.0
|
1.0
|
C
|
E:ILE680
|
3.7
|
93.6
|
1.0
|
O1B
|
E:TPP1301
|
3.7
|
79.5
|
1.0
|
ND2
|
E:ASN678
|
3.8
|
53.9
|
1.0
|
N
|
E:ASP645
|
4.1
|
28.5
|
1.0
|
O
|
E:VAL676
|
4.4
|
38.1
|
1.0
|
O7
|
E:TPP1301
|
4.4
|
101.9
|
1.0
|
N
|
E:ILE680
|
4.4
|
71.8
|
1.0
|
N
|
E:ASN678
|
4.4
|
36.2
|
1.0
|
N
|
E:GLY681
|
4.5
|
105.0
|
1.0
|
CA
|
E:GLY681
|
4.5
|
114.2
|
1.0
|
CB
|
E:ASP645
|
4.5
|
39.9
|
1.0
|
O1A
|
E:TPP1301
|
4.5
|
88.4
|
1.0
|
CB
|
E:ASN678
|
4.6
|
43.4
|
1.0
|
N
|
E:ALA646
|
4.6
|
30.0
|
1.0
|
O
|
E:GLY681
|
4.6
|
128.2
|
1.0
|
CA
|
E:ILE680
|
4.7
|
82.8
|
1.0
|
CA
|
E:ASP645
|
4.8
|
30.3
|
1.0
|
N
|
E:GLN679
|
4.8
|
45.1
|
1.0
|
CA
|
E:ASN678
|
4.8
|
38.5
|
1.0
|
C
|
E:ASN678
|
4.9
|
40.3
|
1.0
|
O2B
|
E:TPP1301
|
4.9
|
80.8
|
1.0
|
C
|
E:GLY644
|
4.9
|
26.1
|
1.0
|
CA
|
E:GLY644
|
5.0
|
25.1
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 8p5x
Go back to
Magnesium Binding Sites List in 8p5x
Magnesium binding site 6 out
of 6 in the Single Particle Cryo-Em Structure of the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi
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 the Complex Between Corynebacterium Glutamicum Homohexameric 2-Oxoglutarate Dehydrogenase Odha and the Fha-Protein Inhibitor Odhi within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg1302
b:40.8
occ:1.00
|
OD1
|
F:ASN678
|
2.3
|
58.0
|
1.0
|
O1A
|
F:TPP1301
|
2.4
|
78.2
|
1.0
|
O
|
F:ILE680
|
2.4
|
100.6
|
1.0
|
O1B
|
F:TPP1301
|
2.9
|
73.0
|
1.0
|
O3A
|
F:TPP1301
|
3.2
|
76.0
|
1.0
|
OD2
|
F:ASP645
|
3.2
|
56.1
|
1.0
|
OD1
|
F:ASP645
|
3.3
|
58.8
|
1.0
|
CG
|
F:ASN678
|
3.3
|
49.6
|
1.0
|
PA
|
F:TPP1301
|
3.4
|
71.2
|
1.0
|
CG
|
F:ASP645
|
3.4
|
53.1
|
1.0
|
PB
|
F:TPP1301
|
3.4
|
63.5
|
1.0
|
C
|
F:ILE680
|
3.6
|
97.6
|
1.0
|
ND2
|
F:ASN678
|
3.7
|
57.8
|
1.0
|
O3B
|
F:TPP1301
|
3.7
|
69.7
|
1.0
|
N
|
F:ASP645
|
4.1
|
29.1
|
1.0
|
O7
|
F:TPP1301
|
4.3
|
91.7
|
1.0
|
N
|
F:ILE680
|
4.4
|
75.3
|
1.0
|
O
|
F:VAL676
|
4.4
|
34.1
|
1.0
|
N
|
F:GLY681
|
4.4
|
111.3
|
1.0
|
N
|
F:ASN678
|
4.4
|
36.6
|
1.0
|
CA
|
F:GLY681
|
4.4
|
122.0
|
1.0
|
O2A
|
F:TPP1301
|
4.5
|
76.0
|
1.0
|
CB
|
F:ASP645
|
4.6
|
41.7
|
1.0
|
O
|
F:GLY681
|
4.6
|
136.6
|
1.0
|
CB
|
F:ASN678
|
4.6
|
44.5
|
1.0
|
CA
|
F:ILE680
|
4.6
|
85.7
|
1.0
|
N
|
F:ALA646
|
4.7
|
32.3
|
1.0
|
N
|
F:GLN679
|
4.8
|
48.0
|
1.0
|
CA
|
F:ASN678
|
4.8
|
40.1
|
1.0
|
CA
|
F:ASP645
|
4.8
|
32.0
|
1.0
|
C
|
F:ASN678
|
4.9
|
43.2
|
1.0
|
O2B
|
F:TPP1301
|
4.9
|
71.7
|
1.0
|
C
|
F:GLY644
|
5.0
|
26.1
|
1.0
|
CG2
|
F:ILE680
|
5.0
|
91.5
|
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 15:55:57 2024
|