Magnesium in PDB 6rdb: Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
Enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
All present enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor:
7.1.2.2;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
(pdb code 6rdb). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor, PDB code: 6rdb:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6rdb
Go back to
Magnesium Binding Sites List in 6rdb
Magnesium binding site 1 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mg1002
b:28.1
occ:1.00
|
OG1
|
T:THR232
|
1.7
|
28.8
|
1.0
|
O1G
|
T:ATP1001
|
2.0
|
30.7
|
1.0
|
O2B
|
T:ATP1001
|
2.1
|
30.7
|
1.0
|
O
|
X:HOH705
|
2.2
|
30.0
|
1.0
|
O
|
T:HOH1105
|
2.4
|
30.0
|
1.0
|
O
|
T:HOH1101
|
2.6
|
30.0
|
1.0
|
CB
|
T:THR232
|
2.9
|
28.8
|
1.0
|
PG
|
T:ATP1001
|
3.4
|
30.7
|
1.0
|
PB
|
T:ATP1001
|
3.4
|
30.7
|
1.0
|
CG2
|
T:THR232
|
3.6
|
28.8
|
1.0
|
O3B
|
T:ATP1001
|
3.7
|
30.7
|
1.0
|
OD2
|
T:ASP325
|
3.9
|
25.5
|
1.0
|
CA
|
T:THR232
|
4.0
|
28.8
|
1.0
|
O3G
|
T:ATP1001
|
4.1
|
30.7
|
1.0
|
N
|
T:THR232
|
4.2
|
28.8
|
1.0
|
OD1
|
T:ASP325
|
4.3
|
25.5
|
1.0
|
O2A
|
T:ATP1001
|
4.4
|
30.7
|
1.0
|
O
|
X:HOH709
|
4.4
|
30.0
|
1.0
|
O3A
|
T:ATP1001
|
4.4
|
30.7
|
1.0
|
O1B
|
T:ATP1001
|
4.4
|
30.7
|
1.0
|
CG
|
T:ASP325
|
4.5
|
25.5
|
1.0
|
O2G
|
T:ATP1001
|
4.5
|
30.7
|
1.0
|
O
|
T:HOH1103
|
4.5
|
30.0
|
1.0
|
O
|
T:HOH1106
|
4.5
|
30.0
|
1.0
|
NH2
|
X:ARG385
|
4.6
|
34.7
|
1.0
|
PA
|
T:ATP1001
|
4.7
|
30.7
|
1.0
|
O1A
|
T:ATP1001
|
4.7
|
30.7
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6rdb
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Magnesium Binding Sites List in 6rdb
Magnesium binding site 2 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Mg1002
b:28.1
occ:1.00
|
O2B
|
U:ATP1001
|
2.2
|
30.7
|
1.0
|
O1G
|
U:ATP1001
|
2.3
|
30.7
|
1.0
|
O
|
U:HOH1105
|
2.3
|
30.0
|
1.0
|
OG1
|
U:THR232
|
2.4
|
29.6
|
1.0
|
O
|
U:HOH1103
|
2.4
|
30.0
|
1.0
|
O
|
U:HOH1107
|
2.6
|
30.0
|
1.0
|
OD2
|
U:ASP325
|
3.4
|
29.4
|
1.0
|
CB
|
U:THR232
|
3.5
|
29.6
|
1.0
|
PB
|
U:ATP1001
|
3.5
|
30.7
|
1.0
|
PG
|
U:ATP1001
|
3.6
|
30.7
|
1.0
|
O
|
U:HOH1108
|
3.9
|
30.0
|
1.0
|
O3B
|
U:ATP1001
|
3.9
|
30.7
|
1.0
|
O
|
U:HOH1102
|
4.2
|
50.0
|
1.0
|
CG
|
U:ASP325
|
4.2
|
29.4
|
1.0
|
N
|
U:THR232
|
4.2
|
29.6
|
1.0
|
OD1
|
U:ASP325
|
4.3
|
29.4
|
1.0
|
CG2
|
U:THR232
|
4.4
|
29.6
|
1.0
|
O1B
|
U:ATP1001
|
4.5
|
30.7
|
1.0
|
CA
|
U:THR232
|
4.5
|
29.6
|
1.0
|
O2G
|
U:ATP1001
|
4.5
|
30.7
|
1.0
|
O2A
|
U:ATP1001
|
4.6
|
30.7
|
1.0
|
O
|
U:HOH1109
|
4.6
|
30.0
|
1.0
|
O3G
|
U:ATP1001
|
4.6
|
30.7
|
1.0
|
O3A
|
U:ATP1001
|
4.6
|
30.7
|
1.0
|
O
|
U:HOH1101
|
4.7
|
30.0
|
1.0
|
OD2
|
U:ASP326
|
4.9
|
28.1
|
1.0
|
PA
|
U:ATP1001
|
5.0
|
30.7
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6rdb
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Magnesium Binding Sites List in 6rdb
Magnesium binding site 3 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg1002
b:28.1
occ:1.00
|
O
|
V:HOH1106
|
2.1
|
30.0
|
1.0
|
O1G
|
V:ATP1001
|
2.2
|
30.7
|
1.0
|
O2B
|
V:ATP1001
|
2.2
|
30.7
|
1.0
|
OG1
|
V:THR232
|
2.3
|
32.0
|
1.0
|
O
|
Y:HOH701
|
2.5
|
30.0
|
1.0
|
O
|
V:HOH1105
|
2.6
|
30.0
|
1.0
|
PG
|
V:ATP1001
|
3.5
|
30.7
|
1.0
|
PB
|
V:ATP1001
|
3.5
|
30.7
|
1.0
|
CB
|
V:THR232
|
3.6
|
32.0
|
1.0
|
O3B
|
V:ATP1001
|
3.6
|
30.7
|
1.0
|
O3G
|
V:ATP1001
|
4.2
|
30.7
|
1.0
|
OD2
|
V:ASP325
|
4.3
|
26.4
|
1.0
|
N
|
V:THR232
|
4.3
|
32.0
|
1.0
|
CG2
|
V:THR232
|
4.4
|
32.0
|
1.0
|
O2A
|
V:ATP1001
|
4.4
|
30.7
|
1.0
|
O1B
|
V:ATP1001
|
4.5
|
30.7
|
1.0
|
O3A
|
V:ATP1001
|
4.5
|
30.7
|
1.0
|
CA
|
V:THR232
|
4.5
|
32.0
|
1.0
|
O
|
V:HOH1107
|
4.6
|
30.0
|
1.0
|
O2G
|
V:ATP1001
|
4.6
|
30.7
|
1.0
|
NH1
|
Y:ARG385
|
4.9
|
46.3
|
1.0
|
PA
|
V:ATP1001
|
4.9
|
30.7
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6rdb
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Magnesium Binding Sites List in 6rdb
Magnesium binding site 4 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Mg602
b:26.4
occ:1.00
|
O
|
X:HOH703
|
0.4
|
30.0
|
1.0
|
OG1
|
X:THR190
|
2.1
|
28.0
|
1.0
|
O
|
X:HOH701
|
2.3
|
30.0
|
1.0
|
O2B
|
X:ADP601
|
2.4
|
34.1
|
1.0
|
O
|
X:HOH704
|
2.4
|
30.0
|
1.0
|
OE2
|
X:GLU215
|
2.9
|
24.0
|
1.0
|
CB
|
X:THR190
|
3.4
|
28.0
|
1.0
|
NH1
|
X:ARG216
|
3.5
|
22.7
|
1.0
|
PB
|
X:ADP601
|
3.8
|
34.1
|
1.0
|
CD
|
X:GLU215
|
3.9
|
24.0
|
1.0
|
OE1
|
X:GLU219
|
4.0
|
26.6
|
1.0
|
CG2
|
X:THR190
|
4.0
|
28.0
|
1.0
|
O3A
|
X:ADP601
|
4.4
|
34.1
|
1.0
|
O1B
|
X:ADP601
|
4.4
|
34.1
|
1.0
|
CA
|
X:THR190
|
4.5
|
28.0
|
1.0
|
OE2
|
X:GLU219
|
4.5
|
26.6
|
1.0
|
N
|
X:THR190
|
4.5
|
28.0
|
1.0
|
OE1
|
X:GLU215
|
4.5
|
24.0
|
1.0
|
CZ
|
X:ARG216
|
4.6
|
22.7
|
1.0
|
O1A
|
X:ADP601
|
4.6
|
34.1
|
1.0
|
CD
|
X:GLU219
|
4.6
|
26.6
|
1.0
|
OD2
|
X:ASP285
|
4.6
|
24.7
|
1.0
|
OD1
|
X:ASP285
|
4.7
|
24.7
|
1.0
|
CG
|
X:GLU215
|
4.7
|
24.0
|
1.0
|
OD1
|
X:ASN286
|
4.7
|
23.2
|
1.0
|
NH2
|
X:ARG216
|
4.8
|
22.7
|
1.0
|
PA
|
X:ADP601
|
4.9
|
34.1
|
1.0
|
O3B
|
X:ADP601
|
4.9
|
34.1
|
1.0
|
O
|
X:HOH702
|
4.9
|
30.0
|
1.0
|
O2A
|
X:ADP601
|
5.0
|
34.1
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6rdb
Go back to
Magnesium Binding Sites List in 6rdb
Magnesium binding site 5 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg602
b:46.6
occ:1.00
|
O3B
|
Y:ADP601
|
2.5
|
48.8
|
1.0
|
O
|
Y:HOH703
|
2.6
|
30.0
|
1.0
|
O
|
Y:HOH702
|
2.8
|
30.0
|
1.0
|
O
|
Y:HOH704
|
2.8
|
30.0
|
1.0
|
OG1
|
Y:THR190
|
2.8
|
45.0
|
1.0
|
OE2
|
Y:GLU215
|
2.8
|
32.2
|
1.0
|
OE2
|
Y:GLU219
|
3.3
|
35.4
|
1.0
|
NH1
|
Y:ARG216
|
3.5
|
31.5
|
1.0
|
CD
|
Y:GLU215
|
3.8
|
32.2
|
1.0
|
OD2
|
Y:ASP285
|
3.8
|
34.0
|
1.0
|
PB
|
Y:ADP601
|
3.8
|
48.8
|
1.0
|
OE1
|
Y:GLU219
|
4.0
|
35.4
|
1.0
|
CD
|
Y:GLU219
|
4.1
|
35.4
|
1.0
|
CB
|
Y:THR190
|
4.1
|
45.0
|
1.0
|
ND2
|
Y:ASN286
|
4.1
|
33.6
|
1.0
|
O2B
|
Y:ADP601
|
4.2
|
48.8
|
1.0
|
OE1
|
Y:GLU215
|
4.5
|
32.2
|
1.0
|
CG
|
Y:GLU215
|
4.6
|
32.2
|
1.0
|
O2A
|
Y:ADP601
|
4.7
|
48.8
|
1.0
|
N
|
Y:THR190
|
4.7
|
45.0
|
1.0
|
CZ
|
Y:ARG216
|
4.7
|
31.5
|
1.0
|
O1B
|
Y:ADP601
|
4.8
|
48.8
|
1.0
|
O3A
|
Y:ADP601
|
4.8
|
48.8
|
1.0
|
NZ
|
Y:LYS189
|
4.8
|
42.4
|
1.0
|
CG
|
Y:ASP285
|
4.9
|
34.0
|
1.0
|
O1A
|
Y:ADP601
|
4.9
|
48.8
|
1.0
|
CA
|
Y:THR190
|
4.9
|
45.0
|
1.0
|
|
Reference:
B.J.Murphy,
N.Klusch,
J.Langer,
D.J.Mills,
O.Yildiz,
W.Kuhlbrandt.
Rotary Substates of Mitochondrial Atp Synthase Reveal the Basis of Flexible F1-Focoupling. Science V. 364 2019.
ISSN: ESSN 1095-9203
PubMed: 31221832
DOI: 10.1126/SCIENCE.AAW9128
Page generated: Tue Oct 1 16:42:14 2024
|