Magnesium in PDB 6rd9: Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
Enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
All present enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map:
7.1.2.2;
Other elements in 6rd9:
The structure of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
(pdb code 6rd9). 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, Composite Map, PDB code: 6rd9:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6rd9
Go back to
Magnesium Binding Sites List in 6rd9
Magnesium binding site 1 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
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, Composite Map within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mg1002
b:43.2
occ:1.00
|
OG1
|
T:THR232
|
2.0
|
43.2
|
1.0
|
O1G
|
T:ATP1001
|
2.0
|
43.0
|
1.0
|
O2B
|
T:ATP1001
|
2.2
|
43.0
|
1.0
|
PG
|
T:ATP1001
|
3.3
|
43.0
|
1.0
|
CB
|
T:THR232
|
3.4
|
43.2
|
1.0
|
PB
|
T:ATP1001
|
3.4
|
43.0
|
1.0
|
O3B
|
T:ATP1001
|
3.7
|
43.0
|
1.0
|
OD2
|
T:ASP325
|
3.7
|
35.9
|
1.0
|
O3G
|
T:ATP1001
|
3.9
|
43.0
|
1.0
|
CG2
|
T:THR232
|
4.0
|
43.2
|
1.0
|
N
|
T:THR232
|
4.3
|
43.2
|
1.0
|
O1B
|
T:ATP1001
|
4.3
|
43.0
|
1.0
|
O2A
|
T:ATP1001
|
4.4
|
43.0
|
1.0
|
CA
|
T:THR232
|
4.4
|
43.2
|
1.0
|
OD1
|
T:ASP325
|
4.4
|
35.9
|
1.0
|
CG
|
T:ASP325
|
4.4
|
35.9
|
1.0
|
O2G
|
T:ATP1001
|
4.5
|
43.0
|
1.0
|
O3A
|
T:ATP1001
|
4.5
|
43.0
|
1.0
|
PA
|
T:ATP1001
|
4.8
|
43.0
|
1.0
|
O1A
|
T:ATP1001
|
5.0
|
43.0
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6rd9
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Magnesium Binding Sites List in 6rd9
Magnesium binding site 2 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
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, Composite Map within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Mg1002
b:55.7
occ:1.00
|
OG1
|
U:THR232
|
2.0
|
45.6
|
1.0
|
O3G
|
U:ATP1001
|
2.1
|
55.4
|
1.0
|
O1B
|
U:ATP1001
|
2.1
|
55.4
|
1.0
|
PG
|
U:ATP1001
|
3.3
|
55.4
|
1.0
|
PB
|
U:ATP1001
|
3.3
|
55.4
|
1.0
|
CB
|
U:THR232
|
3.4
|
45.6
|
1.0
|
O3B
|
U:ATP1001
|
3.6
|
55.4
|
1.0
|
O1A
|
U:ATP1001
|
3.7
|
55.4
|
1.0
|
O1G
|
U:ATP1001
|
3.9
|
55.4
|
1.0
|
OD1
|
U:ASP325
|
3.9
|
38.6
|
1.0
|
CG2
|
U:THR232
|
4.0
|
45.6
|
1.0
|
N
|
U:THR232
|
4.2
|
45.6
|
1.0
|
CA
|
U:THR232
|
4.3
|
45.6
|
1.0
|
OD2
|
U:ASP325
|
4.3
|
38.6
|
1.0
|
O3A
|
U:ATP1001
|
4.4
|
55.4
|
1.0
|
O2B
|
U:ATP1001
|
4.4
|
55.4
|
1.0
|
CG
|
U:ASP325
|
4.5
|
38.6
|
1.0
|
O2G
|
U:ATP1001
|
4.5
|
55.4
|
1.0
|
PA
|
U:ATP1001
|
4.5
|
55.4
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6rd9
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Magnesium Binding Sites List in 6rd9
Magnesium binding site 3 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
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, Composite Map within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg1001
b:43.2
occ:1.00
|
OG1
|
V:THR232
|
2.0
|
48.9
|
1.0
|
O3G
|
V:ATP1000
|
2.0
|
52.2
|
1.0
|
O2B
|
V:ATP1000
|
2.2
|
52.2
|
1.0
|
PG
|
V:ATP1000
|
3.3
|
52.2
|
1.0
|
CB
|
V:THR232
|
3.4
|
48.9
|
1.0
|
PB
|
V:ATP1000
|
3.4
|
52.2
|
1.0
|
O3B
|
V:ATP1000
|
3.6
|
52.2
|
1.0
|
OD1
|
V:ASP325
|
3.7
|
41.6
|
1.0
|
O1G
|
V:ATP1000
|
4.0
|
52.2
|
1.0
|
N
|
V:THR232
|
4.0
|
48.9
|
1.0
|
OD2
|
V:ASP325
|
4.2
|
41.6
|
1.0
|
CG2
|
V:THR232
|
4.2
|
48.9
|
1.0
|
CA
|
V:THR232
|
4.2
|
48.9
|
1.0
|
CG
|
V:ASP325
|
4.3
|
41.6
|
1.0
|
O1B
|
V:ATP1000
|
4.3
|
52.2
|
1.0
|
O2G
|
V:ATP1000
|
4.5
|
52.2
|
1.0
|
OD2
|
V:ASP326
|
4.5
|
43.5
|
1.0
|
O3A
|
V:ATP1000
|
4.6
|
52.2
|
1.0
|
O2A
|
V:ATP1000
|
4.6
|
52.2
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6rd9
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Magnesium Binding Sites List in 6rd9
Magnesium binding site 4 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
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, Composite Map within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Mg602
b:46.1
occ:1.00
|
O2B
|
X:ADP601
|
2.1
|
52.1
|
1.0
|
OG1
|
X:THR190
|
2.1
|
46.6
|
1.0
|
OE2
|
X:GLU215
|
2.4
|
46.8
|
1.0
|
CD
|
X:GLU215
|
3.4
|
46.8
|
1.0
|
CB
|
X:THR190
|
3.4
|
46.6
|
1.0
|
PB
|
X:ADP601
|
3.4
|
52.1
|
1.0
|
NH1
|
X:ARG216
|
3.5
|
43.6
|
1.0
|
O2A
|
X:ADP601
|
3.8
|
52.1
|
1.0
|
O1B
|
X:ADP601
|
3.9
|
52.1
|
1.0
|
OE1
|
X:GLU215
|
4.0
|
46.8
|
1.0
|
OE1
|
X:GLU219
|
4.0
|
51.1
|
1.0
|
CG2
|
X:THR190
|
4.0
|
46.6
|
1.0
|
OE2
|
X:GLU219
|
4.1
|
51.1
|
1.0
|
O3A
|
X:ADP601
|
4.3
|
52.1
|
1.0
|
CG
|
X:GLU215
|
4.4
|
46.8
|
1.0
|
O3B
|
X:ADP601
|
4.4
|
52.1
|
1.0
|
CD
|
X:GLU219
|
4.5
|
51.1
|
1.0
|
CA
|
X:THR190
|
4.5
|
46.6
|
1.0
|
PA
|
X:ADP601
|
4.5
|
52.1
|
1.0
|
N
|
X:THR190
|
4.5
|
46.6
|
1.0
|
OD2
|
X:ASP285
|
4.7
|
44.9
|
1.0
|
CZ
|
X:ARG216
|
4.7
|
43.6
|
1.0
|
OD1
|
X:ASP285
|
4.7
|
44.9
|
1.0
|
ND2
|
X:ASN286
|
4.9
|
40.6
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6rd9
Go back to
Magnesium Binding Sites List in 6rd9
Magnesium binding site 5 out
of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map
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, Composite Map within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Y:Mg602
b:65.5
occ:1.00
|
O3B
|
Y:ADP601
|
2.0
|
76.3
|
1.0
|
OG1
|
Y:THR190
|
2.1
|
67.8
|
1.0
|
OE2
|
Y:GLU215
|
3.3
|
52.5
|
1.0
|
PB
|
Y:ADP601
|
3.4
|
76.3
|
1.0
|
CB
|
Y:THR190
|
3.5
|
67.8
|
1.0
|
OE2
|
Y:GLU219
|
3.6
|
60.7
|
1.0
|
OD2
|
Y:ASP285
|
3.6
|
53.4
|
1.0
|
NH1
|
Y:ARG216
|
3.9
|
53.7
|
1.0
|
O2B
|
Y:ADP601
|
4.0
|
76.3
|
1.0
|
CD
|
Y:GLU215
|
4.1
|
52.5
|
1.0
|
CG2
|
Y:THR190
|
4.1
|
67.8
|
1.0
|
O1B
|
Y:ADP601
|
4.2
|
76.3
|
1.0
|
N
|
Y:THR190
|
4.2
|
67.8
|
1.0
|
OE1
|
Y:GLU219
|
4.3
|
60.7
|
1.0
|
CA
|
Y:THR190
|
4.4
|
67.8
|
1.0
|
CD
|
Y:GLU219
|
4.4
|
60.7
|
1.0
|
O3A
|
Y:ADP601
|
4.5
|
76.3
|
1.0
|
ND2
|
Y:ASN286
|
4.5
|
52.1
|
1.0
|
O2A
|
Y:ADP601
|
4.6
|
76.3
|
1.0
|
CG
|
Y:ASP285
|
4.6
|
53.4
|
1.0
|
CG
|
Y:GLU215
|
4.7
|
52.5
|
1.0
|
OD1
|
Y:ASP285
|
4.7
|
53.4
|
1.0
|
CE
|
Y:LYS189
|
4.8
|
62.5
|
1.0
|
OE1
|
Y:GLU215
|
4.8
|
52.5
|
1.0
|
PA
|
Y:ADP601
|
4.9
|
76.3
|
1.0
|
CB
|
Y:LYS189
|
4.9
|
62.5
|
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
|