Magnesium in PDB 6reu: Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor
Enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor
All present enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor:
7.1.2.2;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor
(pdb code 6reu). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor, PDB code: 6reu:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 6reu
Go back to
Magnesium Binding Sites List in 6reu
Magnesium binding site 1 out
of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
T:Mg1002
b:35.2
occ:1.00
|
O3G
|
T:ATP1001
|
2.1
|
36.8
|
1.0
|
O1G
|
T:ATP1001
|
2.1
|
36.8
|
1.0
|
O2B
|
T:ATP1001
|
2.1
|
36.8
|
1.0
|
PG
|
T:ATP1001
|
2.5
|
36.8
|
1.0
|
OG1
|
T:THR232
|
2.8
|
32.8
|
1.0
|
PB
|
T:ATP1001
|
3.1
|
36.8
|
1.0
|
O3B
|
T:ATP1001
|
3.2
|
36.8
|
1.0
|
NZ
|
T:LYS231
|
3.4
|
32.1
|
1.0
|
O2G
|
T:ATP1001
|
3.9
|
36.8
|
1.0
|
O1B
|
T:ATP1001
|
4.0
|
36.8
|
1.0
|
CE
|
T:LYS231
|
4.0
|
32.1
|
1.0
|
OD1
|
T:ASP325
|
4.2
|
34.3
|
1.0
|
O2A
|
T:ATP1001
|
4.2
|
36.8
|
1.0
|
CB
|
T:THR232
|
4.2
|
32.8
|
1.0
|
N
|
T:THR232
|
4.4
|
32.8
|
1.0
|
O3A
|
T:ATP1001
|
4.5
|
36.8
|
1.0
|
OD2
|
T:ASP325
|
4.9
|
34.3
|
1.0
|
PA
|
T:ATP1001
|
4.9
|
36.8
|
1.0
|
CA
|
T:THR232
|
4.9
|
32.8
|
1.0
|
CG
|
T:ASP325
|
5.0
|
34.3
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 6reu
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Magnesium Binding Sites List in 6reu
Magnesium binding site 2 out
of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
U:Mg1002
b:37.9
occ:1.00
|
O3G
|
U:ATP1001
|
2.0
|
40.5
|
1.0
|
OG1
|
U:THR232
|
2.1
|
33.4
|
1.0
|
O2A
|
U:ATP1001
|
2.6
|
40.5
|
1.0
|
O1B
|
U:ATP1001
|
2.7
|
40.5
|
1.0
|
O3B
|
U:ATP1001
|
2.8
|
40.5
|
1.0
|
PG
|
U:ATP1001
|
2.9
|
40.5
|
1.0
|
CB
|
U:THR232
|
3.1
|
33.4
|
1.0
|
PB
|
U:ATP1001
|
3.3
|
40.5
|
1.0
|
O2G
|
U:ATP1001
|
3.5
|
40.5
|
1.0
|
PA
|
U:ATP1001
|
3.8
|
40.5
|
1.0
|
CG2
|
U:THR232
|
3.9
|
33.4
|
1.0
|
O3A
|
U:ATP1001
|
4.0
|
40.5
|
1.0
|
O1G
|
U:ATP1001
|
4.2
|
40.5
|
1.0
|
N
|
U:THR232
|
4.2
|
33.4
|
1.0
|
CA
|
U:THR232
|
4.3
|
33.4
|
1.0
|
O1A
|
U:ATP1001
|
4.5
|
40.5
|
1.0
|
O2B
|
U:ATP1001
|
4.6
|
40.5
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 6reu
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Magnesium Binding Sites List in 6reu
Magnesium binding site 3 out
of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Mg1002
b:31.4
occ:1.00
|
O3G
|
V:ATP1001
|
2.1
|
37.9
|
1.0
|
OG1
|
V:THR232
|
2.1
|
31.3
|
1.0
|
O1B
|
V:ATP1001
|
2.1
|
37.9
|
1.0
|
O1G
|
V:ATP1001
|
2.1
|
37.9
|
1.0
|
PG
|
V:ATP1001
|
2.4
|
37.9
|
1.0
|
PB
|
V:ATP1001
|
3.1
|
37.9
|
1.0
|
O3B
|
V:ATP1001
|
3.2
|
37.9
|
1.0
|
CB
|
V:THR232
|
3.3
|
31.3
|
1.0
|
O1A
|
V:ATP1001
|
3.7
|
37.9
|
1.0
|
O2G
|
V:ATP1001
|
3.8
|
37.9
|
1.0
|
CG2
|
V:THR232
|
4.1
|
31.3
|
1.0
|
O2B
|
V:ATP1001
|
4.1
|
37.9
|
1.0
|
OD1
|
V:ASP325
|
4.2
|
28.7
|
1.0
|
N
|
V:THR232
|
4.2
|
31.3
|
1.0
|
O3A
|
V:ATP1001
|
4.3
|
37.9
|
1.0
|
CA
|
V:THR232
|
4.4
|
31.3
|
1.0
|
PA
|
V:ATP1001
|
4.4
|
37.9
|
1.0
|
OD2
|
V:ASP326
|
4.4
|
30.1
|
1.0
|
OE1
|
V:GLN264
|
4.6
|
27.3
|
1.0
|
NZ
|
V:LYS231
|
4.6
|
30.8
|
1.0
|
O2A
|
V:ATP1001
|
4.7
|
37.9
|
1.0
|
OD2
|
V:ASP325
|
4.7
|
28.7
|
1.0
|
CE
|
V:LYS231
|
4.8
|
30.8
|
1.0
|
CG
|
V:ASP325
|
4.9
|
28.7
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 6reu
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Magnesium Binding Sites List in 6reu
Magnesium binding site 4 out
of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
X:Mg602
b:37.0
occ:1.00
|
OG1
|
X:THR190
|
1.7
|
38.8
|
1.0
|
O3B
|
X:ADP601
|
2.0
|
43.8
|
1.0
|
CB
|
X:THR190
|
2.5
|
38.8
|
1.0
|
PB
|
X:ADP601
|
2.9
|
43.8
|
1.0
|
O2B
|
X:ADP601
|
2.9
|
43.8
|
1.0
|
N
|
X:THR190
|
3.0
|
38.8
|
1.0
|
O2A
|
X:ADP601
|
3.2
|
43.8
|
1.0
|
CA
|
X:THR190
|
3.3
|
38.8
|
1.0
|
O1A
|
X:ADP601
|
3.4
|
43.8
|
1.0
|
PA
|
X:ADP601
|
3.5
|
43.8
|
1.0
|
O3A
|
X:ADP601
|
3.6
|
43.8
|
1.0
|
CG2
|
X:THR190
|
3.7
|
38.8
|
1.0
|
OE2
|
X:GLU219
|
3.8
|
35.0
|
1.0
|
OE1
|
X:GLU219
|
3.9
|
35.0
|
1.0
|
NH1
|
X:ARG216
|
4.0
|
31.4
|
1.0
|
C
|
X:LYS189
|
4.1
|
36.5
|
1.0
|
O1B
|
X:ADP601
|
4.2
|
43.8
|
1.0
|
CD
|
X:GLU219
|
4.2
|
35.0
|
1.0
|
CB
|
X:LYS189
|
4.3
|
36.5
|
1.0
|
CE
|
X:LYS189
|
4.5
|
36.5
|
1.0
|
N
|
X:LYS189
|
4.5
|
36.5
|
1.0
|
CA
|
X:LYS189
|
4.5
|
36.5
|
1.0
|
C
|
X:THR190
|
4.5
|
38.8
|
1.0
|
NZ
|
X:LYS189
|
4.6
|
36.5
|
1.0
|
N
|
X:VAL191
|
4.9
|
40.5
|
1.0
|
CZ
|
X:ARG216
|
4.9
|
31.4
|
1.0
|
NH2
|
X:ARG216
|
5.0
|
31.4
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 6reu
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Magnesium Binding Sites List in 6reu
Magnesium binding site 5 out
of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
Z:Mg602
b:29.1
occ:1.00
|
O3B
|
Z:ADP601
|
2.1
|
36.6
|
1.0
|
O2B
|
Z:ADP601
|
2.1
|
36.6
|
1.0
|
PB
|
Z:ADP601
|
2.5
|
36.6
|
1.0
|
O3A
|
Z:ADP601
|
3.3
|
36.6
|
1.0
|
OG1
|
Z:THR190
|
3.3
|
33.6
|
1.0
|
CG
|
Z:LYS189
|
3.8
|
30.7
|
1.0
|
O1B
|
Z:ADP601
|
3.9
|
36.6
|
1.0
|
NH2
|
Z:ARG216
|
4.2
|
28.6
|
1.0
|
CD
|
Z:LYS189
|
4.2
|
30.7
|
1.0
|
PA
|
Z:ADP601
|
4.4
|
36.6
|
1.0
|
NH1
|
Z:ARG216
|
4.4
|
28.6
|
1.0
|
ND2
|
Z:ASN286
|
4.5
|
30.8
|
1.0
|
OE2
|
Z:GLU215
|
4.6
|
31.9
|
1.0
|
O2A
|
Z:ADP601
|
4.7
|
36.6
|
1.0
|
OE1
|
Z:GLU215
|
4.7
|
31.9
|
1.0
|
O1A
|
Z:ADP601
|
4.7
|
36.6
|
1.0
|
CB
|
Z:THR190
|
4.8
|
33.6
|
1.0
|
CZ
|
Z:ARG216
|
4.8
|
28.6
|
1.0
|
CE
|
Z:LYS189
|
4.8
|
30.7
|
1.0
|
N
|
Z:THR190
|
4.8
|
33.6
|
1.0
|
CB
|
V:SER400
|
4.9
|
25.4
|
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 16:58:06 2024
|