Magnesium in PDB 7y5c: Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
Enzymatic activity of Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
All present enzymatic activity of Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2):
7.1.2.2;
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
(pdb code 7y5c). 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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2), PDB code: 7y5c:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 7y5c
Go back to
Magnesium Binding Sites List in 7y5c
Magnesium binding site 1 out
of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg600
b:86.0
occ:1.00
|
O1G
|
A:ATP601
|
2.0
|
112.8
|
1.0
|
O3A
|
A:ATP601
|
2.1
|
112.8
|
1.0
|
O3B
|
A:ATP601
|
2.2
|
112.8
|
1.0
|
O1A
|
A:ATP601
|
2.2
|
112.8
|
1.0
|
PB
|
A:ATP601
|
2.2
|
112.8
|
1.0
|
PG
|
A:ATP601
|
2.3
|
112.8
|
1.0
|
PA
|
A:ATP601
|
2.3
|
112.8
|
1.0
|
O1B
|
A:ATP601
|
2.3
|
112.8
|
1.0
|
O3G
|
A:ATP601
|
2.7
|
112.8
|
1.0
|
O2A
|
A:ATP601
|
2.8
|
112.8
|
1.0
|
OG1
|
A:THR179
|
3.5
|
60.0
|
1.0
|
O2B
|
A:ATP601
|
3.7
|
112.8
|
1.0
|
O2G
|
A:ATP601
|
3.8
|
112.8
|
1.0
|
O5'
|
A:ATP601
|
3.8
|
112.8
|
1.0
|
CB
|
A:THR179
|
4.0
|
60.0
|
1.0
|
N
|
A:THR179
|
4.5
|
60.0
|
1.0
|
C5'
|
A:ATP601
|
4.8
|
112.8
|
1.0
|
CA
|
A:GLY177
|
4.9
|
83.0
|
1.0
|
N
|
A:LYS178
|
4.9
|
75.1
|
1.0
|
CA
|
A:THR179
|
4.9
|
60.0
|
1.0
|
N
|
A:GLY177
|
5.0
|
83.0
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 7y5c
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Magnesium Binding Sites List in 7y5c
Magnesium binding site 2 out
of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg600
b:125.0
occ:1.00
|
O1A
|
B:ATP601
|
2.0
|
114.4
|
1.0
|
O3A
|
B:ATP601
|
2.1
|
114.4
|
1.0
|
O3G
|
B:ATP601
|
2.1
|
114.4
|
1.0
|
PG
|
B:ATP601
|
2.3
|
114.4
|
1.0
|
O3B
|
B:ATP601
|
2.3
|
114.4
|
1.0
|
PA
|
B:ATP601
|
2.3
|
114.4
|
1.0
|
PB
|
B:ATP601
|
2.3
|
114.4
|
1.0
|
O1G
|
B:ATP601
|
2.4
|
114.4
|
1.0
|
O1B
|
B:ATP601
|
2.5
|
114.4
|
1.0
|
O2A
|
B:ATP601
|
2.9
|
114.4
|
1.0
|
OG1
|
B:THR179
|
3.3
|
103.6
|
1.0
|
CB
|
B:THR179
|
3.7
|
103.6
|
1.0
|
O5'
|
B:ATP601
|
3.8
|
114.4
|
1.0
|
O2G
|
B:ATP601
|
3.8
|
114.4
|
1.0
|
O2B
|
B:ATP601
|
3.8
|
114.4
|
1.0
|
N
|
B:THR179
|
4.6
|
103.6
|
1.0
|
CG2
|
B:THR179
|
4.7
|
103.6
|
1.0
|
C5'
|
B:ATP601
|
4.8
|
114.4
|
1.0
|
CA
|
B:THR179
|
4.8
|
103.6
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 7y5c
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Magnesium Binding Sites List in 7y5c
Magnesium binding site 3 out
of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg600
b:98.8
occ:1.00
|
O1A
|
C:ATP601
|
2.1
|
115.1
|
1.0
|
O1B
|
C:ATP601
|
2.1
|
115.1
|
1.0
|
O3A
|
C:ATP601
|
2.2
|
115.1
|
1.0
|
O3G
|
C:ATP601
|
2.3
|
115.1
|
1.0
|
PB
|
C:ATP601
|
2.3
|
115.1
|
1.0
|
O3B
|
C:ATP601
|
2.5
|
115.1
|
1.0
|
PA
|
C:ATP601
|
2.6
|
115.1
|
1.0
|
PG
|
C:ATP601
|
2.6
|
115.1
|
1.0
|
OG1
|
C:THR179
|
2.9
|
104.6
|
1.0
|
O1G
|
C:ATP601
|
2.9
|
115.1
|
1.0
|
O2A
|
C:ATP601
|
3.6
|
115.1
|
1.0
|
CG2
|
C:THR179
|
3.6
|
104.6
|
1.0
|
O2B
|
C:ATP601
|
3.8
|
115.1
|
1.0
|
O5'
|
C:ATP601
|
3.8
|
115.1
|
1.0
|
CB
|
C:THR179
|
3.8
|
104.6
|
1.0
|
O2G
|
C:ATP601
|
4.1
|
115.1
|
1.0
|
NZ
|
C:LYS175
|
4.2
|
119.2
|
1.0
|
N
|
C:THR179
|
4.6
|
104.6
|
1.0
|
CA
|
C:THR179
|
4.9
|
104.6
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 7y5c
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Magnesium Binding Sites List in 7y5c
Magnesium binding site 4 out
of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg500
b:82.4
occ:1.00
|
O2A
|
D:ATP501
|
1.9
|
86.3
|
1.0
|
O1B
|
D:ATP501
|
1.9
|
86.3
|
1.0
|
N
|
D:THR167
|
2.1
|
71.3
|
1.0
|
PA
|
D:ATP501
|
2.3
|
86.3
|
1.0
|
O3A
|
D:ATP501
|
2.3
|
86.3
|
1.0
|
PB
|
D:ATP501
|
2.4
|
86.3
|
1.0
|
CB
|
D:THR167
|
2.6
|
71.3
|
1.0
|
OG1
|
D:THR167
|
2.8
|
71.3
|
1.0
|
O1A
|
D:ATP501
|
2.8
|
86.3
|
1.0
|
CA
|
D:THR167
|
2.8
|
71.3
|
1.0
|
N
|
D:LYS166
|
2.9
|
75.8
|
1.0
|
C
|
D:LYS166
|
3.2
|
75.8
|
1.0
|
O2B
|
D:ATP501
|
3.2
|
86.3
|
1.0
|
C
|
D:GLY165
|
3.3
|
78.0
|
1.0
|
CA
|
D:LYS166
|
3.5
|
75.8
|
1.0
|
CG
|
D:LYS166
|
3.7
|
75.8
|
1.0
|
CA
|
D:GLY165
|
3.7
|
78.0
|
1.0
|
N
|
D:VAL168
|
3.8
|
77.4
|
1.0
|
O5'
|
D:ATP501
|
3.8
|
86.3
|
1.0
|
C
|
D:THR167
|
3.8
|
71.3
|
1.0
|
O3B
|
D:ATP501
|
3.9
|
86.3
|
1.0
|
CG2
|
D:THR167
|
4.0
|
71.3
|
1.0
|
N
|
D:GLY165
|
4.0
|
78.0
|
1.0
|
O
|
D:GLY165
|
4.1
|
78.0
|
1.0
|
CB
|
D:LYS166
|
4.2
|
75.8
|
1.0
|
O
|
D:LYS166
|
4.3
|
75.8
|
1.0
|
C5'
|
D:ATP501
|
4.5
|
86.3
|
1.0
|
NZ
|
D:LYS166
|
4.7
|
75.8
|
1.0
|
PG
|
D:ATP501
|
4.9
|
86.3
|
1.0
|
CD
|
D:LYS166
|
5.0
|
75.8
|
1.0
|
O3G
|
D:ATP501
|
5.0
|
86.3
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 7y5c
Go back to
Magnesium Binding Sites List in 7y5c
Magnesium binding site 5 out
of 5 in the Cryo-Em Structure of F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2)
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 F-Atp Synthase From Mycolicibacterium Smegmatis (Rotational State 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg500
b:53.9
occ:1.00
|
O3B
|
F:ATP501
|
2.0
|
64.3
|
1.0
|
O1B
|
F:ATP501
|
2.0
|
64.3
|
1.0
|
OG1
|
F:THR167
|
2.1
|
46.7
|
1.0
|
PB
|
F:ATP501
|
2.4
|
64.3
|
1.0
|
O2G
|
F:ATP501
|
2.7
|
64.3
|
1.0
|
PG
|
F:ATP501
|
2.9
|
64.3
|
1.0
|
CB
|
F:THR167
|
3.1
|
46.7
|
1.0
|
O3A
|
F:ATP501
|
3.4
|
64.3
|
1.0
|
N
|
F:THR167
|
3.5
|
46.7
|
1.0
|
O3G
|
F:ATP501
|
3.5
|
64.3
|
1.0
|
O2B
|
F:ATP501
|
3.7
|
64.3
|
1.0
|
O1A
|
F:ATP501
|
3.9
|
64.3
|
1.0
|
CA
|
F:THR167
|
3.9
|
46.7
|
1.0
|
PA
|
F:ATP501
|
4.0
|
64.3
|
1.0
|
O2A
|
F:ATP501
|
4.1
|
64.3
|
1.0
|
O1G
|
F:ATP501
|
4.1
|
64.3
|
1.0
|
CG2
|
F:THR167
|
4.2
|
46.7
|
1.0
|
N
|
F:LYS166
|
4.5
|
52.3
|
1.0
|
C
|
F:LYS166
|
4.6
|
52.3
|
1.0
|
CB
|
F:LYS166
|
4.8
|
52.3
|
1.0
|
CA
|
F:LYS166
|
4.9
|
52.3
|
1.0
|
|
Reference:
C.F.Wong,
W.G.Saw,
S.Basak,
M.Sano,
H.Ueno,
H.W.Kerk,
D.Litty,
P.Ragunathan,
T.Dick,
V.Muller,
H.Noji,
G.Gruber.
Structural Elements Involved in Atp Hydrolysis Inhibition and Atp Synthesis of Tuberculosis and Nontuberculous Mycobacterial F-Atp Synthase Decipher New Targets For Inhibitors. Antimicrob.Agents Chemother. V. 66 2022.
ISSN: ESSN 1098-6596
PubMed: 36445139
DOI: 10.1128/AAC.01056-22
Page generated: Thu Oct 3 13:29:44 2024
|