Magnesium in PDB 4yxw: Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
Enzymatic activity of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
All present enzymatic activity of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.:
3.6.3.14;
Protein crystallography data
The structure of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate., PDB code: 4yxw
was solved by
J.V.Bason,
M.G.Montgomery,
A.G.W.Leslie,
J.E.Walker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
76.50 /
3.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.353,
123.052,
261.276,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.6 /
27.3
|
Other elements in 4yxw:
The structure of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate. also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
(pdb code 4yxw). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate., PDB code: 4yxw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 4yxw
Go back to
Magnesium Binding Sites List in 4yxw
Magnesium binding site 1 out
of 5 in the Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:48.5
occ:1.00
|
O
|
A:HOH705
|
2.2
|
50.7
|
1.0
|
O
|
A:HOH703
|
2.2
|
49.0
|
1.0
|
O1B
|
A:ANP600
|
2.2
|
48.7
|
1.0
|
O1G
|
A:ANP600
|
2.2
|
48.6
|
1.0
|
O
|
A:HOH704
|
2.2
|
49.2
|
1.0
|
OG1
|
A:THR176
|
2.2
|
50.9
|
1.0
|
PB
|
A:ANP600
|
3.3
|
48.4
|
1.0
|
N3B
|
A:ANP600
|
3.3
|
48.8
|
1.0
|
CB
|
A:THR176
|
3.3
|
51.5
|
1.0
|
PG
|
A:ANP600
|
3.4
|
48.5
|
1.0
|
OD1
|
A:ASP269
|
4.0
|
46.9
|
1.0
|
N
|
A:THR176
|
4.1
|
51.5
|
1.0
|
OD2
|
A:ASP269
|
4.2
|
46.1
|
1.0
|
CA
|
A:THR176
|
4.3
|
52.4
|
1.0
|
O1A
|
A:ANP600
|
4.3
|
47.7
|
1.0
|
O2B
|
A:ANP600
|
4.3
|
48.9
|
1.0
|
O3G
|
A:ANP600
|
4.3
|
47.8
|
1.0
|
CG2
|
A:THR176
|
4.4
|
51.2
|
1.0
|
O2G
|
A:ANP600
|
4.4
|
49.0
|
1.0
|
O3A
|
A:ANP600
|
4.4
|
48.8
|
1.0
|
CG
|
A:ASP269
|
4.5
|
46.9
|
1.0
|
PA
|
A:ANP600
|
4.7
|
48.2
|
1.0
|
O2A
|
A:ANP600
|
4.8
|
48.1
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 4yxw
Go back to
Magnesium Binding Sites List in 4yxw
Magnesium binding site 2 out
of 5 in the Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:53.2
occ:1.00
|
O1B
|
B:ANP600
|
2.2
|
52.9
|
1.0
|
OG1
|
B:THR176
|
2.2
|
52.6
|
1.0
|
O
|
B:HOH705
|
2.2
|
53.5
|
1.0
|
O1G
|
B:ANP600
|
2.2
|
52.9
|
1.0
|
O
|
B:HOH706
|
2.2
|
53.3
|
1.0
|
O
|
B:HOH704
|
2.2
|
52.8
|
1.0
|
CB
|
B:THR176
|
3.3
|
53.4
|
1.0
|
PB
|
B:ANP600
|
3.3
|
52.4
|
1.0
|
PG
|
B:ANP600
|
3.4
|
51.7
|
1.0
|
N3B
|
B:ANP600
|
3.4
|
51.7
|
1.0
|
OD1
|
B:ASP269
|
3.9
|
53.3
|
1.0
|
OD2
|
B:ASP269
|
4.0
|
53.2
|
1.0
|
N
|
B:THR176
|
4.1
|
54.7
|
1.0
|
O1A
|
B:ANP600
|
4.2
|
53.4
|
1.0
|
CA
|
B:THR176
|
4.2
|
54.3
|
1.0
|
O2B
|
B:ANP600
|
4.2
|
52.9
|
1.0
|
CG2
|
B:THR176
|
4.3
|
53.1
|
1.0
|
O3G
|
B:ANP600
|
4.3
|
51.2
|
1.0
|
CG
|
B:ASP269
|
4.4
|
53.2
|
1.0
|
O2G
|
B:ANP600
|
4.4
|
51.7
|
1.0
|
O3A
|
B:ANP600
|
4.5
|
53.9
|
1.0
|
PA
|
B:ANP600
|
4.8
|
54.1
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 4yxw
Go back to
Magnesium Binding Sites List in 4yxw
Magnesium binding site 3 out
of 5 in the Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:50.0
occ:1.00
|
O1B
|
C:ANP600
|
2.2
|
49.1
|
1.0
|
O
|
C:HOH702
|
2.2
|
50.0
|
1.0
|
O1G
|
C:ANP600
|
2.2
|
49.5
|
1.0
|
OG1
|
C:THR176
|
2.2
|
51.5
|
1.0
|
O
|
C:HOH704
|
2.2
|
51.0
|
1.0
|
O
|
C:HOH703
|
2.2
|
53.0
|
1.0
|
PB
|
C:ANP600
|
3.3
|
48.5
|
1.0
|
CB
|
C:THR176
|
3.3
|
53.4
|
1.0
|
PG
|
C:ANP600
|
3.4
|
48.0
|
1.0
|
N3B
|
C:ANP600
|
3.4
|
48.3
|
1.0
|
OD1
|
C:ASP269
|
3.9
|
43.7
|
1.0
|
N
|
C:THR176
|
4.0
|
53.3
|
1.0
|
OD2
|
C:ASP269
|
4.0
|
45.1
|
1.0
|
O2B
|
C:ANP600
|
4.1
|
48.2
|
1.0
|
O2G
|
C:ANP600
|
4.1
|
48.8
|
1.0
|
CA
|
C:THR176
|
4.2
|
53.5
|
1.0
|
CG2
|
C:THR176
|
4.4
|
53.8
|
1.0
|
O1A
|
C:ANP600
|
4.4
|
50.9
|
1.0
|
CG
|
C:ASP269
|
4.4
|
44.4
|
1.0
|
O3A
|
C:ANP600
|
4.5
|
50.4
|
1.0
|
O3G
|
C:ANP600
|
4.5
|
47.6
|
1.0
|
NZ
|
C:LYS175
|
4.8
|
57.0
|
1.0
|
PA
|
C:ANP600
|
4.8
|
51.3
|
1.0
|
CB
|
C:LYS175
|
4.9
|
54.1
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 4yxw
Go back to
Magnesium Binding Sites List in 4yxw
Magnesium binding site 4 out
of 5 in the Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg502
b:55.7
occ:1.00
|
O1G
|
D:ANP501
|
2.2
|
55.9
|
1.0
|
O1B
|
D:ANP501
|
2.2
|
55.6
|
1.0
|
O
|
D:HOH605
|
2.2
|
55.5
|
1.0
|
OG1
|
D:THR163
|
2.2
|
55.1
|
1.0
|
O
|
D:HOH604
|
2.2
|
54.6
|
1.0
|
O
|
D:HOH607
|
2.2
|
54.6
|
1.0
|
CB
|
D:THR163
|
3.4
|
54.8
|
1.0
|
PB
|
D:ANP501
|
3.4
|
55.6
|
1.0
|
PG
|
D:ANP501
|
3.4
|
55.9
|
1.0
|
N3B
|
D:ANP501
|
3.6
|
55.1
|
1.0
|
OD1
|
D:ASP256
|
3.9
|
45.5
|
1.0
|
N
|
D:THR163
|
4.0
|
52.4
|
1.0
|
OD2
|
D:ASP256
|
4.1
|
44.9
|
1.0
|
NH1
|
D:ARG189
|
4.1
|
57.4
|
1.0
|
O1A
|
D:ANP501
|
4.2
|
50.5
|
1.0
|
OE1
|
D:GLU192
|
4.2
|
54.7
|
1.0
|
CA
|
D:THR163
|
4.2
|
54.1
|
1.0
|
OE1
|
D:GLU188
|
4.2
|
57.4
|
1.0
|
O2G
|
D:ANP501
|
4.3
|
55.4
|
1.0
|
CG2
|
D:THR163
|
4.4
|
55.4
|
1.0
|
O2B
|
D:ANP501
|
4.4
|
55.7
|
1.0
|
O3G
|
D:ANP501
|
4.5
|
54.8
|
1.0
|
CG
|
D:ASP256
|
4.5
|
46.1
|
1.0
|
O3A
|
D:ANP501
|
4.5
|
53.6
|
1.0
|
OE2
|
D:GLU192
|
4.5
|
55.9
|
1.0
|
PA
|
D:ANP501
|
4.6
|
51.4
|
1.0
|
CD
|
D:GLU188
|
4.6
|
56.5
|
1.0
|
O2A
|
D:ANP501
|
4.6
|
52.6
|
1.0
|
NH1
|
C:ARG373
|
4.7
|
57.2
|
1.0
|
CB
|
D:LYS162
|
4.8
|
49.8
|
1.0
|
CD
|
D:GLU192
|
4.8
|
55.7
|
1.0
|
CE
|
D:LYS162
|
5.0
|
48.2
|
1.0
|
CG
|
D:GLU188
|
5.0
|
54.9
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 4yxw
Go back to
Magnesium Binding Sites List in 4yxw
Magnesium binding site 5 out
of 5 in the Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Bovine Heart Mitochondrial F1-Atpase Inhibited By Amp-Pnp and Adp in the Presence of Thiophosphate. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg502
b:48.9
occ:1.00
|
O1B
|
F:ANP501
|
2.2
|
49.4
|
1.0
|
O
|
F:HOH608
|
2.2
|
48.5
|
1.0
|
O
|
F:HOH602
|
2.2
|
48.3
|
1.0
|
OG1
|
F:THR163
|
2.2
|
50.9
|
1.0
|
O1G
|
F:ANP501
|
2.2
|
48.8
|
1.0
|
O
|
F:HOH605
|
2.2
|
48.9
|
1.0
|
CB
|
F:THR163
|
3.3
|
51.9
|
1.0
|
PB
|
F:ANP501
|
3.3
|
50.4
|
1.0
|
PG
|
F:ANP501
|
3.4
|
48.4
|
1.0
|
N3B
|
F:ANP501
|
3.4
|
49.5
|
1.0
|
NH1
|
F:ARG189
|
3.8
|
46.9
|
1.0
|
O1A
|
F:ANP501
|
4.0
|
54.3
|
1.0
|
OD2
|
F:ASP256
|
4.0
|
45.8
|
1.0
|
N
|
F:THR163
|
4.1
|
51.7
|
1.0
|
O
|
F:HOH609
|
4.1
|
54.4
|
1.0
|
OE1
|
F:GLU188
|
4.1
|
46.4
|
1.0
|
OE2
|
F:GLU192
|
4.2
|
48.3
|
1.0
|
CA
|
F:THR163
|
4.2
|
51.7
|
1.0
|
CG2
|
F:THR163
|
4.3
|
51.6
|
1.0
|
O3G
|
F:ANP501
|
4.3
|
47.9
|
1.0
|
O2B
|
F:ANP501
|
4.3
|
49.5
|
1.0
|
O2G
|
F:ANP501
|
4.4
|
48.8
|
1.0
|
O3A
|
F:ANP501
|
4.5
|
51.5
|
1.0
|
OD1
|
F:ASP256
|
4.5
|
44.9
|
1.0
|
OE1
|
F:GLU192
|
4.5
|
47.0
|
1.0
|
NH1
|
B:ARG373
|
4.6
|
58.3
|
1.0
|
PA
|
F:ANP501
|
4.6
|
52.9
|
1.0
|
CD
|
F:GLU188
|
4.7
|
47.1
|
1.0
|
CG
|
F:ASP256
|
4.7
|
45.7
|
1.0
|
CD
|
F:GLU192
|
4.8
|
48.1
|
1.0
|
CB
|
F:LYS162
|
4.9
|
51.2
|
1.0
|
O2A
|
F:ANP501
|
4.9
|
52.2
|
1.0
|
CE
|
F:LYS162
|
5.0
|
51.1
|
1.0
|
|
Reference:
J.V.Bason,
M.G.Montgomery,
A.G.Leslie,
J.E.Walker.
How Release of Phosphate From Mammalian F1-Atpase Generates A Rotary Substep. Proc.Natl.Acad.Sci.Usa V. 112 6009 2015.
ISSN: ESSN 1091-6490
PubMed: 25918412
DOI: 10.1073/PNAS.1506465112
Page generated: Sat Sep 28 23:33:20 2024
|