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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:

Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

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

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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

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