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Magnesium in PDB 4asu: F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site

Enzymatic activity of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site

All present enzymatic activity of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site:
3.6.3.14;

Protein crystallography data

The structure of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site, PDB code: 4asu was solved by D.M.Rees, 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) 63.50 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.268, 135.113, 266.355, 90.00, 90.00, 90.00
R / Rfree (%) 24.487 / 28.933

Magnesium Binding Sites:

The binding sites of Magnesium atom in the F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site (pdb code 4asu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site, PDB code: 4asu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 4asu

Go back to Magnesium Binding Sites List in 4asu
Magnesium binding site 1 out of 5 in the F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:35.2
occ:1.00
 OG1 A:THR176 2.0 35.8 1.0
O2B A:ADP600 2.1 33.2 1.0
O A:HOH2023 2.2 34.7 1.0
O A:HOH2022 2.2 36.3 1.0
O A:HOH2021 2.2 36.1 1.0
O A:HOH2020 2.2 33.2 1.0
PB A:ADP600 3.2 34.3 1.0
O1B A:ADP600 3.3 35.1 1.0
CB A:THR176 3.4 36.8 1.0
N A:THR176 3.8 38.0 1.0
OD1 A:ASP269 4.1 33.0 1.0
CA A:THR176 4.1 38.1 1.0
O3B A:ADP600 4.2 33.7 1.0
O1A A:ADP600 4.2 37.3 1.0
OD2 A:ASP269 4.3 32.8 1.0
CG2 A:THR176 4.3 36.6 1.0
O3A A:ADP600 4.4 36.1 1.0
CG A:ASP269 4.6 32.5 1.0
PA A:ADP600 4.6 36.8 1.0
O A:HOH2030 4.7 47.3 1.0
CB A:LYS175 4.7 37.5 1.0
O2A A:ADP600 4.7 36.4 1.0
C A:LYS175 4.8 38.6 1.0
CE A:LYS175 4.9 37.3 1.0
NZ A:LYS175 4.9 37.8 1.0

Magnesium binding site 2 out of 5 in 4asu

Go back to Magnesium Binding Sites List in 4asu
Magnesium binding site 2 out of 5 in the F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:45.1
occ:1.00
 OG1 B:THR176 2.0 30.7 1.0
O B:HOH2032 2.2 43.6 1.0
O B:HOH2029 2.2 45.5 1.0
O B:HOH2030 2.2 46.9 1.0
O B:HOH2028 2.2 43.8 1.0
O2B B:ADP600 2.3 38.1 1.0
CB B:THR176 3.2 31.9 1.0
PB B:ADP600 3.3 40.2 1.0
O1B B:ADP600 3.4 40.3 1.0
N B:THR176 3.8 32.7 1.0
OD1 B:ASP269 3.8 37.0 1.0
OD2 B:ASP269 4.0 37.2 1.0
CA B:THR176 4.0 32.2 1.0
O1A B:ADP600 4.2 40.1 1.0
CG2 B:THR176 4.3 31.7 1.0
O3B B:ADP600 4.3 40.4 1.0
CG B:ASP269 4.4 36.4 1.0
O3A B:ADP600 4.5 39.5 1.0
CB B:LYS175 4.7 32.8 1.0
PA B:ADP600 4.7 38.9 1.0
O2A B:ADP600 4.9 37.1 1.0
C B:LYS175 4.9 33.7 1.0

Magnesium binding site 3 out of 5 in 4asu

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Magnesium binding site 3 out of 5 in the F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:34.9
occ:1.00
 OG1 C:THR176 2.0 30.4 1.0
O C:HOH2021 2.2 33.6 1.0
O C:HOH2019 2.2 32.8 1.0
O C:HOH2020 2.2 32.7 1.0
O C:HOH2018 2.2 34.2 1.0
O2B C:ADP600 2.3 28.4 1.0
CB C:THR176 3.2 30.7 1.0
PB C:ADP600 3.3 29.3 1.0
O1B C:ADP600 3.3 29.4 1.0
N C:THR176 3.9 30.2 1.0
OD2 C:ASP269 4.1 28.7 1.0
CA C:THR176 4.1 30.5 1.0
OD1 C:ASP269 4.2 30.2 1.0
O1A C:ADP600 4.2 30.6 1.0
CG2 C:THR176 4.3 30.3 1.0
O3B C:ADP600 4.4 28.3 1.0
O3A C:ADP600 4.4 29.4 1.0
CG C:ASP269 4.6 29.5 1.0
PA C:ADP600 4.6 29.6 1.0
O2A C:ADP600 4.7 28.0 1.0
CB C:LYS175 4.9 29.4 1.0

Magnesium binding site 4 out of 5 in 4asu

Go back to Magnesium Binding Sites List in 4asu
Magnesium binding site 4 out of 5 in the F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:48.6
occ:1.00
 OG1 D:THR163 1.9 39.4 1.0
O D:HOH2012 2.2 47.6 1.0
O D:HOH2016 2.2 47.0 1.0
O D:HOH2013 2.2 49.4 1.0
O D:HOH2014 2.2 48.8 1.0
O2B D:ADP600 2.4 32.6 1.0
CB D:THR163 3.2 39.0 1.0
PB D:ADP600 3.5 33.6 1.0
O1B D:ADP600 3.7 33.0 1.0
N D:THR163 3.9 37.2 1.0
OD2 D:ASP256 3.9 29.8 1.0
NH1 D:ARG189 4.0 38.4 1.0
OE1 D:GLU188 4.0 34.0 1.0
O1A D:ADP600 4.1 37.2 1.0
CA D:THR163 4.1 38.1 1.0
CG2 D:THR163 4.2 38.5 1.0
OD1 D:ASP256 4.2 29.2 1.0
OE2 D:GLU192 4.3 35.1 1.0
OE1 D:GLU192 4.3 36.5 1.0
CG D:ASP256 4.5 29.9 1.0
O3A D:ADP600 4.6 35.3 1.0
O2A D:ADP600 4.6 36.8 1.0
PA D:ADP600 4.6 37.1 1.0
O3B D:ADP600 4.6 33.6 1.0
CD D:GLU188 4.7 34.6 1.0
CD D:GLU192 4.7 36.2 1.0
CB D:LYS162 4.7 32.2 1.0
O C:HOH2038 4.8 14.9 1.0
CE D:LYS162 4.8 29.3 1.0
O D:HOH2011 4.9 23.4 1.0
C D:LYS162 4.9 36.0 1.0

Magnesium binding site 5 out of 5 in 4asu

Go back to Magnesium Binding Sites List in 4asu
Magnesium binding site 5 out of 5 in the F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of F1-Atpase in Which All Three Catalytic Sites Contain Bound Nucleotide, with Magnesium Ion Released in the Empty Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:32.5
occ:1.00
 OG1 F:THR163 2.0 33.8 1.0
O2B F:ADP600 2.1 36.0 1.0
O F:HOH2025 2.2 32.3 1.0
O F:HOH2027 2.2 33.2 1.0
O B:HOH2031 2.2 35.6 1.0
O F:HOH2026 2.2 31.2 1.0
CB F:THR163 3.1 35.7 1.0
PB F:ADP600 3.3 35.7 1.0
O1B F:ADP600 3.5 34.7 1.0
OE1 F:GLU188 3.6 32.6 1.0
NH1 F:ARG189 3.7 33.0 1.0
N F:THR163 4.0 36.4 1.0
CA F:THR163 4.1 36.5 1.0
CG2 F:THR163 4.1 35.9 1.0
OE2 F:GLU192 4.1 38.4 1.0
O1A F:ADP600 4.1 35.8 1.0
OD2 F:ASP256 4.1 31.8 1.0
O F:HOH2029 4.2 36.1 1.0
O3B F:ADP600 4.3 36.4 1.0
O3A F:ADP600 4.4 36.2 1.0
OD1 F:ASP256 4.4 30.4 1.0
CD F:GLU188 4.5 33.0 1.0
PA F:ADP600 4.5 36.2 1.0
O B:HOH2056 4.5 29.7 1.0
OE1 F:GLU192 4.6 39.2 1.0
O F:HOH2024 4.6 21.9 1.0
O2A F:ADP600 4.6 36.6 1.0
CG F:ASP256 4.7 31.1 1.0
CD F:GLU192 4.8 39.1 1.0
CZ F:ARG189 5.0 33.1 1.0

Reference:

D.M.Rees, M.G.Montgomery, A.G.Leslie, J.E.Walker. Structural Evidence of A New Catalytic Intermediate in the Pathway of Atp Hydrolysis By F1-Atpase From Bovine Heart Mitochondria. Proc.Natl.Acad.Sci.Usa V. 109 11139 2012.
ISSN: ISSN 0027-8424
PubMed: 22733764
DOI: 10.1073/PNAS.1207587109
Page generated: Mon Dec 14 09:09:04 2020

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