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Magnesium in PDB 1w0j: Beryllium Fluoride Inhibited Bovine F1-Atpase

Enzymatic activity of Beryllium Fluoride Inhibited Bovine F1-Atpase

All present enzymatic activity of Beryllium Fluoride Inhibited Bovine F1-Atpase:
3.6.3.14;

Protein crystallography data

The structure of Beryllium Fluoride Inhibited Bovine F1-Atpase, PDB code: 1w0j was solved by R.Kagawa, M.G.Montgomery, K.Braig, J.E.Walker, A.G.W.Leslie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.2
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 283.520, 107.374, 137.936, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.6

Other elements in 1w0j:

The structure of Beryllium Fluoride Inhibited Bovine F1-Atpase also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Beryllium Fluoride Inhibited Bovine F1-Atpase (pdb code 1w0j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Beryllium Fluoride Inhibited Bovine F1-Atpase, PDB code: 1w0j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1w0j

Go back to Magnesium Binding Sites List in 1w0j
Magnesium binding site 1 out of 5 in the Beryllium Fluoride Inhibited Bovine F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1512

b:28.3
occ:1.00
O2B A:ADP1511 1.9 20.9 1.0
O A:HOH2058 2.0 30.4 1.0
O A:HOH2083 2.1 27.0 1.0
O A:HOH2168 2.1 27.2 1.0
OG1 A:THR176 2.1 28.6 1.0
O A:HOH2169 2.1 24.1 1.0
CB A:THR176 3.1 33.4 1.0
PB A:ADP1511 3.2 29.4 1.0
O3B A:ADP1511 3.5 30.0 1.0
N A:THR176 3.9 30.2 1.0
O A:HOH2167 4.0 32.8 1.0
O1A A:ADP1511 4.1 21.6 1.0
OD2 A:ASP269 4.1 40.8 1.0
CG2 A:THR176 4.1 24.5 1.0
CA A:THR176 4.1 33.0 1.0
OD1 A:ASP269 4.1 42.9 1.0
O A:HOH2066 4.3 38.7 1.0
O1B A:ADP1511 4.3 21.1 1.0
O A:HOH2084 4.3 41.7 1.0
O3A A:ADP1511 4.3 29.0 1.0
O D:HOH2050 4.4 48.3 1.0
O A:HOH2166 4.5 32.0 1.0
PA A:ADP1511 4.5 29.1 1.0
O A:HOH2085 4.6 39.1 1.0
CG A:ASP269 4.6 41.3 1.0
O A:HOH2116 4.6 30.2 1.0
O2A A:ADP1511 4.7 32.0 1.0
O A:HOH2090 4.7 48.3 1.0

Magnesium binding site 2 out of 5 in 1w0j

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Magnesium binding site 2 out of 5 in the Beryllium Fluoride Inhibited Bovine F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1512

b:31.9
occ:1.00
O B:HOH2086 2.0 30.1 1.0
O B:HOH2160 2.1 33.6 1.0
O B:HOH2065 2.1 36.2 1.0
O2B B:ADP1511 2.1 32.0 1.0
OG1 B:THR176 2.1 32.8 1.0
O B:HOH2161 2.1 25.0 1.0
CB B:THR176 3.1 35.1 1.0
PB B:ADP1511 3.2 32.5 1.0
O3B B:ADP1511 3.3 29.3 1.0
N B:THR176 3.9 33.4 1.0
O B:HOH2164 3.9 33.5 1.0
O1A B:ADP1511 4.1 26.2 1.0
CA B:THR176 4.1 34.4 1.0
OD2 B:ASP269 4.1 40.5 1.0
OD1 B:ASP269 4.1 32.8 1.0
O B:HOH2163 4.2 28.4 1.0
CG2 B:THR176 4.2 37.9 1.0
O1B B:ADP1511 4.3 27.0 1.0
O3A B:ADP1511 4.4 35.0 1.0
O B:HOH2069 4.5 38.6 1.0
CG B:ASP269 4.6 41.3 1.0
PA B:ADP1511 4.6 33.3 1.0
O B:HOH2087 4.9 47.5 1.0
O2A B:ADP1511 4.9 31.3 1.0
O B:HOH2063 4.9 38.3 1.0
CB B:LYS175 5.0 36.1 1.0

Magnesium binding site 3 out of 5 in 1w0j

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Magnesium binding site 3 out of 5 in the Beryllium Fluoride Inhibited Bovine F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1512

b:24.6
occ:1.00
O C:HOH2064 2.0 21.6 1.0
O2B C:ADP1511 2.0 23.4 1.0
O C:HOH2191 2.0 20.2 1.0
OG1 C:THR176 2.1 23.4 1.0
O C:HOH2090 2.1 21.0 1.0
O C:HOH2063 2.1 30.2 1.0
CB C:THR176 3.2 24.9 1.0
PB C:ADP1511 3.2 25.3 1.0
O3B C:ADP1511 3.4 22.7 1.0
O C:HOH2193 3.9 26.0 1.0
N C:THR176 3.9 25.0 1.0
O C:HOH2091 4.1 34.1 1.0
CA C:THR176 4.1 23.4 1.0
OD2 C:ASP269 4.2 29.1 1.0
O C:HOH2089 4.2 33.9 1.0
OD1 C:ASP269 4.2 26.6 1.0
O C:HOH2192 4.2 24.6 1.0
O1A C:ADP1511 4.2 26.0 1.0
CG2 C:THR176 4.3 20.8 1.0
O1B C:ADP1511 4.3 25.0 1.0
O3A C:ADP1511 4.3 24.6 1.0
O C:HOH2072 4.5 39.3 1.0
O C:HOH2093 4.5 37.3 1.0
PA C:ADP1511 4.6 25.2 1.0
O C:HOH2027 4.7 46.7 1.0
CG C:ASP269 4.7 28.5 1.0
O2A C:ADP1511 4.8 22.4 1.0
O C:HOH2131 4.9 27.9 1.0

Magnesium binding site 4 out of 5 in 1w0j

Go back to Magnesium Binding Sites List in 1w0j
Magnesium binding site 4 out of 5 in the Beryllium Fluoride Inhibited Bovine F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1477

b:30.0
occ:1.00
OG1 D:THR163 2.0 29.8 1.0
O D:HOH2068 2.0 31.4 1.0
F3 D:BEF1478 2.1 23.6 1.0
O D:HOH2063 2.1 37.5 1.0
O2B D:ADP1476 2.1 19.0 1.0
O D:HOH2090 2.2 24.1 1.0
CB D:THR163 3.2 28.3 1.0
BE D:BEF1478 3.4 17.3 1.0
PB D:ADP1476 3.4 19.5 1.0
O1B D:ADP1476 3.7 23.2 1.0
NH1 D:ARG189 3.8 19.2 1.0
OD2 D:ASP256 3.9 32.3 1.0
OE1 D:GLU188 4.0 36.5 1.0
OE2 D:GLU192 4.0 28.7 1.0
CG2 D:THR163 4.0 30.4 1.0
OD1 D:ASP256 4.1 36.6 1.0
O D:HOH2065 4.1 28.7 1.0
N D:THR163 4.1 23.4 1.0
F2 D:BEF1478 4.2 20.4 1.0
CA D:THR163 4.2 25.8 1.0
O D:HOH2064 4.2 36.3 1.0
OE1 D:GLU192 4.3 29.6 1.0
O2A D:ADP1476 4.3 18.3 1.0
O3A D:ADP1476 4.4 24.3 1.0
CD D:GLU188 4.5 34.6 1.0
CG D:ASP256 4.5 32.4 1.0
F1 D:BEF1478 4.5 25.9 1.0
NH1 C:ARG373 4.5 22.6 1.0
CD D:GLU192 4.6 32.6 1.0
O3B D:ADP1476 4.6 20.5 1.0
PA D:ADP1476 4.7 24.2 1.0
CG D:GLU188 4.8 27.0 1.0
O1A D:ADP1476 4.9 27.5 1.0
CE D:LYS162 4.9 21.8 1.0

Magnesium binding site 5 out of 5 in 1w0j

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Magnesium binding site 5 out of 5 in the Beryllium Fluoride Inhibited Bovine F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Beryllium Fluoride Inhibited Bovine F1-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1476

b:25.1
occ:1.00
F3 F:BEF1477 1.9 27.6 1.0
OG1 F:THR163 2.0 28.1 1.0
O2B F:ADP1475 2.1 24.9 1.0
O F:HOH2104 2.1 20.0 1.0
O F:HOH2189 2.1 19.4 1.0
O F:HOH2073 2.1 21.1 1.0
CB F:THR163 3.2 27.3 1.0
BE F:BEF1477 3.2 31.6 1.0
PB F:ADP1475 3.3 25.8 1.0
O1B F:ADP1475 3.5 26.8 1.0
NH1 F:ARG189 3.9 25.3 1.0
N F:THR163 3.9 28.4 1.0
O F:HOH2074 4.0 22.9 1.0
OD2 F:ASP256 4.0 35.9 1.0
OE1 F:GLU188 4.1 46.7 1.0
CA F:THR163 4.1 25.6 1.0
F2 F:BEF1477 4.1 23.4 1.0
O2A F:ADP1475 4.1 26.8 1.0
CG2 F:THR163 4.2 17.6 1.0
OE2 F:GLU192 4.2 34.4 1.0
OD1 F:ASP256 4.3 30.6 1.0
O3B F:ADP1475 4.3 27.7 1.0
O3A F:ADP1475 4.3 23.4 1.0
F1 F:BEF1477 4.4 28.8 1.0
OE1 F:GLU192 4.4 30.0 1.0
CE F:LYS162 4.6 21.8 1.0
CG F:ASP256 4.6 32.5 1.0
PA F:ADP1475 4.7 27.8 1.0
O F:HOH2075 4.7 34.6 1.0
CD F:GLU188 4.7 44.7 1.0
NH1 B:ARG373 4.7 29.8 1.0
NZ F:LYS162 4.7 28.7 1.0
CD F:GLU192 4.8 28.3 1.0
CB F:LYS162 4.8 25.8 1.0
C F:LYS162 5.0 27.5 1.0

Reference:

R.Kagawa, M.G.Montgomery, K.Braig, A.G.W.Leslie, J.E.Walker. The Structure of Bovine F1-Atpase Inhibited By Adp and Beryllium Fluoride Embo J. V. 23 2734 2004.
ISSN: ISSN 0261-4189
PubMed: 15229653
DOI: 10.1038/SJ.EMBOJ.7600293
Page generated: Mon Dec 14 07:00:35 2020

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