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Magnesium in PDB 1h8e: (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)

Enzymatic activity of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)

All present enzymatic activity of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied):
3.6.1.34;

Protein crystallography data

The structure of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied), PDB code: 1h8e was solved by R.I.Menz, 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) 13.5 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 267.700, 106.200, 138.300, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 26.4

Other elements in 1h8e:

The structure of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Aluminium (Al) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) (pdb code 1h8e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied), PDB code: 1h8e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1h8e

Go back to Magnesium Binding Sites List in 1h8e
Magnesium binding site 1 out of 6 in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:33.1
occ:1.00
 O A:HOH2305 2.0 25.5 1.0
O A:HOH2304 2.0 32.0 1.0
O2B A:ADP600 2.1 26.4 1.0
OG1 A:THR176 2.1 35.1 1.0
O A:HOH2102 2.1 26.0 1.0
O A:HOH2148 2.2 28.4 1.0
CB A:THR176 3.2 29.7 1.0
PB A:ADP600 3.3 26.7 1.0
O3B A:ADP600 3.4 27.3 1.0
N A:THR176 3.9 25.9 1.0
CA A:THR176 4.1 29.2 1.0
O A:HOH2147 4.1 35.7 1.0
O2A A:ADP600 4.1 25.0 1.0
O A:HOH2149 4.1 31.0 1.0
OD1 A:ASP269 4.2 29.9 1.0
OD2 A:ASP269 4.2 24.7 1.0
O3A A:ADP600 4.3 28.3 1.0
CG2 A:THR176 4.3 26.0 1.0
O1B A:ADP600 4.3 28.0 1.0
O D:HOH2097 4.4 58.7 1.0
PA A:ADP600 4.5 27.7 1.0
O1A A:ADP600 4.6 28.9 1.0
CG A:ASP269 4.6 31.2 1.0
O A:HOH2191 4.6 29.6 1.0
CB A:LYS175 4.9 27.4 1.0
O A:HOH2042 5.0 45.4 1.0

Magnesium binding site 2 out of 6 in 1h8e

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Magnesium binding site 2 out of 6 in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:35.2
occ:1.00
 O B:HOH2238 2.0 35.2 1.0
OG1 B:THR176 2.0 35.9 1.0
O B:HOH2134 2.0 33.9 1.0
O B:HOH2239 2.1 36.9 1.0
O2B B:ADP600 2.1 34.0 1.0
O B:HOH2098 2.2 40.6 1.0
CB B:THR176 3.2 30.8 1.0
PB B:ADP600 3.4 33.0 1.0
O3B B:ADP600 3.6 30.6 1.0
N B:THR176 3.9 28.8 1.0
OD1 B:ASP269 4.0 31.4 1.0
OD2 B:ASP269 4.1 28.0 1.0
O2A B:ADP600 4.1 32.3 1.0
CA B:THR176 4.1 32.5 1.0
CG2 B:THR176 4.2 33.8 1.0
O B:HOH2136 4.3 38.3 1.0
O B:HOH2236 4.3 51.1 1.0
O1B B:ADP600 4.4 31.9 1.0
O3A B:ADP600 4.4 32.5 1.0
O B:HOH2110 4.4 44.5 1.0
O B:HOH2135 4.4 52.4 1.0
CG B:ASP269 4.5 34.9 1.0
PA B:ADP600 4.6 35.2 1.0
O1A B:ADP600 4.8 33.4 1.0
O B:HOH2185 5.0 32.3 1.0

Magnesium binding site 3 out of 6 in 1h8e

Go back to Magnesium Binding Sites List in 1h8e
Magnesium binding site 3 out of 6 in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:30.6
occ:1.00
 O C:HOH2162 2.0 24.1 1.0
O2B C:ADP600 2.1 28.3 1.0
O C:HOH2317 2.1 24.7 1.0
OG1 C:THR176 2.1 29.3 1.0
O C:HOH2316 2.3 30.2 1.0
O C:HOH2123 2.4 27.5 1.0
CB C:THR176 3.1 26.6 1.0
PB C:ADP600 3.3 27.3 1.0
O3B C:ADP600 3.5 26.0 1.0
N C:THR176 3.9 25.1 1.0
OD2 C:ASP269 4.1 26.5 1.0
CA C:THR176 4.1 27.5 1.0
OD1 C:ASP269 4.2 28.3 1.0
O C:HOH2164 4.2 37.7 1.0
CG2 C:THR176 4.2 23.6 1.0
O2A C:ADP600 4.2 27.2 1.0
O C:HOH2137 4.3 35.3 1.0
O3A C:ADP600 4.3 25.6 1.0
O1B C:ADP600 4.3 25.4 1.0
O C:HOH2163 4.3 34.3 1.0
PA C:ADP600 4.6 28.1 1.0
CG C:ASP269 4.6 31.3 1.0
O1A C:ADP600 4.7 27.0 1.0
O C:HOH2208 4.8 27.5 1.0

Magnesium binding site 4 out of 6 in 1h8e

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Magnesium binding site 4 out of 6 in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:30.6
occ:1.00
 F2 D:ALF620 2.1 37.9 1.0
OG1 D:THR163 2.1 32.5 1.0
O2B D:ADP600 2.1 24.0 1.0
O D:HOH2122 2.2 28.1 1.0
O D:HOH2155 2.2 31.3 1.0
O D:HOH2125 2.2 25.9 1.0
CB D:THR163 3.1 25.7 1.0
PB D:ADP600 3.3 27.4 1.0
F4 D:ALF620 3.4 41.3 1.0
O3B D:ADP600 3.5 29.6 1.0
AL D:ALF620 3.5 37.9 1.0
N D:THR163 3.9 26.8 1.0
OE1 D:GLU188 3.9 29.6 1.0
NH1 D:ARG189 4.0 27.7 1.0
OD2 D:ASP256 4.1 30.8 1.0
CA D:THR163 4.1 27.0 1.0
O3A D:ADP600 4.2 28.6 1.0
O2A D:ADP600 4.2 26.1 1.0
CG2 D:THR163 4.2 21.2 1.0
OE2 D:GLU192 4.3 25.6 1.0
OD1 D:ASP256 4.3 26.5 1.0
F3 D:ALF620 4.4 39.2 1.0
O1B D:ADP600 4.4 27.1 1.0
O D:HOH2120 4.5 24.9 1.0
NH1 C:ARG373 4.5 23.9 1.0
O D:HOH2121 4.5 31.9 1.0
PA D:ADP600 4.5 27.0 1.0
OE1 D:GLU192 4.5 32.8 1.0
CD D:GLU188 4.5 30.4 1.0
O1A D:ADP600 4.6 27.1 1.0
CG D:ASP256 4.6 32.7 1.0
CD D:GLU192 4.8 30.9 1.0
CG D:GLU188 4.8 26.8 1.0
CB D:LYS162 4.9 27.4 1.0
C D:LYS162 5.0 25.6 1.0

Magnesium binding site 5 out of 6 in 1h8e

Go back to Magnesium Binding Sites List in 1h8e
Magnesium binding site 5 out of 6 in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:42.6
occ:1.00
 O E:HOH2177 1.9 40.1 1.0
O E:HOH2180 2.0 47.5 1.0
OG1 E:THR163 2.0 52.6 1.0
O2B E:ADP600 2.1 35.1 1.0
O E:HOH2085 2.2 40.4 1.0
O E:HOH2106 2.4 43.3 1.0
PB E:ADP600 3.3 35.2 1.0
CB E:THR163 3.4 47.0 1.0
O3B E:ADP600 3.4 36.5 1.0
O E:HOH2107 3.9 76.4 1.0
O2A E:ADP600 4.0 39.6 1.0
O3 E:SO4630 4.0 36.1 1.0
N E:THR163 4.0 41.4 1.0
O E:HOH2179 4.1 37.1 1.0
NH1 E:ARG189 4.1 28.4 1.0
OE1 E:GLU192 4.1 48.0 1.0
OD2 E:ASP256 4.2 46.9 1.0
CA E:THR163 4.2 43.4 1.0
O E:HOH2105 4.2 66.7 1.0
O3A E:ADP600 4.2 38.7 1.0
CG2 E:THR163 4.3 55.8 1.0
O1B E:ADP600 4.4 35.4 1.0
PA E:ADP600 4.5 40.0 1.0
NE A:ARG373 4.6 38.3 1.0
O1A E:ADP600 4.6 39.0 1.0
CE E:LYS162 4.7 33.5 1.0
OD1 E:ASP256 4.8 46.0 1.0
O1 E:SO4630 4.8 40.7 1.0
OE2 E:GLU192 4.8 37.8 1.0
CB E:LYS162 4.8 41.2 1.0
CD E:GLU192 4.8 41.4 1.0
CG E:ASP256 4.9 38.8 1.0
NZ E:LYS162 4.9 30.2 1.0
S E:SO4630 5.0 41.2 1.0

Magnesium binding site 6 out of 6 in 1h8e

Go back to Magnesium Binding Sites List in 1h8e
Magnesium binding site 6 out of 6 in the (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of (Adp.ALF4)2(Adp.SO4) Bovine F1-Atpase (All Three Catalytic Sites Occupied) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:28.5
occ:1.00
 F3 F:ALF620 1.9 34.5 1.0
O F:HOH2134 2.0 25.6 1.0
O2B F:ADP600 2.0 26.9 1.0
OG1 F:THR163 2.1 29.9 1.0
O F:HOH2129 2.2 21.4 1.0
O F:HOH2164 2.2 27.3 1.0
CB F:THR163 3.1 22.9 1.0
PB F:ADP600 3.2 25.1 1.0
O3B F:ADP600 3.4 25.3 1.0
AL F:ALF620 3.5 33.9 1.0
F1 F:ALF620 3.8 33.2 1.0
N F:THR163 3.9 26.0 1.0
OE1 F:GLU188 4.0 25.3 1.0
O3A F:ADP600 4.0 25.9 1.0
F2 F:ALF620 4.1 35.7 1.0
O2A F:ADP600 4.1 24.5 1.0
CA F:THR163 4.1 28.9 1.0
NH1 F:ARG189 4.2 21.8 1.0
CG2 F:THR163 4.2 24.1 1.0
OD2 F:ASP256 4.2 26.3 1.0
OE2 F:GLU192 4.2 35.2 1.0
O F:HOH2128 4.3 25.7 1.0
O1B F:ADP600 4.3 26.0 1.0
OD1 F:ASP256 4.3 29.4 1.0
O F:HOH2130 4.3 26.1 1.0
PA F:ADP600 4.4 30.1 1.0
OE1 F:GLU192 4.5 33.8 1.0
O1A F:ADP600 4.5 28.1 1.0
NH1 B:ARG373 4.7 29.3 1.0
CD F:GLU188 4.8 31.8 1.0
CE F:LYS162 4.8 19.5 1.0
CG F:ASP256 4.8 30.3 1.0
CD F:GLU192 4.8 29.9 1.0
NZ F:LYS162 5.0 20.7 1.0
C F:LYS162 5.0 25.5 1.0

Reference:

R.I.Menz, J.E.Walker, A.G.W.Leslie. Structure of Bovine Mitochondrial F1-Atpase with Nucleotide Bound to All Three Catalytic Sites: Implications For the Mechanism of Rotary Catalysis Cell(Cambridge,Mass.) V. 106 331 2001.
ISSN: ISSN 0092-8674
PubMed: 11509182
DOI: 10.1016/S0092-8674(01)00452-4
Page generated: Tue Aug 13 03:54:35 2024

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