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Magnesium in PDB 2jdi: Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide)

Enzymatic activity of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide)

All present enzymatic activity of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide):
3.6.1.34; 3.6.3.14;

Protein crystallography data

The structure of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide), PDB code: 2jdi was solved by M.W.Bowler, 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) 20.00 / 1.9
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.610, 123.130, 261.760, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide) (pdb code 2jdi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide), PDB code: 2jdi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2jdi

Go back to Magnesium Binding Sites List in 2jdi
Magnesium binding site 1 out of 5 in the Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1512

b:16.2
occ:1.00
 O2G A:ANP1511 2.2 13.7 1.0
OG1 A:THR176 2.2 8.0 1.0
O2B A:ANP1511 2.2 8.8 1.0
O A:HOH2150 2.2 9.3 1.0
O A:HOH2200 2.2 6.8 1.0
O A:HOH2347 2.2 10.1 1.0
CB A:THR176 3.2 10.1 1.0
PB A:ANP1511 3.3 10.9 1.0
PG A:ANP1511 3.3 12.3 1.0
N3B A:ANP1511 3.5 11.0 1.0
O A:HOH2355 3.9 15.9 1.0
N A:THR176 4.0 10.2 1.0
OD2 A:ASP269 4.0 11.2 1.0
O1G A:ANP1511 4.1 10.8 1.0
OD1 A:ASP269 4.1 11.7 1.0
CA A:THR176 4.2 11.6 1.0
O A:HOH2348 4.2 16.2 1.0
O A:HOH2202 4.2 14.8 1.0
CG2 A:THR176 4.2 8.5 1.0
O1A A:ANP1511 4.2 15.9 1.0
O A:HOH2201 4.2 17.5 1.0
O A:HOH2168 4.3 14.7 1.0
O A:HOH2353 4.3 20.4 1.0
O1B A:ANP1511 4.3 12.0 1.0
O3A A:ANP1511 4.4 10.7 1.0
O3G A:ANP1511 4.5 8.1 1.0
CG A:ASP269 4.5 13.5 1.0
PA A:ANP1511 4.6 10.0 1.0
O D:HOH2148 4.7 15.3 1.0
O2A A:ANP1511 4.8 11.5 1.0
O A:HOH2354 4.9 18.1 1.0

Magnesium binding site 2 out of 5 in 2jdi

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Magnesium binding site 2 out of 5 in the Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1512

b:15.3
occ:1.00
 OG1 B:THR176 2.2 8.1 1.0
O2G B:ANP1511 2.2 15.2 1.0
O B:HOH2167 2.2 11.6 1.0
O2B B:ANP1511 2.2 11.6 1.0
O B:HOH2223 2.2 11.8 1.0
O B:HOH2345 2.2 10.1 1.0
CB B:THR176 3.2 6.7 1.0
PB B:ANP1511 3.3 10.6 1.0
PG B:ANP1511 3.3 12.4 1.0
N3B B:ANP1511 3.4 11.5 1.0
N B:THR176 3.9 9.5 1.0
O B:HOH2347 3.9 13.9 1.0
OD1 B:ASP269 4.0 14.7 1.0
O1G B:ANP1511 4.1 11.0 1.0
O B:HOH2348 4.1 17.4 1.0
CA B:THR176 4.1 10.7 1.0
O1A B:ANP1511 4.1 10.8 1.0
O B:HOH2343 4.1 28.1 1.0
OD2 B:ASP269 4.2 5.2 1.0
CG2 B:THR176 4.3 7.7 1.0
O1B B:ANP1511 4.3 9.2 1.0
O B:HOH2224 4.3 12.0 1.0
O3A B:ANP1511 4.4 8.8 1.0
O3G B:ANP1511 4.4 12.9 1.0
CG B:ASP269 4.5 15.1 1.0
O B:HOH2225 4.6 20.7 1.0
PA B:ANP1511 4.6 13.9 1.0
O B:HOH2081 4.7 16.4 1.0
O2A B:ANP1511 4.9 16.1 1.0

Magnesium binding site 3 out of 5 in 2jdi

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Magnesium binding site 3 out of 5 in the Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1512

b:13.7
occ:1.00
 OG1 C:THR176 2.2 7.6 1.0
O2G C:ANP1511 2.2 13.4 1.0
O2B C:ANP1511 2.2 13.7 1.0
O C:HOH2144 2.2 11.1 1.0
O C:HOH2192 2.2 9.4 1.0
O C:HOH2363 2.2 12.9 1.0
CB C:THR176 3.2 9.2 1.0
PG C:ANP1511 3.3 14.7 1.0
PB C:ANP1511 3.4 9.9 1.0
N3B C:ANP1511 3.6 17.1 1.0
O C:HOH2367 3.9 23.2 1.0
OD2 C:ASP269 3.9 11.4 1.0
O1G C:ANP1511 4.0 8.2 1.0
N C:THR176 4.0 9.3 1.0
OD1 C:ASP269 4.1 15.4 1.0
O C:HOH2360 4.1 16.1 1.0
CA C:THR176 4.2 10.0 1.0
CG2 C:THR176 4.3 5.0 1.0
O1A C:ANP1511 4.3 12.8 1.0
O F:HOH2183 4.3 16.3 1.0
O1B C:ANP1511 4.4 12.8 1.0
O C:HOH2193 4.4 15.9 1.0
O C:HOH2194 4.4 17.6 1.0
O C:HOH2159 4.4 12.4 1.0
CG C:ASP269 4.4 17.3 1.0
O3A C:ANP1511 4.4 9.6 1.0
O3G C:ANP1511 4.5 13.9 1.0
O F:HOH2193 4.6 11.6 1.0
PA C:ANP1511 4.7 10.6 1.0
O C:HOH2365 4.9 12.8 1.0
O2A C:ANP1511 4.9 11.6 1.0

Magnesium binding site 4 out of 5 in 2jdi

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Magnesium binding site 4 out of 5 in the Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1481

b:14.0
occ:1.00
 OG1 D:THR163 2.2 10.5 1.0
O2G D:ANP1480 2.2 12.9 1.0
O2B D:ANP1480 2.2 8.1 1.0
O D:HOH2166 2.2 13.2 1.0
O D:HOH2213 2.2 14.5 1.0
O D:HOH2384 2.2 8.9 1.0
CB D:THR163 3.1 9.2 1.0
PG D:ANP1480 3.4 16.2 1.0
PB D:ANP1480 3.4 10.7 1.0
N3B D:ANP1480 3.7 9.5 1.0
NH1 D:ARG189 3.7 10.4 1.0
OD2 D:ASP256 3.9 15.2 1.0
N D:THR163 4.0 10.6 1.0
OE1 D:GLU188 4.0 18.9 1.0
OD1 D:ASP256 4.1 10.7 1.0
CG2 D:THR163 4.1 9.2 1.0
CA D:THR163 4.1 11.2 1.0
OE2 D:GLU192 4.1 16.0 1.0
O3G D:ANP1480 4.2 13.6 1.0
O D:HOH2167 4.2 15.2 1.0
O1A D:ANP1480 4.3 14.4 1.0
OE1 D:GLU192 4.3 6.9 1.0
O3A D:ANP1480 4.3 10.2 1.0
NH1 C:ARG373 4.4 9.7 1.0
CG D:ASP256 4.5 12.4 1.0
O1G D:ANP1480 4.5 14.8 1.0
O D:HOH2168 4.6 15.0 1.0
O1B D:ANP1480 4.6 12.7 1.0
PA D:ANP1480 4.6 9.8 1.0
CD D:GLU188 4.6 16.9 1.0
CD D:GLU192 4.6 20.4 1.0
O2A D:ANP1480 4.7 12.1 1.0
CE D:LYS162 4.8 10.5 1.0
CB D:LYS162 4.9 10.3 1.0
CZ D:ARG189 5.0 15.8 1.0

Magnesium binding site 5 out of 5 in 2jdi

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Magnesium binding site 5 out of 5 in the Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ground State Structure of F1-Atpase From Bovine Heart Mitochondria (Bovine F1-Atpase Crystallised in the Absence of Azide) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1480

b:13.3
occ:1.00
 O2G F:ANP1479 2.2 12.5 1.0
OG1 F:THR163 2.2 12.6 1.0
O F:HOH2435 2.2 7.2 1.0
O2B F:ANP1479 2.2 18.2 1.0
O F:HOH2260 2.2 11.8 1.0
O F:HOH2218 2.2 8.2 1.0
CB F:THR163 3.2 8.3 1.0
PB F:ANP1479 3.3 11.5 1.0
PG F:ANP1479 3.4 11.9 1.0
N3B F:ANP1479 3.6 21.9 1.0
OD2 F:ASP256 3.9 10.2 1.0
NH1 F:ARG189 3.9 8.6 1.0
N F:THR163 4.0 10.5 1.0
OE1 F:GLU188 4.0 11.2 1.0
O F:HOH2219 4.1 15.9 1.0
OE2 F:GLU192 4.1 7.3 1.0
CA F:THR163 4.1 11.5 1.0
O1A F:ANP1479 4.2 15.4 1.0
OD1 F:ASP256 4.2 8.7 1.0
CG2 F:THR163 4.2 2.0 1.0
O1G F:ANP1479 4.4 12.1 1.0
O3G F:ANP1479 4.4 19.0 1.0
OE1 F:GLU192 4.4 9.9 1.0
O3A F:ANP1479 4.4 9.0 1.0
O1B F:ANP1479 4.4 8.4 1.0
CG F:ASP256 4.5 13.0 1.0
PA F:ANP1479 4.7 12.7 1.0
CD F:GLU192 4.7 12.3 1.0
CD F:GLU188 4.7 20.7 1.0
CE F:LYS162 4.7 11.4 1.0
NH1 B:ARG373 4.8 8.0 1.0
CB F:LYS162 4.8 11.1 1.0
O F:HOH2220 4.9 16.2 1.0
O2A F:ANP1479 5.0 12.7 1.0

Reference:

M.W.Bowler, M.G.Montgomery, A.G.W.Leslie, J.E.Walker. Ground State Structure of F1-Atpase From Bovine Heart Mitochondria at 1.9 A Resolution J.Biol.Chem. V. 282 14238 2007.
ISSN: ISSN 0021-9258
PubMed: 17350959
DOI: 10.1074/JBC.M700203200
Page generated: Wed Aug 14 00:43:58 2024

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