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Magnesium in PDB 1efr: Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin

Enzymatic activity of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin

All present enzymatic activity of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin:
3.6.1.34;

Protein crystallography data

The structure of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin, PDB code: 1efr was solved by J.P.Abrahams, S.K.Buchanan, M.J.Van Raaij, I.M.Fearnley, 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) 5.50 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 285.700, 107.400, 139.500, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin (pdb code 1efr). 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 Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin, PDB code: 1efr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 1efr

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Magnesium binding site 1 out of 5 in the Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:29.2
occ:1.00
O2G A:ANP600 1.8 30.6 1.0
O A:HOH2032 2.3 32.1 1.0
O2B A:ANP600 2.3 27.5 1.0
N3B A:ANP600 2.8 39.6 1.0
PG A:ANP600 2.9 33.4 1.0
OG1 A:THR176 3.0 31.0 1.0
PB A:ANP600 3.0 32.0 1.0
CB A:THR176 3.7 29.1 1.0
O1G A:ANP600 3.8 40.6 1.0
O3G A:ANP600 3.9 34.9 1.0
O3A A:ANP600 4.1 36.2 1.0
O2A A:ANP600 4.1 39.5 1.0
O1B A:ANP600 4.2 22.9 1.0
N A:THR176 4.2 28.0 1.0
O A:HOH2031 4.3 22.9 1.0
PA A:ANP600 4.4 35.9 1.0
O1A A:ANP600 4.4 31.0 1.0
NZ A:LYS175 4.5 25.9 1.0
CA A:THR176 4.6 28.2 1.0
OD1 A:ASP269 4.8 37.1 1.0
CG2 A:THR176 4.9 23.0 1.0
O A:HOH2012 4.9 39.1 1.0

Magnesium binding site 2 out of 5 in 1efr

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Magnesium binding site 2 out of 5 in the Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:34.4
occ:1.00
O2G B:ANP600 1.8 38.2 1.0
OG1 B:THR176 2.6 34.0 1.0
O2B B:ANP600 2.7 30.8 1.0
O B:HOH2055 3.0 57.6 1.0
PG B:ANP600 3.3 38.0 1.0
CB B:THR176 3.7 38.2 1.0
O B:HOH2056 3.7 35.2 1.0
OD1 B:ASP269 3.8 47.0 1.0
OE1 B:GLN208 3.9 70.3 1.0
PB B:ANP600 4.0 40.5 1.0
N3B B:ANP600 4.1 27.6 1.0
O1G B:ANP600 4.2 41.7 1.0
O3G B:ANP600 4.2 52.4 1.0
O B:HOH2040 4.5 41.3 1.0
N B:THR176 4.5 24.2 1.0
O B:HOH2032 4.6 28.8 1.0
CG B:ASP269 4.6 28.3 1.0
CD B:GLN208 4.7 75.8 1.0
OD2 B:ASP269 4.7 18.9 1.0
CG2 B:THR176 4.7 30.7 1.0
CA B:THR176 4.7 26.7 1.0
NE2 B:GLN208 4.8 50.1 1.0
O1B B:ANP600 5.0 24.8 1.0

Magnesium binding site 3 out of 5 in 1efr

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Magnesium binding site 3 out of 5 in the Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:23.2
occ:1.00
OG1 C:THR176 1.9 34.3 1.0
O2B C:ANP600 2.3 26.3 1.0
O2G C:ANP600 2.4 31.9 1.0
CB C:THR176 3.0 20.4 1.0
PB C:ANP600 3.7 26.5 1.0
PG C:ANP600 3.8 29.8 1.0
N C:THR176 3.9 14.2 1.0
CA C:THR176 4.0 11.2 1.0
CG2 C:THR176 4.0 24.3 1.0
OD2 C:ASP269 4.0 24.8 1.0
N3B C:ANP600 4.0 32.0 1.0
O2A C:ANP600 4.2 36.3 1.0
OD1 C:ASP269 4.3 25.9 1.0
O C:HOH2048 4.4 41.2 1.0
CG C:ASP269 4.5 19.4 1.0
O1G C:ANP600 4.7 27.8 1.0
O1B C:ANP600 4.7 21.0 1.0
O3G C:ANP600 4.8 27.1 1.0
O3A C:ANP600 4.8 27.5 1.0
O1A C:ANP600 4.9 22.0 1.0
PA C:ANP600 4.9 25.5 1.0

Magnesium binding site 4 out of 5 in 1efr

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Magnesium binding site 4 out of 5 in the Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:27.0
occ:1.00
OG1 D:THR163 2.4 33.7 1.0
O2B D:ADP600 2.7 29.2 1.0
CB D:THR163 3.4 25.0 1.0
NH1 D:ARG189 3.6 16.3 1.0
OE1 D:GLU188 3.6 25.9 1.0
OE2 D:GLU192 3.9 32.5 1.0
PB D:ADP600 3.9 27.2 1.0
OE1 D:GLU192 3.9 25.7 1.0
O3B D:ADP600 4.0 27.5 1.0
CD D:GLU188 4.3 26.8 1.0
O D:HOH2022 4.3 22.4 1.0
CD D:GLU192 4.3 22.4 1.0
OD1 D:ASP256 4.3 30.1 1.0
CG2 D:THR163 4.4 30.3 1.0
O C:HOH2082 4.4 22.1 1.0
OD2 D:ASP256 4.5 33.4 1.0
N D:THR163 4.5 23.2 1.0
O2A D:ADP600 4.5 12.5 1.0
CA D:THR163 4.5 22.2 1.0
NH1 C:ARG373 4.8 24.2 1.0
O3A D:ADP600 4.8 29.7 1.0
CZ D:ARG189 4.8 35.4 1.0
CG D:ASP256 4.8 27.6 1.0
CG D:GLU188 4.9 12.5 1.0
O D:HOH2090 4.9 10.1 1.0
PA D:ADP600 5.0 34.0 1.0
O1B D:ADP600 5.0 16.9 1.0
O1A D:ADP600 5.0 15.8 1.0

Magnesium binding site 5 out of 5 in 1efr

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Magnesium binding site 5 out of 5 in the Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bovine Mitochondrial F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:25.3
occ:1.00
O2G F:ANP600 2.2 20.2 1.0
OG1 F:THR163 2.3 31.2 1.0
O2B F:ANP600 2.7 28.4 1.0
CB F:THR163 3.5 16.0 1.0
PG F:ANP600 3.6 33.2 1.0
OE1 F:GLU188 3.7 29.5 1.0
PB F:ANP600 3.7 27.6 1.0
N3B F:ANP600 3.8 28.0 1.0
NH1 F:ARG189 3.9 37.0 1.0
OE2 F:GLU192 3.9 28.7 1.0
OD1 F:ASP256 4.1 33.8 1.0
OE1 F:GLU192 4.1 26.3 1.0
OD2 F:ASP256 4.2 21.3 1.0
O F:HOH2025 4.2 33.7 1.0
O3G F:ANP600 4.3 25.9 1.0
N F:THR163 4.3 24.0 1.0
CD F:GLU188 4.4 42.1 1.0
CD F:GLU192 4.4 41.0 1.0
CA F:THR163 4.4 19.5 1.0
CG2 F:THR163 4.5 9.0 1.0
O2A F:ANP600 4.5 33.0 1.0
CG F:ASP256 4.6 24.4 1.0
O1B F:ANP600 4.6 26.2 1.0
O1G F:ANP600 4.7 27.9 1.0
CE F:LYS162 4.8 14.7 1.0
O B:HOH2081 4.8 17.6 1.0
NH1 B:ARG373 4.9 27.1 1.0
O3A F:ANP600 4.9 27.9 1.0

Reference:

J.P.Abrahams, S.K.Buchanan, M.J.Van Raaij, I.M.Fearnley, A.G.Leslie, J.E.Walker. The Structure of Bovine F1-Atpase Complexed with the Peptide Antibiotic Efrapeptin. Proc.Natl.Acad.Sci.Usa V. 93 9420 1996.
ISSN: ISSN 0027-8424
PubMed: 8790345
DOI: 10.1073/PNAS.93.18.9420
Page generated: Mon Dec 14 05:52:04 2020

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