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Magnesium in PDB 2f43: Rat Liver F1-Atpase

Enzymatic activity of Rat Liver F1-Atpase

All present enzymatic activity of Rat Liver F1-Atpase:
3.6.3.14;

Protein crystallography data

The structure of Rat Liver F1-Atpase, PDB code: 2f43 was solved by C.Chen, A.K.Saxena, W.N.Simcoke, D.N.Garboczi, P.L.Pedersen, Y.H.Ko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 3.00
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 144.567, 144.567, 362.982, 90.00, 90.00, 120.00
R / Rfree (%) 30.6 / 32

Other elements in 2f43:

The structure of Rat Liver F1-Atpase also contains other interesting chemical elements:

Vanadium (V) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rat Liver F1-Atpase (pdb code 2f43). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Rat Liver F1-Atpase, PDB code: 2f43:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2f43

Go back to Magnesium Binding Sites List in 2f43
Magnesium binding site 1 out of 2 in the Rat Liver F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rat Liver F1-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:55.3
occ:1.00
OG1 A:THR176 2.5 71.6 1.0
O2G A:ATP603 2.7 60.4 1.0
O3B A:ATP603 3.0 59.9 1.0
PG A:ATP603 3.2 61.4 1.0
OE1 A:GLN208 3.2 46.0 1.0
O1G A:ATP603 3.4 60.3 1.0
OD1 A:ASP269 3.5 55.0 1.0
CB A:THR176 3.6 70.4 1.0
O3A A:ATP603 3.9 60.7 1.0
PB A:ATP603 4.1 58.6 1.0
CG A:ASP269 4.3 57.5 1.0
OD2 A:ASP269 4.3 59.1 1.0
CD A:GLN208 4.3 45.6 1.0
OD2 A:ASP270 4.3 52.1 1.0
CG2 A:THR176 4.3 68.6 1.0
O1B A:ATP603 4.5 58.0 1.0
O3G A:ATP603 4.6 60.6 1.0
CA A:THR176 4.8 69.7 1.0
CG A:GLN208 4.8 45.1 1.0
N A:THR176 4.8 70.8 1.0
O1A A:ATP603 4.8 62.5 1.0
PA A:ATP603 4.9 63.6 1.0

Magnesium binding site 2 out of 2 in 2f43

Go back to Magnesium Binding Sites List in 2f43
Magnesium binding site 2 out of 2 in the Rat Liver F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rat Liver F1-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg605

b:40.2
occ:1.00
O3B B:ADP604 2.6 98.7 1.0
OG1 B:THR163 2.6 81.1 1.0
O2 B:VO4601 2.9 44.9 1.0
PB B:ADP604 3.1 97.9 1.0
O2B B:ADP604 3.1 97.4 1.0
NH1 B:ARG189 3.1 68.6 1.0
CG B:GLU188 3.2 52.0 1.0
CB B:THR163 3.5 81.8 1.0
O1B B:ADP604 3.5 97.2 1.0
V B:VO4601 3.6 48.4 1.0
OE2 B:GLU188 3.6 50.4 1.0
CD B:GLU188 3.6 52.1 1.0
O3 B:VO4601 3.7 45.5 1.0
OD1 B:ASP256 4.0 64.0 1.0
OD1 B:ASN257 4.2 69.5 1.0
OE1 B:GLU192 4.3 71.0 1.0
CZ B:ARG189 4.4 67.2 1.0
OE1 B:GLU188 4.5 50.0 1.0
CG2 B:THR163 4.5 81.8 1.0
N B:THR163 4.5 81.0 1.0
CB B:GLU188 4.6 53.5 1.0
CA B:THR163 4.6 81.1 1.0
O3A B:ADP604 4.6 99.8 1.0
O1 B:VO4601 4.7 45.2 1.0
CG B:ASP256 4.9 63.5 1.0
OD2 B:ASP256 5.0 64.3 1.0

Reference:

C.Chen, A.K.Saxena, W.N.Simcoke, D.N.Garboczi, P.L.Pedersen, Y.H.Ko. Mitochondrial Atp Synthase: Crystal Structure of the Catalytic F1 Unit in A Vanadate-Induced Transition-Like State and Implications For Mechanism. J.Biol.Chem. V. 281 13777 2006.
ISSN: ISSN 0021-9258
PubMed: 16531409
DOI: 10.1074/JBC.M513369200
Page generated: Mon Dec 14 07:22:10 2020

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