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Magnesium in PDB 3zry: Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase

Enzymatic activity of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase

All present enzymatic activity of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase:
3.6.3.14;

Protein crystallography data

The structure of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase, PDB code: 3zry was solved by M.-F.Giraud, A.Dautant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.63 / 6.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.690, 174.910, 164.260, 90.00, 93.92, 90.00
R / Rfree (%) 31.7 / 33.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase (pdb code 3zry). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase, PDB code: 3zry:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 3zry

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Magnesium binding site 1 out of 5 in the Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:0.8
occ:1.00
 OG1 A:THR178 2.7 0.8 1.0
O1G A:ANP600 2.8 0.6 1.0
O1B A:ANP600 3.0 0.6 1.0
O2G A:ANP600 3.0 0.7 1.0
PG A:ANP600 3.4 0.3 1.0
CB A:THR178 3.6 0.9 1.0
N3B A:ANP600 4.0 0.1 1.0
CG2 A:THR178 4.1 0.1 1.0
PB A:ANP600 4.1 0.7 1.0
O1A A:ANP600 4.4 0.3 1.0
OD2 A:ASP271 4.5 0.3 1.0
OE1 A:GLN210 4.6 0.4 1.0
OD1 A:ASP271 4.6 0.6 1.0
O2A A:ANP600 4.8 0.5 1.0
O3G A:ANP600 4.8 0.6 1.0
CG A:ASP271 4.9 0.5 1.0
PA A:ANP600 4.9 0.6 1.0
O2B A:ANP600 5.0 0.3 1.0
OH A:TYR205 5.0 0.1 1.0
CA A:THR178 5.0 0.5 1.0

Magnesium binding site 2 out of 5 in 3zry

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Magnesium binding site 2 out of 5 in the Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:0.3
occ:1.00
 OG1 B:THR178 2.5 0.2 1.0
O1G B:ANP600 2.6 0.7 1.0
O1B B:ANP600 3.2 0.8 1.0
OD2 B:ASP271 3.2 0.3 1.0
OD1 B:ASP271 3.3 0.9 1.0
CG B:ASP271 3.7 0.9 1.0
CB B:THR178 3.9 0.6 1.0
PG B:ANP600 4.0 0.2 1.0
N B:THR178 4.1 0.9 1.0
PB B:ANP600 4.3 0.8 1.0
CA B:THR178 4.4 0.7 1.0
O3G B:ANP600 4.4 0.3 1.0
CB B:LYS177 4.5 0.3 1.0
O2B B:ANP600 4.7 0.8 1.0
N3B B:ANP600 4.7 0.6 1.0
C B:LYS177 4.9 0.6 1.0
CG1 B:VAL328 4.9 0.3 1.0
CG2 B:THR178 4.9 0.9 1.0
CE B:LYS177 5.0 0.9 1.0

Magnesium binding site 3 out of 5 in 3zry

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Magnesium binding site 3 out of 5 in the Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:0.9
occ:1.00
 OG1 C:THR178 2.6 0.8 1.0
O1G C:ANP600 2.6 0.7 1.0
OD1 C:ASP271 3.3 0.5 1.0
OD2 C:ASP271 3.5 0.3 1.0
O1B C:ANP600 3.5 0.3 1.0
O2G C:ANP600 3.6 0.1 1.0
PG C:ANP600 3.6 0.6 1.0
CG C:ASP271 3.8 0.1 1.0
CB C:THR178 3.9 0.1 1.0
OE1 C:GLN210 4.3 0.4 1.0
PB C:ANP600 4.4 0.7 1.0
N3B C:ANP600 4.5 0.5 1.0
CG2 C:THR178 4.6 0.3 1.0
CD C:GLN210 4.7 0.9 1.0
O2B C:ANP600 4.8 0.8 1.0
O3G C:ANP600 4.9 0.2 1.0
CA C:THR178 4.9 0.7 1.0
N C:THR178 4.9 0.1 1.0

Magnesium binding site 4 out of 5 in 3zry

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Magnesium binding site 4 out of 5 in the Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:0.2
occ:1.00
 OE2 D:GLU193 2.5 0.1 1.0
O1G D:ANP600 2.7 0.2 1.0
OG1 D:THR164 2.8 0.2 1.0
O1B D:ANP600 2.8 0.9 1.0
N3B D:ANP600 2.8 0.1 1.0
NH1 D:ARG190 3.1 0.1 1.0
CB D:THR164 3.1 0.8 1.0
PG D:ANP600 3.2 0.1 1.0
O1A D:ANP600 3.3 0.7 1.0
CD D:GLU193 3.5 0.6 1.0
OE1 D:GLU189 3.5 0.4 1.0
PB D:ANP600 3.6 0.4 1.0
OE1 D:GLU193 3.8 0.4 1.0
O2G D:ANP600 3.8 0.4 1.0
NH1 C:ARG375 3.9 0.9 1.0
CG2 D:THR164 3.9 0.4 1.0
PA D:ANP600 4.0 0.7 1.0
O3A D:ANP600 4.1 0.7 1.0
O2A D:ANP600 4.3 0.0 1.0
CZ D:ARG190 4.3 0.2 1.0
CA D:THR164 4.4 0.9 1.0
N D:THR164 4.5 0.6 1.0
CD D:GLU189 4.6 0.2 1.0
O3G D:ANP600 4.6 0.1 1.0
CG D:GLU193 4.7 0.7 1.0
CD D:ARG190 4.8 0.1 1.0
O2B D:ANP600 4.9 0.2 1.0
NE D:ARG190 5.0 0.6 1.0

Magnesium binding site 5 out of 5 in 3zry

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Magnesium binding site 5 out of 5 in the Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Rotor Architecture in the F(1)-C(10)-Ring Complex of the Yeast F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg700

b:0.9
occ:1.00
 OG1 F:THR164 2.7 0.4 1.0
O1G F:ANP600 2.7 0.4 1.0
OD1 F:ASP256 2.9 0.0 1.0
OE1 F:GLU189 2.9 0.5 1.0
CD F:GLU189 3.0 0.3 1.0
OE2 F:GLU189 3.3 0.3 1.0
CE F:LYS163 3.5 0.7 1.0
O1B F:ANP600 3.8 0.6 1.0
CG F:GLU189 3.8 0.9 1.0
CG F:ASP256 3.8 0.9 1.0
ND2 F:ASN257 3.8 0.5 1.0
OD2 F:ASP256 3.9 0.1 1.0
CB F:THR164 4.1 0.5 1.0
PG F:ANP600 4.2 0.1 1.0
NZ F:LYS163 4.3 0.6 1.0
N F:THR164 4.3 0.8 1.0
CB F:ASN257 4.4 0.2 1.0
O3G F:ANP600 4.5 0.5 1.0
CD F:LYS163 4.6 0.0 1.0
CA F:THR164 4.6 0.2 1.0
CG F:ASN257 4.6 0.5 1.0
PB F:ANP600 4.7 0.0 1.0
CB F:ALA309 4.8 0.4 1.0
CB F:LYS163 4.8 0.1 1.0
O2B F:ANP600 4.9 0.7 1.0
CG2 F:THR164 4.9 0.1 1.0
OE1 F:GLU193 4.9 0.3 1.0
N3B F:ANP600 4.9 0.6 1.0

Reference:

M.-F.Giraud, P.Paumard, C.Sanchez, D.Brethes, J.Velours, A.Dautant. Rotor Architecture in the Yeast and Bovine F(1)-C-Ring Complexes of F-Atp Synthase. J.Struct.Biol. V. 177 490 2012.
ISSN: ISSN 1047-8477
PubMed: 22119846
DOI: 10.1016/J.JSB.2011.10.015
Page generated: Thu Aug 15 14:04:08 2024

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