Atomistry » Magnesium » PDB 3zia-3zx4 » 3zry
Atomistry »
  Magnesium »
    PDB 3zia-3zx4 »
      3zry »

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

Go back to Magnesium Binding Sites List in 3zry
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

Go back to Magnesium Binding Sites List in 3zry
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

Go back to Magnesium Binding Sites List in 3zry
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

Go back to Magnesium Binding Sites List in 3zry
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

Go back to Magnesium Binding Sites List in 3zry
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: Mon Aug 11 05:20:48 2025

Last articles

Mg in 4DPG
Mg in 4DQP
Mg in 4DQQ
Mg in 4DPM
Mg in 4DPV
Mg in 4DQI
Mg in 4DOB
Mg in 4DOC
Mg in 4DMZ
Mg in 4DOA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy