Atomistry » Magnesium » PDB 3zi8-3zwk » 3zry
Atomistry »
  Magnesium »
    PDB 3zi8-3zwk »
      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 Dec 14 09:04:27 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy