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Magnesium in PDB 2xok: Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution

Enzymatic activity of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution

All present enzymatic activity of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution:
3.6.1.34;

Protein crystallography data

The structure of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution, PDB code: 2xok was solved by D.Stock, 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) 20.00 / 3.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.352, 173.711, 137.889, 90.00, 91.77, 90.00
R / Rfree (%) 21 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution (pdb code 2xok). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution, PDB code: 2xok:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2xok

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Magnesium binding site 1 out of 5 in the Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg700

b:66.8
occ:1.00
 O2B A:ANP600 2.0 60.6 1.0
O2G A:ANP600 2.0 79.7 1.0
OG1 A:THR178 2.1 70.5 1.0
PG A:ANP600 3.1 80.3 1.0
CB A:THR178 3.3 67.6 1.0
PB A:ANP600 3.3 68.8 1.0
O1G A:ANP600 3.4 88.8 1.0
N3B A:ANP600 3.7 70.2 1.0
O1B A:ANP600 4.1 65.4 1.0
CG2 A:THR178 4.1 68.8 1.0
OD1 A:ASP271 4.2 85.2 1.0
O2A A:ANP600 4.2 68.3 1.0
OD2 A:ASP271 4.3 86.0 1.0
CA A:THR178 4.4 68.2 1.0
N A:THR178 4.4 69.1 1.0
O3A A:ANP600 4.5 72.5 1.0
O3G A:ANP600 4.5 82.7 1.0
O1A A:ANP600 4.6 66.6 1.0
CG A:ASP271 4.6 84.2 1.0
PA A:ANP600 4.7 63.7 1.0

Magnesium binding site 2 out of 5 in 2xok

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Magnesium binding site 2 out of 5 in the Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg700

b:86.4
occ:1.00
 O2G B:ANP600 1.8 0.2 1.0
OG1 B:THR178 1.9 0.5 1.0
O2B B:ANP600 2.6 0.3 1.0
CB B:THR178 3.1 0.9 1.0
PG B:ANP600 3.3 0.7 1.0
O2A B:ANP600 3.4 0.2 1.0
PB B:ANP600 3.9 0.3 1.0
N3B B:ANP600 4.0 0.1 1.0
N B:THR178 4.0 0.2 1.0
CG2 B:THR178 4.1 0.2 1.0
O1G B:ANP600 4.1 0.4 1.0
CA B:THR178 4.1 0.1 1.0
OD2 B:ASP271 4.1 0.6 1.0
PA B:ANP600 4.4 0.8 1.0
O3G B:ANP600 4.4 0.8 1.0
O1A B:ANP600 4.5 0.7 1.0
O3A B:ANP600 4.7 0.3 1.0
OD1 B:ASP271 4.7 0.3 1.0
CG B:ASP271 4.9 0.2 1.0

Magnesium binding site 3 out of 5 in 2xok

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Magnesium binding site 3 out of 5 in the Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg700

b:80.4
occ:1.00
 O2G C:ANP600 1.8 77.4 1.0
OG1 C:THR178 2.0 61.9 1.0
O2B C:ANP600 2.1 63.0 1.0
PG C:ANP600 3.0 74.4 1.0
CB C:THR178 3.1 60.2 1.0
PB C:ANP600 3.4 59.4 1.0
O1G C:ANP600 3.5 80.9 1.0
N3B C:ANP600 3.7 70.2 1.0
O2A C:ANP600 3.8 72.3 1.0
OD2 C:ASP271 4.0 71.4 1.0
CG2 C:THR178 4.0 51.4 1.0
N C:THR178 4.0 59.2 1.0
CA C:THR178 4.1 60.8 1.0
OD1 C:ASP271 4.2 75.6 1.0
O1B C:ANP600 4.3 51.6 1.0
O3G C:ANP600 4.4 83.0 1.0
CG C:ASP271 4.6 72.2 1.0
O3A C:ANP600 4.6 64.6 1.0
PA C:ANP600 4.7 69.9 1.0

Magnesium binding site 4 out of 5 in 2xok

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Magnesium binding site 4 out of 5 in the Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg700

b:71.6
occ:1.00
 O2G D:ANP600 1.8 0.3 1.0
OG1 D:THR164 2.1 70.0 1.0
O2B D:ANP600 2.3 75.0 1.0
CB D:THR164 2.8 71.6 1.0
PG D:ANP600 2.9 0.2 1.0
N3B D:ANP600 3.0 96.2 1.0
OE2 D:GLU193 3.2 88.9 1.0
PB D:ANP600 3.3 70.5 1.0
O2A D:ANP600 3.4 72.8 1.0
OE1 D:GLU189 3.4 92.2 1.0
NH1 D:ARG190 3.6 80.9 1.0
N D:THR164 3.8 71.4 1.0
CG2 D:THR164 3.8 72.2 1.0
CA D:THR164 3.9 69.7 1.0
CD D:GLU193 4.0 85.4 1.0
O1G D:ANP600 4.0 0.5 1.0
O3G D:ANP600 4.1 0.2 1.0
PA D:ANP600 4.1 67.8 1.0
OE1 D:GLU193 4.1 94.2 1.0
O3A D:ANP600 4.2 70.8 1.0
O1A D:ANP600 4.2 69.1 1.0
NH1 C:ARG375 4.4 97.0 1.0
CD D:GLU189 4.4 95.0 1.0
O1B D:ANP600 4.5 71.2 1.0
OD2 D:ASP256 4.7 90.5 1.0
CZ D:ARG190 4.9 73.0 1.0
OD1 D:ASP256 5.0 87.8 1.0

Magnesium binding site 5 out of 5 in 2xok

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Magnesium binding site 5 out of 5 in the Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Refined Structure of Yeast F1C10 Atpase Complex to 3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg700

b:53.0
occ:1.00
 O2G F:ANP600 1.6 58.5 1.0
OG1 F:THR164 1.8 61.0 1.0
O2B F:ANP600 2.3 39.6 1.0
OE1 F:GLU189 2.8 0.1 1.0
CB F:THR164 2.9 66.1 1.0
PG F:ANP600 3.1 72.1 1.0
PB F:ANP600 3.3 52.0 1.0
N3B F:ANP600 3.4 56.6 1.0
OE2 F:GLU193 3.6 0.2 1.0
CD F:GLU189 3.7 0.9 1.0
N F:THR164 3.9 61.5 1.0
NH1 F:ARG190 3.9 92.4 1.0
CG2 F:THR164 3.9 69.8 1.0
CA F:THR164 4.0 65.8 1.0
O2A F:ANP600 4.0 49.8 1.0
O1G F:ANP600 4.1 75.7 1.0
OE2 F:GLU189 4.2 0.9 1.0
CE F:LYS163 4.2 41.4 1.0
OE1 F:GLU193 4.2 1.0 1.0
O3G F:ANP600 4.2 72.5 1.0
O3A F:ANP600 4.3 61.7 1.0
CD F:GLU193 4.3 98.0 1.0
OD1 F:ASP256 4.4 0.7 1.0
NH1 B:ARG375 4.4 71.8 1.0
PA F:ANP600 4.5 61.9 1.0
O1B F:ANP600 4.6 59.7 1.0
NZ F:LYS163 4.7 49.2 1.0
O1A F:ANP600 4.7 55.5 1.0
CG F:GLU189 4.8 0.6 1.0
OD2 F:ASP256 4.8 94.7 1.0

Reference:

D.Stock, A.G.Leslie, J.E.Walker. Molecular Architecture of the Rotary Motor in Atp Synthase. Science V. 286 1700 1999.
ISSN: ISSN 0036-8075
PubMed: 10576729
DOI: 10.1126/SCIENCE.286.5445.1700
Page generated: Mon Dec 14 07:47:10 2020

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