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Magnesium in PDB 4b2q: Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average

Enzymatic activity of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average

All present enzymatic activity of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average:
3.6.3.14;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average (pdb code 4b2q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average, PDB code: 4b2q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 4b2q

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Magnesium binding site 1 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


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A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1512

b:68.3
occ:1.00
 OG1 A:THR178 2.4 73.3 1.0
O2B A:ATP1511 2.4 68.3 1.0
O2G A:ATP1511 2.7 68.3 1.0
OD2 A:ASP271 3.3 73.3 1.0
PB A:ATP1511 3.6 68.3 1.0
CB A:THR178 3.6 73.3 1.0
PG A:ATP1511 3.8 68.3 1.0
NE2 A:GLN210 3.8 73.3 1.0
O1B A:ATP1511 4.0 68.3 1.0
O1G A:ATP1511 4.0 68.3 1.0
OD1 A:ASP271 4.0 73.3 1.0
CG A:ASP271 4.1 73.3 1.0
O3B A:ATP1511 4.2 68.3 1.0
O2A A:ATP1511 4.3 68.3 1.0
CG2 A:THR178 4.4 73.3 1.0
CA A:THR178 4.7 73.3 1.0
N A:THR178 4.7 73.3 1.0
O3A A:ATP1511 4.9 68.3 1.0
OH A:TYR205 4.9 73.3 1.0

Magnesium binding site 2 out of 10 in 4b2q

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Magnesium binding site 2 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


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A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1511

b:0.4
occ:1.00
 OG1 B:THR178 2.1 0.6 1.0
O2B B:ATP1510 2.3 0.4 1.0
O1G B:ATP1510 2.3 0.4 1.0
O2G B:ATP1510 2.4 0.4 1.0
PG B:ATP1510 2.7 0.4 1.0
CB B:THR178 3.0 0.6 1.0
N B:THR178 3.1 0.6 1.0
PB B:ATP1510 3.2 0.4 1.0
O3B B:ATP1510 3.3 0.4 1.0
CA B:THR178 3.6 0.6 1.0
OD1 B:ASP271 3.6 0.6 1.0
CB B:LYS177 3.7 0.6 1.0
O1B B:ATP1510 3.9 0.4 1.0
C B:LYS177 3.9 0.6 1.0
O3G B:ATP1510 4.1 0.4 1.0
O2A B:ATP1510 4.1 0.4 1.0
CE B:LYS177 4.2 0.6 1.0
CA B:LYS177 4.2 0.6 1.0
OD2 B:ASP271 4.2 0.6 1.0
CG B:ASP271 4.2 0.6 1.0
CG2 B:THR178 4.3 0.6 1.0
N B:LYS177 4.3 0.6 1.0
NZ B:LYS177 4.5 0.6 1.0
O3A B:ATP1510 4.6 0.4 1.0
CG B:LYS177 4.7 0.6 1.0
CG1 B:VAL328 4.9 0.6 1.0
C B:THR178 4.9 0.6 1.0
O B:LYS177 4.9 0.6 1.0
PA B:ATP1510 5.0 0.4 1.0
CD B:LYS177 5.0 0.6 1.0

Magnesium binding site 3 out of 10 in 4b2q

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Magnesium binding site 3 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1512

b:71.6
occ:1.00
 OG1 C:THR178 2.2 63.7 1.0
O2B C:ATP1511 2.3 71.6 1.0
O1G C:ATP1511 2.4 71.6 1.0
O2G C:ATP1511 2.6 71.6 1.0
PG C:ATP1511 2.9 71.6 1.0
CB C:THR178 3.4 63.7 1.0
PB C:ATP1511 3.4 71.6 1.0
OD2 C:ASP271 3.5 63.7 1.0
O3B C:ATP1511 3.7 71.6 1.0
OD1 C:ASP271 4.1 63.7 1.0
O1B C:ATP1511 4.1 71.6 1.0
CG2 C:THR178 4.2 63.7 1.0
NE2 C:GLN210 4.2 63.7 1.0
CG C:ASP271 4.2 63.7 1.0
O3G C:ATP1511 4.3 71.6 1.0
N C:THR178 4.5 63.7 1.0
CA C:THR178 4.5 63.7 1.0
O2A C:ATP1511 4.7 71.6 1.0
O3A C:ATP1511 4.8 71.6 1.0

Magnesium binding site 4 out of 10 in 4b2q

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Magnesium binding site 4 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1477

b:71.6
occ:1.00
 OG1 D:THR164 2.4 75.0 1.0
O2B D:ADP1476 2.5 71.6 1.0
O1B D:ADP1476 3.0 71.6 1.0
O2A D:ADP1476 3.0 71.6 1.0
PB D:ADP1476 3.2 71.6 1.0
OE1 D:GLU189 3.5 75.0 1.0
CB D:THR164 3.6 75.0 1.0
OE2 D:GLU193 3.9 75.0 1.0
PA D:ADP1476 3.9 71.6 1.0
NH1 D:ARG190 3.9 75.0 1.0
O3A D:ADP1476 4.0 71.6 1.0
N D:THR164 4.3 75.0 1.0
O1A D:ADP1476 4.4 71.6 1.0
CA D:THR164 4.5 75.0 1.0
O3B D:ADP1476 4.5 71.6 1.0
CG2 D:THR164 4.6 75.0 1.0
CD D:GLU189 4.6 75.0 1.0
OE1 D:GLU193 4.7 75.0 1.0
CD D:GLU193 4.7 75.0 1.0
OD2 D:ASP256 5.0 75.0 1.0
CZ D:ARG190 5.0 75.0 1.0

Magnesium binding site 5 out of 10 in 4b2q

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Magnesium binding site 5 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1480

b:0.4
occ:1.00
 O2B F:ADP1479 2.3 0.4 1.0
OG1 F:THR164 2.4 89.4 1.0
OE1 F:GLU189 2.9 89.4 1.0
PB F:ADP1479 3.4 0.4 1.0
CB F:THR164 3.6 89.4 1.0
OD1 F:ASP256 3.7 89.4 1.0
O3B F:ADP1479 3.9 0.4 1.0
CD F:GLU189 3.9 89.4 1.0
O1B F:ADP1479 4.0 0.4 1.0
OD2 F:ASP256 4.0 89.4 1.0
OE1 F:GLU193 4.2 89.4 1.0
NH1 F:ARG190 4.2 89.4 1.0
CG F:ASP256 4.3 89.4 1.0
N F:THR164 4.4 89.4 1.0
OE2 F:GLU189 4.5 89.4 1.0
O2A F:ADP1479 4.5 0.4 1.0
OE2 F:GLU193 4.5 89.4 1.0
CA F:THR164 4.6 89.4 1.0
CG2 F:THR164 4.6 89.4 1.0
NH1 B:ARG375 4.6 0.6 1.0
O3A F:ADP1479 4.7 0.4 1.0
CD F:GLU193 4.8 89.4 1.0
CE F:LYS163 5.0 89.4 1.0

Magnesium binding site 6 out of 10 in 4b2q

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Magnesium binding site 6 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1512

b:68.3
occ:1.00
 OG1 a:THR178 2.4 73.3 1.0
O2B a:ATP1511 2.4 68.3 1.0
O2G a:ATP1511 2.7 68.3 1.0
OD2 a:ASP271 3.3 73.3 1.0
PB a:ATP1511 3.6 68.3 1.0
CB a:THR178 3.6 73.3 1.0
PG a:ATP1511 3.8 68.3 1.0
NE2 a:GLN210 3.8 73.3 1.0
O1B a:ATP1511 4.0 68.3 1.0
O1G a:ATP1511 4.0 68.3 1.0
OD1 a:ASP271 4.0 73.3 1.0
CG a:ASP271 4.1 73.3 1.0
O3B a:ATP1511 4.2 68.3 1.0
O2A a:ATP1511 4.3 68.3 1.0
CG2 a:THR178 4.4 73.3 1.0
CA a:THR178 4.7 73.3 1.0
N a:THR178 4.7 73.3 1.0
O3A a:ATP1511 4.9 68.3 1.0
OH a:TYR205 4.9 73.3 1.0

Magnesium binding site 7 out of 10 in 4b2q

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Magnesium binding site 7 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg1511

b:0.4
occ:1.00
 OG1 b:THR178 2.1 0.6 1.0
O2B b:ATP1510 2.3 0.4 1.0
O1G b:ATP1510 2.3 0.4 1.0
O2G b:ATP1510 2.4 0.4 1.0
PG b:ATP1510 2.7 0.4 1.0
CB b:THR178 3.0 0.6 1.0
N b:THR178 3.1 0.6 1.0
PB b:ATP1510 3.2 0.4 1.0
O3B b:ATP1510 3.3 0.4 1.0
CA b:THR178 3.6 0.6 1.0
OD1 b:ASP271 3.6 0.6 1.0
CB b:LYS177 3.7 0.6 1.0
O1B b:ATP1510 3.9 0.4 1.0
C b:LYS177 3.9 0.6 1.0
O3G b:ATP1510 4.1 0.4 1.0
O2A b:ATP1510 4.1 0.4 1.0
CE b:LYS177 4.2 0.6 1.0
CA b:LYS177 4.2 0.6 1.0
OD2 b:ASP271 4.2 0.6 1.0
CG b:ASP271 4.2 0.6 1.0
CG2 b:THR178 4.3 0.6 1.0
N b:LYS177 4.3 0.6 1.0
NZ b:LYS177 4.5 0.6 1.0
O3A b:ATP1510 4.6 0.4 1.0
CG b:LYS177 4.7 0.6 1.0
CG1 b:VAL328 4.9 0.6 1.0
C b:THR178 4.9 0.6 1.0
O b:LYS177 4.9 0.6 1.0
PA b:ATP1510 5.0 0.4 1.0
CD b:LYS177 5.0 0.6 1.0

Magnesium binding site 8 out of 10 in 4b2q

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Magnesium binding site 8 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Mg1512

b:71.6
occ:1.00
 OG1 c:THR178 2.2 63.7 1.0
O2B c:ATP1511 2.3 71.6 1.0
O1G c:ATP1511 2.4 71.6 1.0
O2G c:ATP1511 2.6 71.6 1.0
PG c:ATP1511 2.9 71.6 1.0
CB c:THR178 3.4 63.7 1.0
PB c:ATP1511 3.4 71.6 1.0
OD2 c:ASP271 3.5 63.7 1.0
O3B c:ATP1511 3.7 71.6 1.0
OD1 c:ASP271 4.1 63.7 1.0
O1B c:ATP1511 4.1 71.6 1.0
CG2 c:THR178 4.2 63.7 1.0
NE2 c:GLN210 4.2 63.7 1.0
CG c:ASP271 4.2 63.7 1.0
O3G c:ATP1511 4.3 71.6 1.0
N c:THR178 4.5 63.7 1.0
CA c:THR178 4.5 63.7 1.0
O2A c:ATP1511 4.7 71.6 1.0
O3A c:ATP1511 4.8 71.6 1.0

Magnesium binding site 9 out of 10 in 4b2q

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Magnesium binding site 9 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Mg1477

b:71.6
occ:1.00
 OG1 d:THR164 2.4 75.0 1.0
O2B d:ADP1476 2.5 71.6 1.0
O1B d:ADP1476 3.0 71.6 1.0
O2A d:ADP1476 3.0 71.6 1.0
PB d:ADP1476 3.2 71.6 1.0
OE1 d:GLU189 3.5 75.0 1.0
CB d:THR164 3.6 75.0 1.0
OE2 d:GLU193 3.9 75.0 1.0
PA d:ADP1476 3.9 71.6 1.0
NH1 d:ARG190 3.9 75.0 1.0
O3A d:ADP1476 4.0 71.6 1.0
N d:THR164 4.3 75.0 1.0
O1A d:ADP1476 4.4 71.6 1.0
CA d:THR164 4.5 75.0 1.0
O3B d:ADP1476 4.5 71.6 1.0
CG2 d:THR164 4.6 75.0 1.0
CD d:GLU189 4.6 75.0 1.0
OE1 d:GLU193 4.7 75.0 1.0
CD d:GLU193 4.7 75.0 1.0
OD2 d:ASP256 5.0 75.0 1.0
CZ d:ARG190 5.0 75.0 1.0

Magnesium binding site 10 out of 10 in 4b2q

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Magnesium binding site 10 out of 10 in the Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Model of the Yeast F1FO-Atp Synthase Dimer Based on Subtomogram Average within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Mg1480

b:0.4
occ:1.00
 O2B f:ADP1479 2.3 0.4 1.0
OG1 f:THR164 2.4 89.4 1.0
OE1 f:GLU189 2.9 89.4 1.0
PB f:ADP1479 3.4 0.4 1.0
CB f:THR164 3.6 89.4 1.0
OD1 f:ASP256 3.7 89.4 1.0
O3B f:ADP1479 3.9 0.4 1.0
CD f:GLU189 3.9 89.4 1.0
O1B f:ADP1479 4.0 0.4 1.0
OD2 f:ASP256 4.0 89.4 1.0
OE1 f:GLU193 4.2 89.4 1.0
NH1 f:ARG190 4.2 89.4 1.0
CG f:ASP256 4.3 89.4 1.0
N f:THR164 4.4 89.4 1.0
OE2 f:GLU189 4.5 89.4 1.0
O2A f:ADP1479 4.5 0.4 1.0
OE2 f:GLU193 4.5 89.4 1.0
CA f:THR164 4.6 89.4 1.0
CG2 f:THR164 4.6 89.4 1.0
NH1 b:ARG375 4.6 0.6 1.0
O3A f:ADP1479 4.7 0.4 1.0
CD f:GLU193 4.8 89.4 1.0
CE f:LYS163 5.0 89.4 1.0

Reference:

K.M.Davies, C.Anselmi, I.Wittig, J.D.Faraldo-Gomez, W.Kuhlbrandt. Structure of the Yeast F1FO-Atp Synthase Dimer and Its Role in Shaping the Mitochondrial Cristae. Proc.Natl.Acad.Sci.Usa V. 109 13602 2012.
ISSN: ISSN 0027-8424
PubMed: 22864911
DOI: 10.1073/PNAS.1204593109
Page generated: Thu Aug 15 15:14:56 2024

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