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Magnesium in PDB 6rd9: Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map

Enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map

All present enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map:
7.1.2.2;

Other elements in 6rd9:

The structure of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map (pdb code 6rd9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map, PDB code: 6rd9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6rd9

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Magnesium binding site 1 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1002

b:43.2
occ:1.00
 OG1 T:THR232 2.0 43.2 1.0
O1G T:ATP1001 2.0 43.0 1.0
O2B T:ATP1001 2.2 43.0 1.0
PG T:ATP1001 3.3 43.0 1.0
CB T:THR232 3.4 43.2 1.0
PB T:ATP1001 3.4 43.0 1.0
O3B T:ATP1001 3.7 43.0 1.0
OD2 T:ASP325 3.7 35.9 1.0
O3G T:ATP1001 3.9 43.0 1.0
CG2 T:THR232 4.0 43.2 1.0
N T:THR232 4.3 43.2 1.0
O1B T:ATP1001 4.3 43.0 1.0
O2A T:ATP1001 4.4 43.0 1.0
CA T:THR232 4.4 43.2 1.0
OD1 T:ASP325 4.4 35.9 1.0
CG T:ASP325 4.4 35.9 1.0
O2G T:ATP1001 4.5 43.0 1.0
O3A T:ATP1001 4.5 43.0 1.0
PA T:ATP1001 4.8 43.0 1.0
O1A T:ATP1001 5.0 43.0 1.0

Magnesium binding site 2 out of 5 in 6rd9

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Magnesium binding site 2 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1002

b:55.7
occ:1.00
 OG1 U:THR232 2.0 45.6 1.0
O3G U:ATP1001 2.1 55.4 1.0
O1B U:ATP1001 2.1 55.4 1.0
PG U:ATP1001 3.3 55.4 1.0
PB U:ATP1001 3.3 55.4 1.0
CB U:THR232 3.4 45.6 1.0
O3B U:ATP1001 3.6 55.4 1.0
O1A U:ATP1001 3.7 55.4 1.0
O1G U:ATP1001 3.9 55.4 1.0
OD1 U:ASP325 3.9 38.6 1.0
CG2 U:THR232 4.0 45.6 1.0
N U:THR232 4.2 45.6 1.0
CA U:THR232 4.3 45.6 1.0
OD2 U:ASP325 4.3 38.6 1.0
O3A U:ATP1001 4.4 55.4 1.0
O2B U:ATP1001 4.4 55.4 1.0
CG U:ASP325 4.5 38.6 1.0
O2G U:ATP1001 4.5 55.4 1.0
PA U:ATP1001 4.5 55.4 1.0

Magnesium binding site 3 out of 5 in 6rd9

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Magnesium binding site 3 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1001

b:43.2
occ:1.00
 OG1 V:THR232 2.0 48.9 1.0
O3G V:ATP1000 2.0 52.2 1.0
O2B V:ATP1000 2.2 52.2 1.0
PG V:ATP1000 3.3 52.2 1.0
CB V:THR232 3.4 48.9 1.0
PB V:ATP1000 3.4 52.2 1.0
O3B V:ATP1000 3.6 52.2 1.0
OD1 V:ASP325 3.7 41.6 1.0
O1G V:ATP1000 4.0 52.2 1.0
N V:THR232 4.0 48.9 1.0
OD2 V:ASP325 4.2 41.6 1.0
CG2 V:THR232 4.2 48.9 1.0
CA V:THR232 4.2 48.9 1.0
CG V:ASP325 4.3 41.6 1.0
O1B V:ATP1000 4.3 52.2 1.0
O2G V:ATP1000 4.5 52.2 1.0
OD2 V:ASP326 4.5 43.5 1.0
O3A V:ATP1000 4.6 52.2 1.0
O2A V:ATP1000 4.6 52.2 1.0

Magnesium binding site 4 out of 5 in 6rd9

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Magnesium binding site 4 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg602

b:46.1
occ:1.00
 O2B X:ADP601 2.1 52.1 1.0
OG1 X:THR190 2.1 46.6 1.0
OE2 X:GLU215 2.4 46.8 1.0
CD X:GLU215 3.4 46.8 1.0
CB X:THR190 3.4 46.6 1.0
PB X:ADP601 3.4 52.1 1.0
NH1 X:ARG216 3.5 43.6 1.0
O2A X:ADP601 3.8 52.1 1.0
O1B X:ADP601 3.9 52.1 1.0
OE1 X:GLU215 4.0 46.8 1.0
OE1 X:GLU219 4.0 51.1 1.0
CG2 X:THR190 4.0 46.6 1.0
OE2 X:GLU219 4.1 51.1 1.0
O3A X:ADP601 4.3 52.1 1.0
CG X:GLU215 4.4 46.8 1.0
O3B X:ADP601 4.4 52.1 1.0
CD X:GLU219 4.5 51.1 1.0
CA X:THR190 4.5 46.6 1.0
PA X:ADP601 4.5 52.1 1.0
N X:THR190 4.5 46.6 1.0
OD2 X:ASP285 4.7 44.9 1.0
CZ X:ARG216 4.7 43.6 1.0
OD1 X:ASP285 4.7 44.9 1.0
ND2 X:ASN286 4.9 40.6 1.0

Magnesium binding site 5 out of 5 in 6rd9

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Magnesium binding site 5 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Composite Map within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg602

b:65.5
occ:1.00
 O3B Y:ADP601 2.0 76.3 1.0
OG1 Y:THR190 2.1 67.8 1.0
OE2 Y:GLU215 3.3 52.5 1.0
PB Y:ADP601 3.4 76.3 1.0
CB Y:THR190 3.5 67.8 1.0
OE2 Y:GLU219 3.6 60.7 1.0
OD2 Y:ASP285 3.6 53.4 1.0
NH1 Y:ARG216 3.9 53.7 1.0
O2B Y:ADP601 4.0 76.3 1.0
CD Y:GLU215 4.1 52.5 1.0
CG2 Y:THR190 4.1 67.8 1.0
O1B Y:ADP601 4.2 76.3 1.0
N Y:THR190 4.2 67.8 1.0
OE1 Y:GLU219 4.3 60.7 1.0
CA Y:THR190 4.4 67.8 1.0
CD Y:GLU219 4.4 60.7 1.0
O3A Y:ADP601 4.5 76.3 1.0
ND2 Y:ASN286 4.5 52.1 1.0
O2A Y:ADP601 4.6 76.3 1.0
CG Y:ASP285 4.6 53.4 1.0
CG Y:GLU215 4.7 52.5 1.0
OD1 Y:ASP285 4.7 53.4 1.0
CE Y:LYS189 4.8 62.5 1.0
OE1 Y:GLU215 4.8 52.5 1.0
PA Y:ADP601 4.9 76.3 1.0
CB Y:LYS189 4.9 62.5 1.0

Reference:

B.J.Murphy, N.Klusch, J.Langer, D.J.Mills, O.Yildiz, W.Kuhlbrandt. Rotary Substates of Mitochondrial Atp Synthase Reveal the Basis of Flexible F1-Focoupling. Science V. 364 2019.
ISSN: ESSN 1095-9203
PubMed: 31221832
DOI: 10.1126/SCIENCE.AAW9128
Page generated: Tue Oct 1 16:42:14 2024

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