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Magnesium in PDB 6rdb: Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor

Enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor

All present enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor:
7.1.2.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor (pdb code 6rdb). 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, Focussed Refinement of F1 Head and Rotor, PDB code: 6rdb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6rdb

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Magnesium binding site 1 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor


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, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1002

b:28.1
occ:1.00
 OG1 T:THR232 1.7 28.8 1.0
O1G T:ATP1001 2.0 30.7 1.0
O2B T:ATP1001 2.1 30.7 1.0
O X:HOH705 2.2 30.0 1.0
O T:HOH1105 2.4 30.0 1.0
O T:HOH1101 2.6 30.0 1.0
CB T:THR232 2.9 28.8 1.0
PG T:ATP1001 3.4 30.7 1.0
PB T:ATP1001 3.4 30.7 1.0
CG2 T:THR232 3.6 28.8 1.0
O3B T:ATP1001 3.7 30.7 1.0
OD2 T:ASP325 3.9 25.5 1.0
CA T:THR232 4.0 28.8 1.0
O3G T:ATP1001 4.1 30.7 1.0
N T:THR232 4.2 28.8 1.0
OD1 T:ASP325 4.3 25.5 1.0
O2A T:ATP1001 4.4 30.7 1.0
O X:HOH709 4.4 30.0 1.0
O3A T:ATP1001 4.4 30.7 1.0
O1B T:ATP1001 4.4 30.7 1.0
CG T:ASP325 4.5 25.5 1.0
O2G T:ATP1001 4.5 30.7 1.0
O T:HOH1103 4.5 30.0 1.0
O T:HOH1106 4.5 30.0 1.0
NH2 X:ARG385 4.6 34.7 1.0
PA T:ATP1001 4.7 30.7 1.0
O1A T:ATP1001 4.7 30.7 1.0

Magnesium binding site 2 out of 5 in 6rdb

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Magnesium binding site 2 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor


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, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1002

b:28.1
occ:1.00
 O2B U:ATP1001 2.2 30.7 1.0
O1G U:ATP1001 2.3 30.7 1.0
O U:HOH1105 2.3 30.0 1.0
OG1 U:THR232 2.4 29.6 1.0
O U:HOH1103 2.4 30.0 1.0
O U:HOH1107 2.6 30.0 1.0
OD2 U:ASP325 3.4 29.4 1.0
CB U:THR232 3.5 29.6 1.0
PB U:ATP1001 3.5 30.7 1.0
PG U:ATP1001 3.6 30.7 1.0
O U:HOH1108 3.9 30.0 1.0
O3B U:ATP1001 3.9 30.7 1.0
O U:HOH1102 4.2 50.0 1.0
CG U:ASP325 4.2 29.4 1.0
N U:THR232 4.2 29.6 1.0
OD1 U:ASP325 4.3 29.4 1.0
CG2 U:THR232 4.4 29.6 1.0
O1B U:ATP1001 4.5 30.7 1.0
CA U:THR232 4.5 29.6 1.0
O2G U:ATP1001 4.5 30.7 1.0
O2A U:ATP1001 4.6 30.7 1.0
O U:HOH1109 4.6 30.0 1.0
O3G U:ATP1001 4.6 30.7 1.0
O3A U:ATP1001 4.6 30.7 1.0
O U:HOH1101 4.7 30.0 1.0
OD2 U:ASP326 4.9 28.1 1.0
PA U:ATP1001 5.0 30.7 1.0

Magnesium binding site 3 out of 5 in 6rdb

Go back to Magnesium Binding Sites List in 6rdb
Magnesium binding site 3 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor


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, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1002

b:28.1
occ:1.00
 O V:HOH1106 2.1 30.0 1.0
O1G V:ATP1001 2.2 30.7 1.0
O2B V:ATP1001 2.2 30.7 1.0
OG1 V:THR232 2.3 32.0 1.0
O Y:HOH701 2.5 30.0 1.0
O V:HOH1105 2.6 30.0 1.0
PG V:ATP1001 3.5 30.7 1.0
PB V:ATP1001 3.5 30.7 1.0
CB V:THR232 3.6 32.0 1.0
O3B V:ATP1001 3.6 30.7 1.0
O3G V:ATP1001 4.2 30.7 1.0
OD2 V:ASP325 4.3 26.4 1.0
N V:THR232 4.3 32.0 1.0
CG2 V:THR232 4.4 32.0 1.0
O2A V:ATP1001 4.4 30.7 1.0
O1B V:ATP1001 4.5 30.7 1.0
O3A V:ATP1001 4.5 30.7 1.0
CA V:THR232 4.5 32.0 1.0
O V:HOH1107 4.6 30.0 1.0
O2G V:ATP1001 4.6 30.7 1.0
NH1 Y:ARG385 4.9 46.3 1.0
PA V:ATP1001 4.9 30.7 1.0

Magnesium binding site 4 out of 5 in 6rdb

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Magnesium binding site 4 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor


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, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg602

b:26.4
occ:1.00
 O X:HOH703 0.4 30.0 1.0
OG1 X:THR190 2.1 28.0 1.0
O X:HOH701 2.3 30.0 1.0
O2B X:ADP601 2.4 34.1 1.0
O X:HOH704 2.4 30.0 1.0
OE2 X:GLU215 2.9 24.0 1.0
CB X:THR190 3.4 28.0 1.0
NH1 X:ARG216 3.5 22.7 1.0
PB X:ADP601 3.8 34.1 1.0
CD X:GLU215 3.9 24.0 1.0
OE1 X:GLU219 4.0 26.6 1.0
CG2 X:THR190 4.0 28.0 1.0
O3A X:ADP601 4.4 34.1 1.0
O1B X:ADP601 4.4 34.1 1.0
CA X:THR190 4.5 28.0 1.0
OE2 X:GLU219 4.5 26.6 1.0
N X:THR190 4.5 28.0 1.0
OE1 X:GLU215 4.5 24.0 1.0
CZ X:ARG216 4.6 22.7 1.0
O1A X:ADP601 4.6 34.1 1.0
CD X:GLU219 4.6 26.6 1.0
OD2 X:ASP285 4.6 24.7 1.0
OD1 X:ASP285 4.7 24.7 1.0
CG X:GLU215 4.7 24.0 1.0
OD1 X:ASN286 4.7 23.2 1.0
NH2 X:ARG216 4.8 22.7 1.0
PA X:ADP601 4.9 34.1 1.0
O3B X:ADP601 4.9 34.1 1.0
O X:HOH702 4.9 30.0 1.0
O2A X:ADP601 5.0 34.1 1.0

Magnesium binding site 5 out of 5 in 6rdb

Go back to Magnesium Binding Sites List in 6rdb
Magnesium binding site 5 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor


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, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg602

b:46.6
occ:1.00
 O3B Y:ADP601 2.5 48.8 1.0
O Y:HOH703 2.6 30.0 1.0
O Y:HOH702 2.8 30.0 1.0
O Y:HOH704 2.8 30.0 1.0
OG1 Y:THR190 2.8 45.0 1.0
OE2 Y:GLU215 2.8 32.2 1.0
OE2 Y:GLU219 3.3 35.4 1.0
NH1 Y:ARG216 3.5 31.5 1.0
CD Y:GLU215 3.8 32.2 1.0
OD2 Y:ASP285 3.8 34.0 1.0
PB Y:ADP601 3.8 48.8 1.0
OE1 Y:GLU219 4.0 35.4 1.0
CD Y:GLU219 4.1 35.4 1.0
CB Y:THR190 4.1 45.0 1.0
ND2 Y:ASN286 4.1 33.6 1.0
O2B Y:ADP601 4.2 48.8 1.0
OE1 Y:GLU215 4.5 32.2 1.0
CG Y:GLU215 4.6 32.2 1.0
O2A Y:ADP601 4.7 48.8 1.0
N Y:THR190 4.7 45.0 1.0
CZ Y:ARG216 4.7 31.5 1.0
O1B Y:ADP601 4.8 48.8 1.0
O3A Y:ADP601 4.8 48.8 1.0
NZ Y:LYS189 4.8 42.4 1.0
CG Y:ASP285 4.9 34.0 1.0
O1A Y:ADP601 4.9 48.8 1.0
CA Y:THR190 4.9 45.0 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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