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Magnesium in PDB 6rdg: Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, Focussed Refinement of F1 Head and Rotor

Enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, Focussed Refinement of F1 Head and Rotor

All present enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, 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 3, Focussed Refinement of F1 Head and Rotor (pdb code 6rdg). 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 3, Focussed Refinement of F1 Head and Rotor, PDB code: 6rdg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6rdg

Go back to Magnesium Binding Sites List in 6rdg
Magnesium binding site 1 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, 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 3, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1002

b:35.2
occ:1.00
 O T:HOH1107 2.4 30.0 1.0
O3G T:ATP1001 2.4 36.8 1.0
O T:HOH1104 2.5 30.0 1.0
O T:HOH1105 2.5 30.0 1.0
O2B T:ATP1001 2.5 36.8 1.0
OG1 T:THR232 2.6 32.8 1.0
CB T:THR232 3.1 32.8 1.0
OD2 T:ASP325 3.6 34.3 1.0
PG T:ATP1001 3.7 36.8 1.0
PB T:ATP1001 3.7 36.8 1.0
N T:THR232 3.8 32.8 1.0
O3B T:ATP1001 3.8 36.8 1.0
OD1 T:ASP325 3.9 34.3 1.0
CA T:THR232 4.0 32.8 1.0
CG T:ASP325 4.1 34.3 1.0
CG2 T:THR232 4.3 32.8 1.0
O2A T:ATP1001 4.5 36.8 1.0
O1G T:ATP1001 4.6 36.8 1.0
CB T:LYS231 4.7 32.1 1.0
O2G T:ATP1001 4.7 36.8 1.0
O1B T:ATP1001 4.8 36.8 1.0
O T:HOH1101 4.8 30.0 1.0
O3A T:ATP1001 4.8 36.8 1.0
OD2 T:ASP326 4.8 36.6 1.0
O X:HOH702 4.9 30.0 1.0
C T:LYS231 4.9 32.1 1.0

Magnesium binding site 2 out of 5 in 6rdg

Go back to Magnesium Binding Sites List in 6rdg
Magnesium binding site 2 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, 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 3, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1002

b:37.9
occ:1.00
 O U:HOH1105 2.3 30.0 1.0
O1B U:ATP1001 2.3 40.5 1.0
OG1 U:THR232 2.5 33.4 1.0
O3G U:ATP1001 2.6 40.5 1.0
O U:HOH1103 2.8 30.0 1.0
O U:HOH1109 2.9 30.0 1.0
CB U:THR232 3.5 33.4 1.0
PB U:ATP1001 3.7 40.5 1.0
O U:HOH1108 3.7 30.0 1.0
PG U:ATP1001 3.9 40.5 1.0
O3B U:ATP1001 4.0 40.5 1.0
OD1 U:ASP325 4.1 29.5 1.0
O U:HOH1107 4.2 30.0 1.0
O2A U:ATP1001 4.3 40.5 1.0
CG2 U:THR232 4.4 33.4 1.0
O U:HOH1102 4.4 30.0 1.0
OD2 U:ASP325 4.4 29.5 1.0
N U:THR232 4.5 33.4 1.0
CA U:THR232 4.6 33.4 1.0
CG U:ASP325 4.6 29.5 1.0
O3A U:ATP1001 4.6 40.5 1.0
O2B U:ATP1001 4.7 40.5 1.0
NE2 U:GLN264 4.8 29.7 1.0
O1G U:ATP1001 4.8 40.5 1.0
PA U:ATP1001 4.8 40.5 1.0
O2G U:ATP1001 4.8 40.5 1.0
O1A U:ATP1001 4.9 40.5 1.0
OD2 U:ASP326 4.9 33.1 1.0

Magnesium binding site 3 out of 5 in 6rdg

Go back to Magnesium Binding Sites List in 6rdg
Magnesium binding site 3 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, 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 3, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1002

b:31.4
occ:1.00
 O1G V:ATP1001 2.4 37.9 1.0
O V:HOH1103 2.5 30.0 1.0
O1B V:ATP1001 2.6 37.9 1.0
OG1 V:THR232 2.7 31.3 1.0
O V:HOH1108 2.8 30.0 1.0
OD1 V:ASP325 3.4 28.7 1.0
O V:HOH1104 3.7 30.0 1.0
O V:HOH1106 3.7 30.0 1.0
PG V:ATP1001 3.8 37.9 1.0
PB V:ATP1001 3.9 37.9 1.0
O1A V:ATP1001 3.9 37.9 1.0
CB V:THR232 3.9 31.3 1.0
O3B V:ATP1001 4.1 37.9 1.0
CG V:ASP325 4.3 28.7 1.0
OD2 V:ASP325 4.5 28.7 1.0
CG2 V:THR232 4.6 31.3 1.0
O V:HOH1110 4.7 30.0 1.0
NE2 V:GLN264 4.7 27.3 1.0
O3G V:ATP1001 4.7 37.9 1.0
O2G V:ATP1001 4.7 37.9 1.0
O3A V:ATP1001 4.8 37.9 1.0
N V:THR232 4.8 31.3 1.0
O2B V:ATP1001 4.9 37.9 1.0
CD V:GLN264 5.0 27.3 1.0
CA V:THR232 5.0 31.3 1.0

Magnesium binding site 4 out of 5 in 6rdg

Go back to Magnesium Binding Sites List in 6rdg
Magnesium binding site 4 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, 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 3, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg602

b:37.0
occ:1.00
 OG1 X:THR190 2.1 38.8 1.0
O X:HOH701 2.3 30.0 1.0
O2B X:ADP601 2.5 43.8 1.0
OE2 X:GLU215 3.3 31.9 1.0
NH1 X:ARG216 3.4 31.4 1.0
CB X:THR190 3.5 38.8 1.0
OE2 X:GLU219 3.6 35.0 1.0
PB X:ADP601 3.9 43.8 1.0
OE1 X:GLU219 4.2 35.0 1.0
CD X:GLU215 4.2 31.9 1.0
CG2 X:THR190 4.2 38.8 1.0
O1B X:ADP601 4.2 43.8 1.0
CD X:GLU219 4.3 35.0 1.0
N X:THR190 4.4 38.8 1.0
O X:HOH703 4.4 30.0 1.0
OD2 X:ASP285 4.4 33.0 1.0
OD1 X:ASP285 4.5 33.0 1.0
CA X:THR190 4.5 38.8 1.0
ND2 X:ASN286 4.6 31.1 1.0
CZ X:ARG216 4.6 31.4 1.0
O1A X:ADP601 4.7 43.8 1.0
O3B X:ADP601 4.8 43.8 1.0
O3A X:ADP601 4.9 43.8 1.0
NZ X:LYS189 4.9 36.5 1.0
CG X:ASP285 4.9 33.0 1.0
OE1 X:GLU215 4.9 31.9 1.0
CG X:GLU215 4.9 31.9 1.0
CE X:LYS189 5.0 36.5 1.0
O2A X:ADP601 5.0 43.8 1.0

Magnesium binding site 5 out of 5 in 6rdg

Go back to Magnesium Binding Sites List in 6rdg
Magnesium binding site 5 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 3, 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 3, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg602

b:29.1
occ:1.00
 O Z:HOH702 2.2 30.0 1.0
O Z:HOH704 2.3 30.0 1.0
OG1 Z:THR190 2.4 33.6 1.0
O3B Z:ADP601 2.5 36.6 1.0
OE1 Z:GLU215 2.6 31.9 1.0
CD Z:GLU215 3.3 31.9 1.0
O Z:HOH701 3.6 30.0 1.0
CB Z:THR190 3.7 33.6 1.0
OE2 Z:GLU219 3.8 32.2 1.0
PB Z:ADP601 3.9 36.6 1.0
OE2 Z:GLU215 3.9 31.9 1.0
CG Z:GLU215 4.2 31.9 1.0
CG2 Z:THR190 4.2 33.6 1.0
O2B Z:ADP601 4.2 36.6 1.0
OD1 Z:ASP285 4.3 33.9 1.0
ND2 Z:ASN286 4.3 30.8 1.0
OE1 Z:GLU219 4.3 32.2 1.0
O V:HOH1101 4.4 30.0 1.0
CD Z:GLU219 4.5 32.2 1.0
NZ Z:LYS189 4.5 30.7 1.0
CG Z:LYS189 4.6 30.7 1.0
OD2 Z:ASP285 4.6 33.9 1.0
CD Z:LYS189 4.6 30.7 1.0
NH1 Z:ARG216 4.7 28.6 1.0
O3A Z:ADP601 4.8 36.6 1.0
O2A Z:ADP601 4.8 36.6 1.0
CG Z:ASP285 4.8 33.9 1.0
CA Z:THR190 4.8 33.6 1.0
O1B Z:ADP601 4.8 36.6 1.0
N Z:THR190 4.9 33.6 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 16:44:41 2024

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