Atomistry » Magnesium » PDB 6rdk-6rf8 » 6red
Atomistry »
  Magnesium »
    PDB 6rdk-6rf8 »
      6red »

Magnesium in PDB 6red: Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, Focussed Refinement of F1 Head and Rotor

Enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, Focussed Refinement of F1 Head and Rotor

All present enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, Focussed Refinement of F1 Head and Rotor:
7.1.2.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, Focussed Refinement of F1 Head and Rotor (pdb code 6red). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, Focussed Refinement of F1 Head and Rotor, PDB code: 6red:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6red

Go back to Magnesium Binding Sites List in 6red
Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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
 OG1 T:THR232 2.2 32.8 1.0
O3G T:ATP1001 2.3 36.8 1.0
O2B T:ATP1001 2.5 36.8 1.0
OD2 T:ASP325 3.2 34.3 1.0
PG T:ATP1001 3.4 36.8 1.0
CB T:THR232 3.6 32.8 1.0
O1G T:ATP1001 3.6 36.8 1.0
PB T:ATP1001 3.7 36.8 1.0
O3B T:ATP1001 4.0 36.8 1.0
CG T:ASP325 4.0 34.3 1.0
OD1 T:ASP325 4.1 34.3 1.0
CG2 T:THR232 4.2 32.8 1.0
N T:THR232 4.3 32.8 1.0
CA T:THR232 4.5 32.8 1.0
O1B T:ATP1001 4.6 36.8 1.0
OD2 T:ASP326 4.6 36.6 1.0
O2A T:ATP1001 4.7 36.8 1.0
O2G T:ATP1001 4.7 36.8 1.0
NE2 T:GLN264 4.9 32.4 1.0
O3A T:ATP1001 5.0 36.8 1.0

Magnesium binding site 2 out of 5 in 6red

Go back to Magnesium Binding Sites List in 6red
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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
 O3G U:ATP1001 2.2 40.5 1.0
OG1 U:THR232 2.3 33.4 1.0
O1B U:ATP1001 2.6 40.5 1.0
OD1 U:ASP325 3.4 29.5 1.0
PG U:ATP1001 3.4 40.5 1.0
CB U:THR232 3.7 33.4 1.0
PB U:ATP1001 3.7 40.5 1.0
O1G U:ATP1001 3.8 40.5 1.0
O3B U:ATP1001 3.9 40.5 1.0
CG U:ASP325 4.2 29.5 1.0
OD2 U:ASP326 4.2 33.1 1.0
OD1 U:ASP326 4.2 33.1 1.0
OD2 U:ASP325 4.3 29.5 1.0
CG2 U:THR232 4.4 33.4 1.0
NE2 U:GLN264 4.4 29.7 1.0
N U:THR232 4.4 33.4 1.0
CG U:ASP326 4.5 33.1 1.0
O2B U:ATP1001 4.5 40.5 1.0
CA U:THR232 4.6 33.4 1.0
O2G U:ATP1001 4.7 40.5 1.0
O2A U:ATP1001 4.8 40.5 1.0
O3A U:ATP1001 5.0 40.5 1.0
CD U:GLN264 5.0 29.7 1.0

Magnesium binding site 3 out of 5 in 6red

Go back to Magnesium Binding Sites List in 6red
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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
 OG1 V:THR232 2.3 31.3 1.0
O1B V:ATP1001 2.6 37.9 1.0
O1G V:ATP1001 2.7 37.9 1.0
OD1 V:ASP325 3.0 28.7 1.0
O3G V:ATP1001 3.6 37.9 1.0
PG V:ATP1001 3.6 37.9 1.0
CB V:THR232 3.6 31.3 1.0
CG V:ASP325 3.8 28.7 1.0
PB V:ATP1001 3.9 37.9 1.0
OD2 V:ASP325 4.1 28.7 1.0
CG2 V:THR232 4.2 31.3 1.0
O3B V:ATP1001 4.2 37.9 1.0
NE2 V:GLN264 4.3 27.3 1.0
OD2 V:ASP326 4.3 30.1 1.0
O2B V:ATP1001 4.5 37.9 1.0
N V:THR232 4.6 31.3 1.0
CA V:THR232 4.6 31.3 1.0
O1A V:ATP1001 4.9 37.9 1.0
O2G V:ATP1001 5.0 37.9 1.0

Magnesium binding site 4 out of 5 in 6red

Go back to Magnesium Binding Sites List in 6red
Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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
O2B X:ADP601 2.4 43.8 1.0
OE2 X:GLU215 3.1 31.9 1.0
O1B X:ADP601 3.3 43.8 1.0
PB X:ADP601 3.3 43.8 1.0
CB X:THR190 3.5 38.8 1.0
NH1 X:ARG216 3.5 31.4 1.0
OE2 X:GLU219 3.7 35.0 1.0
CD X:GLU215 4.2 31.9 1.0
OE1 X:GLU219 4.2 35.0 1.0
CG2 X:THR190 4.2 38.8 1.0
O3B X:ADP601 4.3 43.8 1.0
N X:THR190 4.4 38.8 1.0
CD X:GLU219 4.4 35.0 1.0
OD1 X:ASP285 4.4 33.0 1.0
OD2 X:ASP285 4.4 33.0 1.0
CA X:THR190 4.5 38.8 1.0
NZ X:LYS189 4.5 36.5 1.0
O1A X:ADP601 4.5 43.8 1.0
ND2 X:ASN286 4.5 31.1 1.0
O3A X:ADP601 4.5 43.8 1.0
CZ X:ARG216 4.7 31.4 1.0
CE X:LYS189 4.8 36.5 1.0
CG X:ASP285 4.8 33.0 1.0
OE1 X:GLU215 4.9 31.9 1.0
PA X:ADP601 4.9 43.8 1.0

Magnesium binding site 5 out of 5 in 6red

Go back to Magnesium Binding Sites List in 6red
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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 Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3A, 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
 O3B Z:ADP601 2.4 36.6 1.0
OG1 Z:THR190 2.4 33.6 1.0
OE1 Z:GLU215 2.6 31.9 1.0
CD Z:GLU215 3.4 31.9 1.0
PB Z:ADP601 3.6 36.6 1.0
CB Z:THR190 3.7 33.6 1.0
NH1 Z:ARG216 3.8 28.6 1.0
O2B Z:ADP601 3.9 36.6 1.0
OE1 Z:GLU219 3.9 32.2 1.0
OE2 Z:GLU219 4.0 32.2 1.0
OE2 Z:GLU215 4.0 31.9 1.0
CG Z:GLU215 4.3 31.9 1.0
OD1 Z:ASP285 4.3 33.9 1.0
O2A Z:ADP601 4.3 36.6 1.0
CG2 Z:THR190 4.4 33.6 1.0
ND2 Z:ASN286 4.4 30.8 1.0
CD Z:GLU219 4.4 32.2 1.0
NZ Z:LYS189 4.5 30.7 1.0
OD2 Z:ASP285 4.5 33.9 1.0
O1B Z:ADP601 4.6 36.6 1.0
O3A Z:ADP601 4.7 36.6 1.0
CG Z:ASP285 4.7 33.9 1.0
CA Z:THR190 4.7 33.6 1.0
N Z:THR190 4.8 33.6 1.0
CZ Z:ARG216 4.8 28.6 1.0
PA Z:ADP601 4.9 36.6 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: Wed Aug 13 15:43:06 2025

Last articles

Mg in 9MOB
Mg in 9MOA
Mg in 9MO8
Mg in 9MO9
Mg in 9MO7
Mg in 9MME
Mg in 9MO6
Mg in 9MO5
Mg in 9MO4
Mg in 9MMI
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy