Atomistry » Magnesium » PDB 6rdk-6rf8 » 6re0
Atomistry »
  Magnesium »
    PDB 6rdk-6rf8 »
      6re0 »

Magnesium in PDB 6re0: Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement

Enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement

All present enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement:
7.1.2.2;

Other elements in 6re0:

The structure of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement (pdb code 6re0). 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 2A, Monomer-Masked Refinement, PDB code: 6re0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6re0

Go back to Magnesium Binding Sites List in 6re0
Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement


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 2A, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1002

b:15.0
occ:1.00
 OG1 T:THR232 2.3 13.0 1.0
O1G T:ATP1001 2.4 29.9 1.0
O2B T:ATP1001 2.5 29.9 1.0
OD2 T:ASP325 3.4 16.0 1.0
PG T:ATP1001 3.4 29.9 1.0
PB T:ATP1001 3.5 29.9 1.0
O3G T:ATP1001 3.6 29.9 1.0
CB T:THR232 3.7 13.0 1.0
O3B T:ATP1001 3.9 29.9 1.0
O1B T:ATP1001 4.0 29.9 1.0
OD2 T:ASP326 4.0 11.8 1.0
NE2 T:GLN264 4.1 10.9 1.0
CG T:ASP325 4.2 16.0 1.0
OD1 T:ASP325 4.2 16.0 1.0
CG2 T:THR232 4.3 13.0 1.0
N T:THR232 4.4 13.0 1.0
CA T:THR232 4.6 13.0 1.0
CE T:LYS231 4.7 9.7 1.0
O2G T:ATP1001 4.8 29.9 1.0
CG T:ASP326 4.9 11.8 1.0
O3A T:ATP1001 4.9 29.9 1.0

Magnesium binding site 2 out of 5 in 6re0

Go back to Magnesium Binding Sites List in 6re0
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement


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 2A, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1002

b:13.6
occ:1.00
 OG1 U:THR232 2.3 19.0 1.0
O1B U:ATP1001 2.5 29.1 1.0
O1G U:ATP1001 2.7 29.1 1.0
PB U:ATP1001 3.6 29.1 1.0
PG U:ATP1001 3.7 29.1 1.0
OD1 U:ASP325 3.7 18.2 1.0
O3G U:ATP1001 3.7 29.1 1.0
CB U:THR232 3.7 19.0 1.0
OD2 U:ASP325 3.9 18.2 1.0
O2B U:ATP1001 3.9 29.1 1.0
CG U:ASP325 4.1 18.2 1.0
O3B U:ATP1001 4.1 29.1 1.0
OE1 U:GLN264 4.3 15.6 1.0
N U:THR232 4.3 19.0 1.0
CG2 U:THR232 4.4 19.0 1.0
CA U:THR232 4.5 19.0 1.0
CE U:LYS231 4.8 18.6 1.0
OD1 U:ASP326 4.9 15.3 1.0
O3A U:ATP1001 4.9 29.1 1.0
CD U:GLN264 5.0 15.6 1.0

Magnesium binding site 3 out of 5 in 6re0

Go back to Magnesium Binding Sites List in 6re0
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement


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 2A, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1002

b:13.2
occ:1.00
 OG1 V:THR232 2.3 13.8 1.0
O3B V:ATP1001 2.4 24.7 1.0
O1G V:ATP1001 2.6 24.7 1.0
O2B V:ATP1001 3.0 24.7 1.0
PG V:ATP1001 3.0 24.7 1.0
PB V:ATP1001 3.1 24.7 1.0
O3A V:ATP1001 3.2 24.7 1.0
CB V:THR232 3.4 13.8 1.0
O2G V:ATP1001 3.8 24.7 1.0
CG2 V:THR232 4.0 13.8 1.0
O3G V:ATP1001 4.3 24.7 1.0
O1A V:ATP1001 4.4 24.7 1.0
PA V:ATP1001 4.5 24.7 1.0
O1B V:ATP1001 4.5 24.7 1.0
CA V:THR232 4.6 13.8 1.0
N V:THR232 4.6 13.8 1.0
OD1 V:ASP325 4.6 8.2 1.0
OE1 V:GLN264 4.7 9.9 1.0
OD1 V:ASP326 5.0 8.2 1.0

Magnesium binding site 4 out of 5 in 6re0

Go back to Magnesium Binding Sites List in 6re0
Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement


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 2A, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg602

b:10.2
occ:1.00
 O3B Y:ADP601 2.2 17.0 1.0
OG1 Y:THR190 2.5 11.0 1.0
OE1 Y:GLU215 3.0 10.6 1.0
OE2 Y:GLU219 3.5 11.7 1.0
PB Y:ADP601 3.5 17.0 1.0
CD Y:GLU215 3.6 10.6 1.0
CB Y:THR190 3.7 11.0 1.0
NH1 Y:ARG216 3.8 11.4 1.0
OE1 Y:GLU219 3.9 11.7 1.0
O2B Y:ADP601 3.9 17.0 1.0
CG Y:GLU215 4.0 10.6 1.0
O2A Y:ADP601 4.1 17.0 1.0
CD Y:GLU219 4.1 11.7 1.0
CG2 Y:THR190 4.2 11.0 1.0
OD1 Y:ASP285 4.2 10.2 1.0
OE2 Y:GLU215 4.3 10.6 1.0
O1B Y:ADP601 4.4 17.0 1.0
OD2 Y:ASP285 4.5 10.2 1.0
O3A Y:ADP601 4.6 17.0 1.0
CZ Y:ARG216 4.6 11.4 1.0
ND2 Y:ASN286 4.7 12.0 1.0
CG Y:ASP285 4.7 10.2 1.0
NH2 Y:ARG216 4.9 11.4 1.0
PA Y:ADP601 4.9 17.0 1.0
CA Y:THR190 4.9 11.0 1.0
CB Y:GLU215 4.9 10.6 1.0
N Y:THR190 5.0 11.0 1.0

Magnesium binding site 5 out of 5 in 6re0

Go back to Magnesium Binding Sites List in 6re0
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Monomer-Masked Refinement


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 2A, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg602

b:28.9
occ:1.00
 OG1 Z:THR190 2.2 30.0 1.0
O3B Z:ADP601 2.4 35.2 1.0
OE2 Z:GLU219 3.2 20.4 1.0
OE1 Z:GLU215 3.3 17.4 1.0
CB Z:THR190 3.6 30.0 1.0
PB Z:ADP601 3.8 35.2 1.0
CD Z:GLU215 3.8 17.4 1.0
NH1 Z:ARG216 3.8 17.6 1.0
ND2 Z:ASN286 3.9 18.7 1.0
OE1 Z:GLU219 3.9 20.4 1.0
CD Z:GLU219 4.0 20.4 1.0
O2B Z:ADP601 4.2 35.2 1.0
OE2 Z:GLU215 4.2 17.4 1.0
CG2 Z:THR190 4.3 30.0 1.0
OD1 Z:ASP285 4.3 17.6 1.0
OD2 Z:ASP285 4.4 17.6 1.0
O3A Z:ADP601 4.4 35.2 1.0
N Z:THR190 4.5 30.0 1.0
CA Z:THR190 4.6 30.0 1.0
CG Z:GLU215 4.6 17.4 1.0
O2A Z:ADP601 4.7 35.2 1.0
NZ Z:LYS189 4.7 27.4 1.0
CG Z:ASP285 4.8 17.6 1.0
NH2 V:ARG429 4.9 31.5 1.0
O1B Z:ADP601 4.9 35.2 1.0
PA Z:ADP601 4.9 35.2 1.0
CG Z:ASN286 5.0 18.7 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 15:40:09 2025

Last articles

Mg in 7EFN
Mg in 7EFM
Mg in 7EFL
Mg in 7EDZ
Mg in 7EF6
Mg in 7EF7
Mg in 7EDX
Mg in 7ED9
Mg in 7ED6
Mg in 7EDD
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy