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Magnesium in PDB 6ref: Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, Monomer-Masked Refinement

Enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, Monomer-Masked Refinement

All present enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, Monomer-Masked Refinement:
7.1.2.2;

Other elements in 6ref:

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

Magnesium binding site 1 out of 5 in 6ref

Go back to Magnesium Binding Sites List in 6ref
Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, 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 3B, Monomer-Masked Refinement 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 2.6 36.8 1.0
OD2 T:ASP325 3.1 34.3 1.0
CB T:THR232 3.5 32.8 1.0
PG T:ATP1001 3.6 36.8 1.0
PB T:ATP1001 3.9 36.8 1.0
O3B T:ATP1001 4.0 36.8 1.0
CG2 T:THR232 4.1 32.8 1.0
CG T:ASP325 4.1 34.3 1.0
O1G T:ATP1001 4.2 36.8 1.0
NE2 T:GLN264 4.3 32.4 1.0
O2A T:ATP1001 4.4 36.8 1.0
OD1 T:ASP325 4.4 34.3 1.0
CA T:THR232 4.6 32.8 1.0
N T:THR232 4.6 32.8 1.0
O1B T:ATP1001 4.8 36.8 1.0
O2G T:ATP1001 4.8 36.8 1.0
OD2 T:ASP326 4.8 36.6 1.0
CD T:GLN264 5.0 32.4 1.0
O3A T:ATP1001 5.0 36.8 1.0

Magnesium binding site 2 out of 5 in 6ref

Go back to Magnesium Binding Sites List in 6ref
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, 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 3B, Monomer-Masked Refinement 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 2.2 33.4 1.0
O1B U:ATP1001 2.5 40.5 1.0
OD1 U:ASP325 3.5 29.5 1.0
PG U:ATP1001 3.6 40.5 1.0
CB U:THR232 3.6 33.4 1.0
PB U:ATP1001 3.7 40.5 1.0
O3B U:ATP1001 3.9 40.5 1.0
OD2 U:ASP325 4.1 29.5 1.0
CG U:ASP325 4.2 29.5 1.0
O1G U:ATP1001 4.2 40.5 1.0
OD1 U:ASP326 4.3 33.1 1.0
CG2 U:THR232 4.3 33.4 1.0
OD2 U:ASP326 4.4 33.1 1.0
O2B U:ATP1001 4.4 40.5 1.0
N U:THR232 4.5 33.4 1.0
CA U:THR232 4.6 33.4 1.0
O2A U:ATP1001 4.6 40.5 1.0
CG U:ASP326 4.7 33.1 1.0
O2G U:ATP1001 4.7 40.5 1.0
NE2 U:GLN264 4.8 29.7 1.0
O3A U:ATP1001 4.9 40.5 1.0

Magnesium binding site 3 out of 5 in 6ref

Go back to Magnesium Binding Sites List in 6ref
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, 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 3B, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1002

b:31.4
occ:1.00
 OG1 V:THR232 2.2 31.3 1.0
O1B V:ATP1001 2.5 37.9 1.0
O3G V:ATP1001 2.7 37.9 1.0
O1G V:ATP1001 3.1 37.9 1.0
PG V:ATP1001 3.4 37.9 1.0
OD2 V:ASP325 3.5 28.7 1.0
CB V:THR232 3.5 31.3 1.0
PB V:ATP1001 3.8 37.9 1.0
OD1 V:ASP325 4.0 28.7 1.0
CG2 V:THR232 4.0 31.3 1.0
O3B V:ATP1001 4.1 37.9 1.0
O1A V:ATP1001 4.1 37.9 1.0
CG V:ASP325 4.1 28.7 1.0
OD2 V:ASP326 4.2 30.1 1.0
NE2 V:GLN264 4.5 27.3 1.0
CA V:THR232 4.6 31.3 1.0
N V:THR232 4.6 31.3 1.0
O2B V:ATP1001 4.8 37.9 1.0
O2G V:ATP1001 4.8 37.9 1.0
CG V:ASP326 4.9 30.1 1.0
CD V:GLN264 4.9 27.3 1.0
O3A V:ATP1001 4.9 37.9 1.0

Magnesium binding site 4 out of 5 in 6ref

Go back to Magnesium Binding Sites List in 6ref
Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, 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 3B, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg602

b:37.0
occ:1.00
 OG1 X:THR190 2.3 38.8 1.0
O2B X:ADP601 2.3 43.8 1.0
OE2 X:GLU215 3.1 31.9 1.0
PB X:ADP601 3.5 43.8 1.0
OE2 X:GLU219 3.6 35.0 1.0
CB X:THR190 3.7 38.8 1.0
NH1 X:ARG216 3.7 31.4 1.0
CD X:GLU215 3.9 31.9 1.0
O1B X:ADP601 4.0 43.8 1.0
OE1 X:GLU219 4.1 35.0 1.0
O3B X:ADP601 4.3 43.8 1.0
CD X:GLU219 4.3 35.0 1.0
OD1 X:ASP285 4.3 33.0 1.0
ND2 X:ASN286 4.3 31.1 1.0
CG2 X:THR190 4.4 38.8 1.0
N X:THR190 4.4 38.8 1.0
OD2 X:ASP285 4.4 33.0 1.0
OE1 X:GLU215 4.4 31.9 1.0
O1A X:ADP601 4.5 43.8 1.0
CA X:THR190 4.6 38.8 1.0
CG X:GLU215 4.6 31.9 1.0
O3A X:ADP601 4.7 43.8 1.0
CG X:ASP285 4.8 33.0 1.0
CE X:LYS189 4.9 36.5 1.0

Magnesium binding site 5 out of 5 in 6ref

Go back to Magnesium Binding Sites List in 6ref
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 3B, 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 3B, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg602

b:29.1
occ:1.00
 OG1 Z:THR190 2.3 33.6 1.0
OE1 Z:GLU215 2.3 31.9 1.0
O3B Z:ADP601 2.3 36.6 1.0
NH1 Z:ARG216 3.0 28.6 1.0
CD Z:GLU215 3.1 31.9 1.0
OE2 Z:GLU215 3.6 31.9 1.0
CB Z:THR190 3.6 33.6 1.0
OE1 Z:GLU219 3.6 32.2 1.0
O2A Z:ADP601 3.7 36.6 1.0
PB Z:ADP601 3.7 36.6 1.0
OE2 Z:GLU219 3.8 32.2 1.0
CG2 Z:THR190 4.1 33.6 1.0
CD Z:GLU219 4.1 32.2 1.0
O2B Z:ADP601 4.2 36.6 1.0
CG Z:GLU215 4.2 31.9 1.0
CZ Z:ARG216 4.2 28.6 1.0
OD2 Z:ASP285 4.5 33.9 1.0
O3A Z:ADP601 4.6 36.6 1.0
NH2 Z:ARG216 4.6 28.6 1.0
PA Z:ADP601 4.6 36.6 1.0
ND2 Z:ASN286 4.7 30.8 1.0
OD1 Z:ASP285 4.7 33.9 1.0
CA Z:THR190 4.7 33.6 1.0
O1B Z:ADP601 4.8 36.6 1.0
N Z:THR190 4.8 33.6 1.0
CG Z:ASP285 5.0 33.9 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 15:43:13 2025

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