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Magnesium in PDB 6rdx: Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, Monomer-Masked Refinement

Enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, Monomer-Masked Refinement

All present enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, Monomer-Masked Refinement:
7.1.2.2;

Other elements in 6rdx:

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

Magnesium binding site 1 out of 5 in 6rdx

Go back to Magnesium Binding Sites List in 6rdx
Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, 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 1F, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg1002

b:28.1
occ:1.00
 O2B T:ATP1001 2.1 30.7 1.0
OG1 T:THR232 2.4 28.8 1.0
O1G T:ATP1001 2.7 30.7 1.0
O3G T:ATP1001 2.9 30.7 1.0
PG T:ATP1001 3.3 30.7 1.0
PB T:ATP1001 3.4 30.7 1.0
CB T:THR232 3.7 28.8 1.0
O3B T:ATP1001 3.8 30.7 1.0
OD1 T:ASP325 3.9 25.5 1.0
OD2 T:ASP326 4.2 25.6 1.0
O1B T:ATP1001 4.2 30.7 1.0
OD2 T:ASP325 4.2 25.5 1.0
OE1 T:GLN264 4.5 26.6 1.0
CG T:ASP325 4.5 25.5 1.0
CG2 T:THR232 4.5 28.8 1.0
N T:THR232 4.6 28.8 1.0
O3A T:ATP1001 4.6 30.7 1.0
CA T:THR232 4.7 28.8 1.0
O2G T:ATP1001 4.7 30.7 1.0
CD T:GLN264 4.8 26.6 1.0
CG T:ASP326 4.9 25.6 1.0
O2A T:ATP1001 5.0 30.7 1.0

Magnesium binding site 2 out of 5 in 6rdx

Go back to Magnesium Binding Sites List in 6rdx
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, 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 1F, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1002

b:28.1
occ:1.00
 O2B U:ATP1001 2.3 30.7 1.0
OG1 U:THR232 2.4 29.6 1.0
O1G U:ATP1001 2.6 30.7 1.0
PB U:ATP1001 3.4 30.7 1.0
OD2 U:ASP326 3.5 28.1 1.0
PG U:ATP1001 3.6 30.7 1.0
O3G U:ATP1001 3.6 30.7 1.0
O1B U:ATP1001 3.7 30.7 1.0
CB U:THR232 3.9 29.6 1.0
OD1 U:ASP325 3.9 29.4 1.0
O3B U:ATP1001 4.0 30.7 1.0
OE1 U:GLN264 4.0 26.4 1.0
OD2 U:ASP325 4.2 29.4 1.0
CG U:ASP326 4.5 28.1 1.0
CG U:ASP325 4.5 29.4 1.0
N U:THR232 4.5 29.6 1.0
CG2 U:THR232 4.6 29.6 1.0
CA U:THR232 4.7 29.6 1.0
O3A U:ATP1001 4.8 30.7 1.0
NE2 U:GLN264 4.8 26.4 1.0
CD U:GLN264 4.8 26.4 1.0
O2A U:ATP1001 4.9 30.7 1.0
OD1 U:ASP326 4.9 28.1 1.0
CE U:LYS231 4.9 24.4 1.0
O2G U:ATP1001 5.0 30.7 1.0

Magnesium binding site 3 out of 5 in 6rdx

Go back to Magnesium Binding Sites List in 6rdx
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, 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 1F, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1002

b:28.1
occ:1.00
 OG1 V:THR232 2.2 32.0 1.0
O1G V:ATP1001 2.3 30.7 1.0
O2B V:ATP1001 2.5 30.7 1.0
OD1 V:ASP325 3.2 26.4 1.0
PB V:ATP1001 3.2 30.7 1.0
O1B V:ATP1001 3.3 30.7 1.0
PG V:ATP1001 3.5 30.7 1.0
CB V:THR232 3.7 32.0 1.0
O3G V:ATP1001 3.8 30.7 1.0
OD2 V:ASP325 3.8 26.4 1.0
O3B V:ATP1001 3.9 30.7 1.0
CG V:ASP325 3.9 26.4 1.0
OD2 V:ASP326 4.4 27.8 1.0
CG2 V:THR232 4.4 32.0 1.0
N V:THR232 4.4 32.0 1.0
OD1 V:ASP326 4.5 27.8 1.0
CA V:THR232 4.5 32.0 1.0
CG V:ASP326 4.7 27.8 1.0
O3A V:ATP1001 4.7 30.7 1.0
O2G V:ATP1001 4.8 30.7 1.0
NZ V:LYS231 4.8 30.4 1.0
CE V:LYS231 4.9 30.4 1.0

Magnesium binding site 4 out of 5 in 6rdx

Go back to Magnesium Binding Sites List in 6rdx
Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, 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 1F, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg602

b:26.4
occ:1.00
 OE2 X:GLU215 2.1 24.0 1.0
NH1 X:ARG216 2.3 22.7 1.0
OG1 X:THR190 2.4 28.0 1.0
OE1 X:GLU219 2.7 26.6 1.0
O2B X:ADP601 2.8 34.1 1.0
OE2 X:GLU219 3.1 26.6 1.0
CB X:THR190 3.2 28.0 1.0
CD X:GLU215 3.2 24.0 1.0
CD X:GLU219 3.3 26.6 1.0
CZ X:ARG216 3.5 22.7 1.0
CG2 X:THR190 3.5 28.0 1.0
NH2 X:ARG216 4.0 22.7 1.0
CG X:GLU215 4.0 24.0 1.0
OE1 X:GLU215 4.1 24.0 1.0
PB X:ADP601 4.3 34.1 1.0
O1A X:ADP601 4.5 34.1 1.0
NE X:ARG216 4.5 22.7 1.0
CA X:THR190 4.6 28.0 1.0
CB X:GLU215 4.6 24.0 1.0
OD1 X:ASP285 4.6 24.7 1.0
O2A X:ADP601 4.7 34.1 1.0
CG X:GLU219 4.7 26.6 1.0
OD2 X:ASP285 4.8 24.7 1.0
CD X:ARG216 4.8 22.7 1.0
PA X:ADP601 4.9 34.1 1.0
N X:THR190 4.9 28.0 1.0
O3A X:ADP601 5.0 34.1 1.0

Magnesium binding site 5 out of 5 in 6rdx

Go back to Magnesium Binding Sites List in 6rdx
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1F, 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 1F, Monomer-Masked Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg602

b:46.6
occ:1.00
 OE2 Y:GLU215 2.1 32.2 1.0
O3B Y:ADP601 2.3 48.8 1.0
OG1 Y:THR190 2.3 45.0 1.0
OE2 Y:GLU219 2.4 35.4 1.0
CD Y:GLU215 3.3 32.2 1.0
CD Y:GLU219 3.4 35.4 1.0
CB Y:THR190 3.4 45.0 1.0
OE1 Y:GLU219 3.6 35.4 1.0
PB Y:ADP601 3.6 48.8 1.0
NH1 Y:ARG216 3.7 31.5 1.0
OE1 Y:GLU215 4.0 32.2 1.0
CG2 Y:THR190 4.1 45.0 1.0
O1B Y:ADP601 4.2 48.8 1.0
CG Y:GLU215 4.3 32.2 1.0
O2B Y:ADP601 4.4 48.8 1.0
CA Y:THR190 4.6 45.0 1.0
O2A Y:ADP601 4.6 48.8 1.0
OD1 Y:ASP285 4.7 34.0 1.0
N Y:THR190 4.7 45.0 1.0
OD2 Y:ASP285 4.7 34.0 1.0
O3A Y:ADP601 4.7 48.8 1.0
CG Y:GLU219 4.8 35.4 1.0
CZ Y:ARG216 4.9 31.5 1.0
ND2 Y:ASN286 4.9 33.6 1.0
NZ Y:LYS189 4.9 42.4 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 15:39:14 2025

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