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Magnesium in PDB 6rdz: Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Composite Map

Enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Composite Map

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

Other elements in 6rdz:

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

Magnesium binding site 1 out of 5 in 6rdz

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


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, Composite Map 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 6rdz

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


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, Composite Map 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 6rdz

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


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, Composite Map 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 6rdz

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Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 2A, Composite Map


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, Composite Map 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 6rdz

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


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, Composite Map 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 15:39:23 2025

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