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

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

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

Other elements in 6rdu:

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

Magnesium binding site 1 out of 5 in 6rdu

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

b:28.1
occ:1.00
 OG1 T:THR232 2.1 28.8 1.0
O2B T:ATP1001 2.5 30.7 1.0
OD2 T:ASP325 3.1 25.5 1.0
O1G T:ATP1001 3.2 30.7 1.0
CB T:THR232 3.5 28.8 1.0
PB T:ATP1001 3.7 30.7 1.0
O3G T:ATP1001 3.8 30.7 1.0
CG T:ASP325 3.9 25.5 1.0
PG T:ATP1001 4.0 30.7 1.0
OD1 T:ASP325 4.0 25.5 1.0
N T:THR232 4.1 28.8 1.0
CG2 T:THR232 4.2 28.8 1.0
OD2 T:ASP326 4.2 25.6 1.0
O1B T:ATP1001 4.2 30.7 1.0
CA T:THR232 4.2 28.8 1.0
NE2 T:GLN264 4.4 26.6 1.0
O3B T:ATP1001 4.4 30.7 1.0
CB T:LYS231 4.8 26.2 1.0
CE T:LYS231 5.0 26.2 1.0
C T:LYS231 5.0 26.2 1.0

Magnesium binding site 2 out of 5 in 6rdu

Go back to Magnesium Binding Sites List in 6rdu
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1E, 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 1E, 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 2.2 30.7 1.0
OG1 U:THR232 2.3 29.6 1.0
O1G U:ATP1001 2.7 30.7 1.0
O3G U:ATP1001 3.0 30.7 1.0
PG U:ATP1001 3.3 30.7 1.0
PB U:ATP1001 3.5 30.7 1.0
CB U:THR232 3.5 29.6 1.0
OD2 U:ASP325 3.7 29.4 1.0
O3B U:ATP1001 3.9 30.7 1.0
NE2 U:GLN264 4.1 26.4 1.0
CG2 U:THR232 4.1 29.6 1.0
O1B U:ATP1001 4.2 30.7 1.0
O2A U:ATP1001 4.3 30.7 1.0
OE1 U:GLN264 4.5 26.4 1.0
CG U:ASP325 4.6 29.4 1.0
CA U:THR232 4.7 29.6 1.0
OD1 U:ASP325 4.7 29.4 1.0
O3A U:ATP1001 4.7 30.7 1.0
N U:THR232 4.7 29.6 1.0
O2G U:ATP1001 4.7 30.7 1.0
CD U:GLN264 4.8 26.4 1.0
OD2 U:ASP326 4.9 28.1 1.0
PA U:ATP1001 5.0 30.7 1.0

Magnesium binding site 3 out of 5 in 6rdu

Go back to Magnesium Binding Sites List in 6rdu
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1E, 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 1E, 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 2.1 32.0 1.0
O1G V:ATP1001 2.3 30.7 1.0
O2B V:ATP1001 3.2 30.7 1.0
OD1 V:ASP325 3.4 26.4 1.0
CB V:THR232 3.4 32.0 1.0
PG V:ATP1001 3.7 30.7 1.0
OE1 V:GLN264 3.8 28.7 1.0
OD2 V:ASP325 3.9 26.4 1.0
CG V:ASP325 4.0 26.4 1.0
CG2 V:THR232 4.0 32.0 1.0
O2G V:ATP1001 4.1 30.7 1.0
OD2 V:ASP326 4.3 27.8 1.0
O3B V:ATP1001 4.4 30.7 1.0
PB V:ATP1001 4.4 30.7 1.0
CA V:THR232 4.4 32.0 1.0
OD1 V:ASP326 4.4 27.8 1.0
CD V:GLN264 4.5 28.7 1.0
N V:THR232 4.5 32.0 1.0
CG V:ASP326 4.7 27.8 1.0
O3G V:ATP1001 4.8 30.7 1.0
NE2 V:GLN264 4.9 28.7 1.0
OH V:TYR259 4.9 22.2 1.0
O2A V:ATP1001 5.0 30.7 1.0

Magnesium binding site 4 out of 5 in 6rdu

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

b:26.4
occ:1.00
 O2B X:ADP601 2.3 34.1 1.0
OG1 X:THR190 2.4 28.0 1.0
OE2 X:GLU215 3.1 24.0 1.0
PB X:ADP601 3.5 34.1 1.0
CB X:THR190 3.8 28.0 1.0
O1B X:ADP601 3.8 34.1 1.0
CD X:GLU215 3.9 24.0 1.0
NH1 X:ARG216 4.0 22.7 1.0
OD2 X:ASP285 4.2 24.7 1.0
O3B X:ADP601 4.3 34.1 1.0
OE2 X:GLU219 4.4 26.6 1.0
CG X:GLU215 4.5 24.0 1.0
CG2 X:THR190 4.5 28.0 1.0
OE1 X:GLU215 4.5 24.0 1.0
N X:THR190 4.6 28.0 1.0
O1A X:ADP601 4.6 34.1 1.0
OE1 X:GLU219 4.6 26.6 1.0
NZ X:LYS189 4.7 24.2 1.0
CA X:THR190 4.7 28.0 1.0
O3A X:ADP601 4.7 34.1 1.0
OD1 X:ASP285 4.8 24.7 1.0
CG X:ASP285 4.9 24.7 1.0
CG X:LYS189 4.9 24.2 1.0
CE X:LYS189 4.9 24.2 1.0
ND2 X:ASN286 4.9 23.2 1.0
CD X:GLU219 5.0 26.6 1.0
PA X:ADP601 5.0 34.1 1.0
CZ X:ARG216 5.0 22.7 1.0

Magnesium binding site 5 out of 5 in 6rdu

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

b:46.6
occ:1.00
 O3B Y:ADP601 2.3 48.8 1.0
OG1 Y:THR190 2.4 45.0 1.0
OE2 Y:GLU215 3.1 32.2 1.0
NH1 Y:ARG216 3.5 31.5 1.0
PB Y:ADP601 3.6 48.8 1.0
OE2 Y:GLU219 3.6 35.4 1.0
CB Y:THR190 3.8 45.0 1.0
CD Y:GLU215 3.8 32.2 1.0
O2B Y:ADP601 4.0 48.8 1.0
OE1 Y:GLU219 4.3 35.4 1.0
CD Y:GLU219 4.3 35.4 1.0
O1B Y:ADP601 4.3 48.8 1.0
OE1 Y:GLU215 4.4 32.2 1.0
ND2 Y:ASN286 4.4 33.6 1.0
O2A Y:ADP601 4.4 48.8 1.0
CZ Y:ARG216 4.4 31.5 1.0
CG2 Y:THR190 4.4 45.0 1.0
OD1 Y:ASP285 4.5 34.0 1.0
CG Y:GLU215 4.5 32.2 1.0
NZ Y:LYS189 4.7 42.4 1.0
NH2 Y:ARG216 4.7 31.5 1.0
N Y:THR190 4.7 45.0 1.0
O3A Y:ADP601 4.8 48.8 1.0
OD2 Y:ASP285 4.8 34.0 1.0
CA Y:THR190 4.8 45.0 1.0
PA Y:ADP601 4.9 48.8 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: Mon Dec 14 23:57:46 2020

Last articles

Cl in 6COG
Cl in 6CST
Cl in 6CTW
Cl in 6CTZ
Cl in 6CTT
Cl in 6CSP
Cl in 6CU9
Cl in 6CTX
Cl in 6CTU
Cl in 6CTP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy