Atomistry » Magnesium » PDB 6rdi-6rev » 6rdp
Atomistry »
  Magnesium »
    PDB 6rdi-6rev »
      6rdp »

Magnesium in PDB 6rdp: Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor

Enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor

All present enzymatic activity of Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor:
7.1.2.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor (pdb code 6rdp). 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 1C, Focussed Refinement of F1 Head and Rotor, PDB code: 6rdp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6rdp

Go back to Magnesium Binding Sites List in 6rdp
Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor


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 1C, Focussed Refinement of F1 Head and Rotor 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
O1G T:ATP1001 2.2 30.7 1.0
O2B T:ATP1001 2.3 30.7 1.0
O3G T:ATP1001 2.9 30.7 1.0
PG T:ATP1001 3.0 30.7 1.0
CB T:THR232 3.4 28.8 1.0
PB T:ATP1001 3.5 30.7 1.0
O3B T:ATP1001 3.7 30.7 1.0
OD2 T:ASP325 4.0 25.5 1.0
CG2 T:THR232 4.1 28.8 1.0
O2A T:ATP1001 4.2 30.7 1.0
O2G T:ATP1001 4.4 30.7 1.0
O3A T:ATP1001 4.4 30.7 1.0
N T:THR232 4.5 28.8 1.0
CA T:THR232 4.5 28.8 1.0
OD1 T:ASP325 4.6 25.5 1.0
PA T:ATP1001 4.7 30.7 1.0
O1B T:ATP1001 4.7 30.7 1.0
CG T:ASP325 4.7 25.5 1.0
O1A T:ATP1001 4.8 30.7 1.0

Magnesium binding site 2 out of 5 in 6rdp

Go back to Magnesium Binding Sites List in 6rdp
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor


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 1C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Mg1002

b:28.1
occ:1.00
 O2B U:ATP1001 2.1 30.7 1.0
OG1 U:THR232 2.1 29.6 1.0
O1G U:ATP1001 2.5 30.7 1.0
O3G U:ATP1001 2.6 30.7 1.0
PG U:ATP1001 3.0 30.7 1.0
PB U:ATP1001 3.3 30.7 1.0
CB U:THR232 3.5 29.6 1.0
O3B U:ATP1001 3.6 30.7 1.0
OD2 U:ASP325 3.6 29.4 1.0
O1B U:ATP1001 4.1 30.7 1.0
CG2 U:THR232 4.2 29.6 1.0
N U:THR232 4.3 29.6 1.0
O2G U:ATP1001 4.4 30.7 1.0
O2A U:ATP1001 4.4 30.7 1.0
CA U:THR232 4.4 29.6 1.0
CG U:ASP325 4.4 29.4 1.0
OD1 U:ASP325 4.5 29.4 1.0
O3A U:ATP1001 4.6 30.7 1.0
OD2 U:ASP326 4.7 28.1 1.0
PA U:ATP1001 4.9 30.7 1.0

Magnesium binding site 3 out of 5 in 6rdp

Go back to Magnesium Binding Sites List in 6rdp
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor


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 1C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg1002

b:28.1
occ:1.00
 OG1 V:THR232 2.0 32.0 1.0
O3G V:ATP1001 2.1 30.7 1.0
O2B V:ATP1001 2.3 30.7 1.0
PG V:ATP1001 3.3 30.7 1.0
CB V:THR232 3.3 32.0 1.0
PB V:ATP1001 3.5 30.7 1.0
O1G V:ATP1001 3.7 30.7 1.0
O3B V:ATP1001 3.7 30.7 1.0
CG2 V:THR232 3.9 32.0 1.0
OD2 V:ASP325 4.1 26.4 1.0
O2A V:ATP1001 4.2 30.7 1.0
OD1 V:ASP325 4.3 26.4 1.0
CA V:THR232 4.4 32.0 1.0
N V:THR232 4.4 32.0 1.0
O2G V:ATP1001 4.6 30.7 1.0
O3A V:ATP1001 4.6 30.7 1.0
CG V:ASP325 4.6 26.4 1.0
NH1 Y:ARG385 4.6 46.3 1.0
O1B V:ATP1001 4.6 30.7 1.0
PA V:ATP1001 4.8 30.7 1.0
NE2 V:GLN264 4.9 28.7 1.0
OD2 V:ASP326 4.9 27.8 1.0

Magnesium binding site 4 out of 5 in 6rdp

Go back to Magnesium Binding Sites List in 6rdp
Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor


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 1C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg602

b:26.4
occ:1.00
 OG1 X:THR190 2.3 28.0 1.0
O2B X:ADP601 2.4 34.1 1.0
OE2 X:GLU215 2.6 24.0 1.0
CD X:GLU215 3.5 24.0 1.0
CB X:THR190 3.6 28.0 1.0
PB X:ADP601 3.7 34.1 1.0
NH1 X:ARG216 3.7 22.7 1.0
O3B X:ADP601 3.9 34.1 1.0
OE2 X:GLU219 4.1 26.6 1.0
OE1 X:GLU219 4.2 26.6 1.0
OE1 X:GLU215 4.2 24.0 1.0
OD1 X:ASP285 4.3 24.7 1.0
OD2 X:ASP285 4.3 24.7 1.0
CG2 X:THR190 4.3 28.0 1.0
ND2 X:ASN286 4.4 23.2 1.0
CG X:GLU215 4.4 24.0 1.0
N X:THR190 4.6 28.0 1.0
CD X:GLU219 4.6 26.6 1.0
CA X:THR190 4.6 28.0 1.0
O3A X:ADP601 4.6 34.1 1.0
CG X:ASP285 4.6 24.7 1.0
CZ X:ARG216 4.7 22.7 1.0
O1B X:ADP601 4.7 34.1 1.0
NH2 X:ARG216 4.9 22.7 1.0
O1A X:ADP601 5.0 34.1 1.0
O2A X:ADP601 5.0 34.1 1.0

Magnesium binding site 5 out of 5 in 6rdp

Go back to Magnesium Binding Sites List in 6rdp
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Polytomella F-Atp Synthase, Rotary Substate 1C, Focussed Refinement of F1 Head and Rotor


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 1C, Focussed Refinement of F1 Head and Rotor within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg602

b:46.6
occ:1.00
 OG1 Y:THR190 2.3 45.0 1.0
O3B Y:ADP601 2.3 48.8 1.0
OE2 Y:GLU215 2.5 32.2 1.0
OE2 Y:GLU219 3.4 35.4 1.0
CD Y:GLU215 3.4 32.2 1.0
PB Y:ADP601 3.7 48.8 1.0
CB Y:THR190 3.7 45.0 1.0
NH1 Y:ARG216 3.8 31.5 1.0
OE1 Y:GLU215 4.1 32.2 1.0
OD2 Y:ASP285 4.1 34.0 1.0
OE1 Y:GLU219 4.2 35.4 1.0
CD Y:GLU219 4.2 35.4 1.0
CG Y:GLU215 4.2 32.2 1.0
CG2 Y:THR190 4.3 45.0 1.0
O1B Y:ADP601 4.3 48.8 1.0
OD1 Y:ASP285 4.3 34.0 1.0
O2B Y:ADP601 4.4 48.8 1.0
N Y:THR190 4.5 45.0 1.0
CG Y:ASP285 4.6 34.0 1.0
CA Y:THR190 4.6 45.0 1.0
ND2 Y:ASN286 4.7 33.6 1.0
O3A Y:ADP601 4.8 48.8 1.0
O2A Y:ADP601 4.9 48.8 1.0
CE Y:LYS189 5.0 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: Tue Oct 1 16:47:21 2024

Last articles

Cl in 8SMQ
Cl in 8SQO
Cl in 8SPI
Cl in 8SQP
Cl in 8SPG
Cl in 8SPH
Cl in 8SP4
Cl in 8SPD
Cl in 8SP8
Cl in 8SPC
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy