Atomistry » Magnesium » PDB 6r5l-6rdg » 6rdb
Atomistry »
  Magnesium »
    PDB 6r5l-6rdg »
      6rdb »

Magnesium in PDB 6rdb: Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor

Enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor

All present enzymatic activity of Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor:
7.1.2.2;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor (pdb code 6rdb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, Focussed Refinement of F1 Head and Rotor, PDB code: 6rdb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6rdb

Go back to Magnesium Binding Sites List in 6rdb
Magnesium binding site 1 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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 Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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 1.7 28.8 1.0
O1G T:ATP1001 2.0 30.7 1.0
O2B T:ATP1001 2.1 30.7 1.0
O X:HOH705 2.2 30.0 1.0
O T:HOH1105 2.4 30.0 1.0
O T:HOH1101 2.6 30.0 1.0
CB T:THR232 2.9 28.8 1.0
PG T:ATP1001 3.4 30.7 1.0
PB T:ATP1001 3.4 30.7 1.0
CG2 T:THR232 3.6 28.8 1.0
O3B T:ATP1001 3.7 30.7 1.0
OD2 T:ASP325 3.9 25.5 1.0
CA T:THR232 4.0 28.8 1.0
O3G T:ATP1001 4.1 30.7 1.0
N T:THR232 4.2 28.8 1.0
OD1 T:ASP325 4.3 25.5 1.0
O2A T:ATP1001 4.4 30.7 1.0
O X:HOH709 4.4 30.0 1.0
O3A T:ATP1001 4.4 30.7 1.0
O1B T:ATP1001 4.4 30.7 1.0
CG T:ASP325 4.5 25.5 1.0
O2G T:ATP1001 4.5 30.7 1.0
O T:HOH1103 4.5 30.0 1.0
O T:HOH1106 4.5 30.0 1.0
NH2 X:ARG385 4.6 34.7 1.0
PA T:ATP1001 4.7 30.7 1.0
O1A T:ATP1001 4.7 30.7 1.0

Magnesium binding site 2 out of 5 in 6rdb

Go back to Magnesium Binding Sites List in 6rdb
Magnesium binding site 2 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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 Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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 2.2 30.7 1.0
O1G U:ATP1001 2.3 30.7 1.0
O U:HOH1105 2.3 30.0 1.0
OG1 U:THR232 2.4 29.6 1.0
O U:HOH1103 2.4 30.0 1.0
O U:HOH1107 2.6 30.0 1.0
OD2 U:ASP325 3.4 29.4 1.0
CB U:THR232 3.5 29.6 1.0
PB U:ATP1001 3.5 30.7 1.0
PG U:ATP1001 3.6 30.7 1.0
O U:HOH1108 3.9 30.0 1.0
O3B U:ATP1001 3.9 30.7 1.0
O U:HOH1102 4.2 50.0 1.0
CG U:ASP325 4.2 29.4 1.0
N U:THR232 4.2 29.6 1.0
OD1 U:ASP325 4.3 29.4 1.0
CG2 U:THR232 4.4 29.6 1.0
O1B U:ATP1001 4.5 30.7 1.0
CA U:THR232 4.5 29.6 1.0
O2G U:ATP1001 4.5 30.7 1.0
O2A U:ATP1001 4.6 30.7 1.0
O U:HOH1109 4.6 30.0 1.0
O3G U:ATP1001 4.6 30.7 1.0
O3A U:ATP1001 4.6 30.7 1.0
O U:HOH1101 4.7 30.0 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 6rdb

Go back to Magnesium Binding Sites List in 6rdb
Magnesium binding site 3 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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 Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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
 O V:HOH1106 2.1 30.0 1.0
O1G V:ATP1001 2.2 30.7 1.0
O2B V:ATP1001 2.2 30.7 1.0
OG1 V:THR232 2.3 32.0 1.0
O Y:HOH701 2.5 30.0 1.0
O V:HOH1105 2.6 30.0 1.0
PG V:ATP1001 3.5 30.7 1.0
PB V:ATP1001 3.5 30.7 1.0
CB V:THR232 3.6 32.0 1.0
O3B V:ATP1001 3.6 30.7 1.0
O3G V:ATP1001 4.2 30.7 1.0
OD2 V:ASP325 4.3 26.4 1.0
N V:THR232 4.3 32.0 1.0
CG2 V:THR232 4.4 32.0 1.0
O2A V:ATP1001 4.4 30.7 1.0
O1B V:ATP1001 4.5 30.7 1.0
O3A V:ATP1001 4.5 30.7 1.0
CA V:THR232 4.5 32.0 1.0
O V:HOH1107 4.6 30.0 1.0
O2G V:ATP1001 4.6 30.7 1.0
NH1 Y:ARG385 4.9 46.3 1.0
PA V:ATP1001 4.9 30.7 1.0

Magnesium binding site 4 out of 5 in 6rdb

Go back to Magnesium Binding Sites List in 6rdb
Magnesium binding site 4 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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 Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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
 O X:HOH703 0.4 30.0 1.0
OG1 X:THR190 2.1 28.0 1.0
O X:HOH701 2.3 30.0 1.0
O2B X:ADP601 2.4 34.1 1.0
O X:HOH704 2.4 30.0 1.0
OE2 X:GLU215 2.9 24.0 1.0
CB X:THR190 3.4 28.0 1.0
NH1 X:ARG216 3.5 22.7 1.0
PB X:ADP601 3.8 34.1 1.0
CD X:GLU215 3.9 24.0 1.0
OE1 X:GLU219 4.0 26.6 1.0
CG2 X:THR190 4.0 28.0 1.0
O3A X:ADP601 4.4 34.1 1.0
O1B X:ADP601 4.4 34.1 1.0
CA X:THR190 4.5 28.0 1.0
OE2 X:GLU219 4.5 26.6 1.0
N X:THR190 4.5 28.0 1.0
OE1 X:GLU215 4.5 24.0 1.0
CZ X:ARG216 4.6 22.7 1.0
O1A X:ADP601 4.6 34.1 1.0
CD X:GLU219 4.6 26.6 1.0
OD2 X:ASP285 4.6 24.7 1.0
OD1 X:ASP285 4.7 24.7 1.0
CG X:GLU215 4.7 24.0 1.0
OD1 X:ASN286 4.7 23.2 1.0
NH2 X:ARG216 4.8 22.7 1.0
PA X:ADP601 4.9 34.1 1.0
O3B X:ADP601 4.9 34.1 1.0
O X:HOH702 4.9 30.0 1.0
O2A X:ADP601 5.0 34.1 1.0

Magnesium binding site 5 out of 5 in 6rdb

Go back to Magnesium Binding Sites List in 6rdb
Magnesium binding site 5 out of 5 in the Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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 Cryoem Structure of Polytomella F-Atp Synthase, Primary Rotary State 1, 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
 O3B Y:ADP601 2.5 48.8 1.0
O Y:HOH703 2.6 30.0 1.0
O Y:HOH702 2.8 30.0 1.0
O Y:HOH704 2.8 30.0 1.0
OG1 Y:THR190 2.8 45.0 1.0
OE2 Y:GLU215 2.8 32.2 1.0
OE2 Y:GLU219 3.3 35.4 1.0
NH1 Y:ARG216 3.5 31.5 1.0
CD Y:GLU215 3.8 32.2 1.0
OD2 Y:ASP285 3.8 34.0 1.0
PB Y:ADP601 3.8 48.8 1.0
OE1 Y:GLU219 4.0 35.4 1.0
CD Y:GLU219 4.1 35.4 1.0
CB Y:THR190 4.1 45.0 1.0
ND2 Y:ASN286 4.1 33.6 1.0
O2B Y:ADP601 4.2 48.8 1.0
OE1 Y:GLU215 4.5 32.2 1.0
CG Y:GLU215 4.6 32.2 1.0
O2A Y:ADP601 4.7 48.8 1.0
N Y:THR190 4.7 45.0 1.0
CZ Y:ARG216 4.7 31.5 1.0
O1B Y:ADP601 4.8 48.8 1.0
O3A Y:ADP601 4.8 48.8 1.0
NZ Y:LYS189 4.8 42.4 1.0
CG Y:ASP285 4.9 34.0 1.0
O1A Y:ADP601 4.9 48.8 1.0
CA Y:THR190 4.9 45.0 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 16:42:14 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy