Atomistry » Magnesium » PDB 6r5n-6rdh » 6rdb
Atomistry »
  Magnesium »
    PDB 6r5n-6rdh »
      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

Mg in 1JPM
Mg in 1JQX
Mg in 1JQV
Mg in 1JP4
Mg in 1JQH
Mg in 1JNK
Mg in 1JM6
Mg in 1JMS
Mg in 1JM1
Mg in 1JLS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy