Atomistry » Magnesium » PDB 8p4a-8pdy » 8p4o
Atomistry »
  Magnesium »
    PDB 8p4a-8pdy »
      8p4o »

Magnesium in PDB 8p4o: Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx

Enzymatic activity of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx

All present enzymatic activity of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx:
2.5.1.6; 5.6.1.7;

Other elements in 8p4o:

The structure of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx also contains other interesting chemical elements:

Fluorine (F) 21 atoms
Potassium (K) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx (pdb code 8p4o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx, PDB code: 8p4o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8p4o

Go back to Magnesium Binding Sites List in 8p4o
Magnesium binding site 1 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx


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 A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:26.2
occ:1.00
O A:HOH1703 2.0 24.7 1.0
O A:HOH1701 2.0 26.0 1.0
F1 A:BEF1602 2.1 30.4 1.0
OD2 A:ASP87 2.1 29.0 1.0
O2B A:ADP1600 2.1 21.7 1.0
O2A A:ADP1600 2.9 21.7 1.0
CG A:ASP87 3.0 29.0 1.0
OD1 A:ASP87 3.2 29.0 1.0
PB A:ADP1600 3.4 21.7 1.0
BE A:BEF1602 3.6 30.4 1.0
O3B A:ADP1600 3.8 21.7 1.0
O3A A:ADP1600 4.0 21.7 1.0
OD2 A:ASP398 4.0 34.5 1.0
PA A:ADP1600 4.0 21.7 1.0
O A:SER151 4.1 30.7 1.0
OG A:SER151 4.3 30.7 1.0
CB A:ASP87 4.3 29.0 1.0
O A:HOH1702 4.4 24.9 1.0
F3 A:BEF1602 4.4 30.4 1.0
N A:GLY88 4.4 26.8 1.0
F2 A:BEF1602 4.4 30.4 1.0
O5' A:ADP1600 4.6 21.7 1.0
CG A:ASP398 4.6 34.5 1.0
O1B A:ADP1600 4.6 21.7 1.0
CB A:ASP398 4.8 34.5 1.0
CA A:ASP87 4.8 29.0 1.0
CA A:SER151 4.9 30.7 1.0
C A:SER151 5.0 30.7 1.0

Magnesium binding site 2 out of 7 in 8p4o

Go back to Magnesium Binding Sites List in 8p4o
Magnesium binding site 2 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx


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 A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:30.2
occ:1.00
O B:HOH1702 2.0 31.5 1.0
O B:HOH1701 2.0 25.4 1.0
F1 B:BEF1602 2.0 29.9 1.0
O2B B:ADP1600 2.0 23.0 1.0
O2A B:ADP1600 2.0 23.0 1.0
OD1 B:ASP87 3.0 29.6 1.0
PB B:ADP1600 3.0 23.0 1.0
PA B:ADP1600 3.2 23.0 1.0
O3A B:ADP1600 3.3 23.0 1.0
O3B B:ADP1600 3.4 23.0 1.0
BE B:BEF1602 3.5 29.9 1.0
CG B:ASP87 3.9 29.6 1.0
OD2 B:ASP87 4.0 29.6 1.0
O5' B:ADP1600 4.0 23.0 1.0
F3 B:BEF1602 4.3 29.9 1.0
O B:HOH1703 4.3 25.0 1.0
F2 B:BEF1602 4.4 29.9 1.0
OD2 B:ASP398 4.4 35.0 1.0
O B:SER151 4.4 30.6 1.0
O1B B:ADP1600 4.4 23.0 1.0
O1A B:ADP1600 4.4 23.0 1.0
K B:K1603 4.7 36.5 1.0
C5' B:ADP1600 4.7 23.0 1.0
OG B:SER151 4.8 30.6 1.0
N B:GLY88 4.9 26.7 1.0

Magnesium binding site 3 out of 7 in 8p4o

Go back to Magnesium Binding Sites List in 8p4o
Magnesium binding site 3 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx


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 A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1601

b:34.6
occ:1.00
O C:HOH1701 2.0 31.6 1.0
O C:HOH1702 2.0 34.4 1.0
OD1 C:ASP87 2.4 32.3 1.0
CG C:ASP87 2.6 32.3 1.0
F1 C:BEF1602 2.6 38.4 1.0
O2B C:ADP1600 2.6 51.5 1.0
OD2 C:ASP87 3.0 32.3 1.0
CB C:ASP87 3.3 32.3 1.0
O2A C:ADP1600 3.5 51.5 1.0
PB C:ADP1600 3.8 51.5 1.0
O3B C:ADP1600 3.9 51.5 1.0
OG C:SER151 3.9 28.5 1.0
BE C:BEF1602 4.0 38.4 1.0
O C:HOH1703 4.1 29.7 1.0
OD2 C:ASP398 4.1 34.6 1.0
CA C:ASP87 4.1 32.3 1.0
O C:SER151 4.4 28.5 1.0
N C:GLY88 4.4 31.1 1.0
F2 C:BEF1602 4.5 38.4 1.0
CG C:ASP398 4.6 34.6 1.0
CB C:ASP398 4.6 34.6 1.0
O3A C:ADP1600 4.6 51.5 1.0
PA C:ADP1600 4.7 51.5 1.0
C C:ASP87 4.9 32.3 1.0
CB C:SER151 4.9 28.5 1.0
CA C:SER151 5.0 28.5 1.0
O1B C:ADP1600 5.0 51.5 1.0

Magnesium binding site 4 out of 7 in 8p4o

Go back to Magnesium Binding Sites List in 8p4o
Magnesium binding site 4 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx


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 A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1601

b:39.1
occ:1.00
O D:HOH1701 2.0 41.8 1.0
OD1 D:ASP87 2.0 36.1 1.0
O D:HOH1702 2.0 37.1 1.0
F1 D:BEF1602 2.0 41.0 1.0
O2B D:ADP1600 2.0 51.5 1.0
CG D:ASP87 2.7 36.1 1.0
OD2 D:ASP87 2.7 36.1 1.0
O2A D:ADP1600 3.0 51.5 1.0
PB D:ADP1600 3.2 51.5 1.0
BE D:BEF1602 3.4 41.0 1.0
O3B D:ADP1600 3.5 51.5 1.0
O3A D:ADP1600 3.9 51.5 1.0
PA D:ADP1600 4.0 51.5 1.0
CB D:ASP87 4.1 36.1 1.0
F2 D:BEF1602 4.2 41.0 1.0
O D:HOH1703 4.2 28.7 1.0
N D:GLY88 4.2 33.6 1.0
OD1 D:ASP398 4.4 38.6 1.0
O D:SER151 4.4 32.7 1.0
F3 D:BEF1602 4.5 41.0 1.0
O1B D:ADP1600 4.5 51.5 1.0
OG D:SER151 4.5 32.7 1.0
CA D:ASP87 4.6 36.1 1.0
O5' D:ADP1600 4.7 51.5 1.0
CG D:ASP398 4.7 38.6 1.0
CB D:ASP398 4.9 38.6 1.0
C D:ASP87 5.0 36.1 1.0
CA D:SER151 5.0 32.7 1.0

Magnesium binding site 5 out of 7 in 8p4o

Go back to Magnesium Binding Sites List in 8p4o
Magnesium binding site 5 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx


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 A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1601

b:41.7
occ:1.00
O E:HOH1702 2.0 32.1 1.0
O E:HOH1701 2.0 33.9 1.0
O2B E:ADP1600 2.1 51.5 1.0
F1 E:BEF1602 2.1 39.7 1.0
O2A E:ADP1600 2.1 51.5 1.0
PB E:ADP1600 3.2 51.5 1.0
PA E:ADP1600 3.3 51.5 1.0
O3A E:ADP1600 3.5 51.5 1.0
BE E:BEF1602 3.6 39.7 1.0
OD2 E:ASP87 3.6 32.7 1.0
O3B E:ADP1600 3.7 51.5 1.0
O E:HOH1703 3.8 34.2 1.0
CG E:ASP87 4.0 32.7 1.0
O5' E:ADP1600 4.2 51.5 1.0
O E:SER151 4.3 32.2 1.0
OD1 E:ASP87 4.3 32.7 1.0
F3 E:BEF1602 4.4 39.7 1.0
F2 E:BEF1602 4.5 39.7 1.0
O1B E:ADP1600 4.5 51.5 1.0
O1A E:ADP1600 4.5 51.5 1.0
OD2 E:ASP398 4.7 34.4 1.0
CB E:ASP87 4.7 32.7 1.0
C5' E:ADP1600 4.9 51.5 1.0
CA E:SER151 4.9 32.2 1.0
C E:SER151 5.0 32.2 1.0

Magnesium binding site 6 out of 7 in 8p4o

Go back to Magnesium Binding Sites List in 8p4o
Magnesium binding site 6 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1601

b:42.8
occ:1.00
O F:HOH1701 2.0 33.5 1.0
O F:HOH1702 2.0 34.9 1.0
O2B F:ADP1600 2.0 51.5 1.0
O2A F:ADP1600 2.0 51.5 1.0
F1 F:BEF1602 2.1 40.8 1.0
OD1 F:ASP87 3.1 35.5 1.0
PB F:ADP1600 3.1 51.5 1.0
PA F:ADP1600 3.2 51.5 1.0
O3A F:ADP1600 3.4 51.5 1.0
O3B F:ADP1600 3.6 51.5 1.0
BE F:BEF1602 3.6 40.8 1.0
OD2 F:ASP87 3.8 35.5 1.0
CG F:ASP87 3.8 35.5 1.0
O5' F:ADP1600 4.0 51.5 1.0
OD2 F:ASP398 4.2 36.5 1.0
O F:SER151 4.2 32.5 1.0
F3 F:BEF1602 4.3 40.8 1.0
O1B F:ADP1600 4.4 51.5 1.0
O F:HOH1703 4.4 28.9 1.0
O1A F:ADP1600 4.5 51.5 1.0
F2 F:BEF1602 4.5 40.8 1.0
C5' F:ADP1600 4.6 51.5 1.0
K F:K1603 4.7 39.2 1.0
OG F:SER151 4.8 32.5 1.0

Magnesium binding site 7 out of 7 in 8p4o

Go back to Magnesium Binding Sites List in 8p4o
Magnesium binding site 7 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Ordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1601

b:38.2
occ:1.00
O G:HOH1702 2.0 32.8 1.0
F1 G:BEF1602 2.0 41.0 1.0
O G:HOH1701 2.0 34.2 1.0
O2B G:ADP1600 2.1 51.5 1.0
O2A G:ADP1600 2.2 51.5 1.0
OD1 G:ASP87 2.5 34.9 1.0
OD2 G:ASP87 3.1 34.9 1.0
CG G:ASP87 3.2 34.9 1.0
PB G:ADP1600 3.3 51.5 1.0
PA G:ADP1600 3.4 51.5 1.0
BE G:BEF1602 3.5 41.0 1.0
O3A G:ADP1600 3.6 51.5 1.0
O3B G:ADP1600 3.7 51.5 1.0
O5' G:ADP1600 4.2 51.5 1.0
O G:HOH1703 4.3 25.3 1.0
F2 G:BEF1602 4.3 41.0 1.0
F3 G:BEF1602 4.4 41.0 1.0
O G:SER151 4.5 30.5 1.0
OD2 G:ASP398 4.5 34.4 1.0
O1B G:ADP1600 4.6 51.5 1.0
N G:GLY88 4.6 33.5 1.0
CB G:ASP87 4.6 34.9 1.0
O1A G:ADP1600 4.6 51.5 1.0
C5' G:ADP1600 4.8 51.5 1.0

Reference:

J.Wagner, A.I.Caravajal, F.Beck, A.Bracher, W.Wan, S.Bohn, R.Koerner, W.Baumeister, R.Fernandez-Busnadiego, F.U.Hartl. Visualizing Chaperonin Function in Situ By Cryo-Electron Tomography Nature 2024.
ISSN: ESSN 1476-4687
Page generated: Fri Oct 4 15:47:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy