Atomistry » Magnesium » PDB 8p0g-8p5u » 8p4o
Atomistry »
  Magnesium »
    PDB 8p0g-8p5u »
      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

Cl in 5WII
Cl in 5WIU
Cl in 5WGZ
Cl in 5WGY
Cl in 5WHH
Cl in 5WGX
Cl in 5WGW
Cl in 5WGI
Cl in 5WGV
Cl in 5WGU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy