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Magnesium in PDB 8p4n: Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered Substrate Metk in the Presence of Adp-Befx

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

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

Other elements in 8p4n:

The structure of Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx (pdb code 8p4n). 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 Disordered Substrate Metk in the Presence of Adp-Befx, PDB code: 8p4n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8p4n

Go back to Magnesium Binding Sites List in 8p4n
Magnesium binding site 1 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1601

b:22.0
occ:1.00
 O A:HOH2001 1.8 6.5 1.0
OD1 A:ASP87 1.9 6.7 1.0
O A:HOH2005 2.0 6.4 1.0
O2B A:ADP1600 2.1 5.9 1.0
CG A:ASP87 2.6 6.7 1.0
OD2 A:ASP87 2.7 6.7 1.0
F1 A:BEF1602 2.8 4.0 1.0
O2A A:ADP1600 3.4 5.9 1.0
PB A:ADP1600 3.6 5.9 1.0
OG A:SER151 3.7 7.7 1.0
CB A:ASP87 4.0 6.7 1.0
N A:GLY88 4.2 5.0 1.0
O3B A:ADP1600 4.2 5.9 1.0
BE A:BEF1602 4.2 4.0 1.0
O A:SER151 4.2 7.7 1.0
O1B A:ADP1600 4.5 5.9 1.0
O3A A:ADP1600 4.5 5.9 1.0
PA A:ADP1600 4.6 5.9 1.0
CA A:ASP87 4.6 6.7 1.0
O A:HOH2013 4.7 6.5 1.0
CA A:SER151 4.7 7.7 1.0
CB A:SER151 4.7 7.7 1.0
CB A:ASP398 4.8 8.5 1.0
F2 A:BEF1602 4.9 4.0 1.0
C A:ASP87 4.9 6.7 1.0
O A:HOH2017 4.9 7.3 1.0
O A:HOH2008 4.9 7.9 1.0
C A:SER151 4.9 7.7 1.0
CA A:GLY88 5.0 5.0 1.0

Magnesium binding site 2 out of 7 in 8p4n

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Magnesium binding site 2 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1601

b:6.4
occ:1.00
 O B:HOH1702 1.9 6.2 1.0
O B:HOH1703 2.0 8.4 1.0
OD2 B:ASP87 2.0 7.6 1.0
OD1 B:ASP87 2.2 7.6 1.0
CG B:ASP87 2.3 7.6 1.0
O2B B:ADP1600 2.7 22.0 1.0
F1 B:BEF1602 3.0 10.8 1.0
O2A B:ADP1600 3.5 22.0 1.0
CB B:ASP87 3.8 7.6 1.0
PB B:ADP1600 3.9 22.0 1.0
OG B:SER151 4.1 8.7 1.0
O3B B:ADP1600 4.1 22.0 1.0
N B:GLY88 4.2 7.8 1.0
O B:HOH1712 4.3 17.2 1.0
BE B:BEF1602 4.4 10.8 1.0
O B:SER151 4.5 8.7 1.0
CA B:ASP87 4.5 7.6 1.0
CB B:SER151 4.5 8.7 1.0
CA B:SER151 4.6 8.7 1.0
OD1 B:ASP398 4.7 9.2 1.0
PA B:ADP1600 4.7 22.0 1.0
O3A B:ADP1600 4.8 22.0 1.0
F2 B:BEF1602 4.9 10.8 1.0
C B:ASP87 4.9 7.6 1.0
CB B:ASP398 5.0 9.2 1.0

Magnesium binding site 3 out of 7 in 8p4n

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Magnesium binding site 3 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1601

b:8.2
occ:1.00
 O C:HOH2001 1.8 8.3 1.0
O C:HOH2005 1.9 7.9 1.0
OD2 C:ASP87 2.0 9.2 1.0
O2B C:ADP1600 2.2 22.0 1.0
F1 C:BEF1602 2.3 11.0 1.0
OD1 C:ASP87 2.3 9.2 1.0
CG C:ASP87 2.4 9.2 1.0
PB C:ADP1600 3.5 22.0 1.0
BE C:BEF1602 3.5 11.0 1.0
O2A C:ADP1600 3.6 22.0 1.0
CB C:ASP87 3.8 9.2 1.0
O3B C:ADP1600 3.9 22.0 1.0
N C:GLY88 4.2 7.8 1.0
F2 C:BEF1602 4.2 11.0 1.0
CA C:ASP87 4.3 9.2 1.0
O C:SER151 4.3 8.1 1.0
O3A C:ADP1600 4.4 22.0 1.0
CB C:ASP398 4.5 10.0 1.0
O1B C:ADP1600 4.6 22.0 1.0
PA C:ADP1600 4.6 22.0 1.0
O C:HOH2017 4.7 9.1 1.0
F3 C:BEF1602 4.7 11.0 1.0
C C:ASP87 4.8 9.2 1.0
CG C:ASP398 4.8 10.0 1.0
CB C:SER151 4.9 8.1 1.0
CA C:SER151 4.9 8.1 1.0
OD2 C:ASP398 4.9 10.0 1.0
O C:HOH2016 5.0 16.2 1.0

Magnesium binding site 4 out of 7 in 8p4n

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Magnesium binding site 4 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1601

b:3.9
occ:1.00
 O D:HOH2001 1.9 6.5 1.0
OD1 D:ASP87 1.9 5.6 1.0
O D:HOH2007 2.0 22.0 1.0
F1 D:BEF1602 2.1 3.6 1.0
O2B D:ADP1600 2.4 5.3 1.0
CG D:ASP87 2.7 5.6 1.0
OD2 D:ASP87 3.0 5.6 1.0
O2A D:ADP1600 3.0 5.3 1.0
BE D:BEF1602 3.4 3.6 1.0
PB D:ADP1600 3.5 5.3 1.0
O3B D:ADP1600 3.5 5.3 1.0
F2 D:BEF1602 3.9 3.6 1.0
OD2 D:ASP398 4.0 9.7 1.0
CB D:ASP87 4.1 5.6 1.0
N D:GLY88 4.1 5.3 1.0
PA D:ADP1600 4.2 5.3 1.0
O3A D:ADP1600 4.2 5.3 1.0
O D:HOH2016 4.2 5.8 1.0
O D:SER151 4.5 9.0 1.0
CA D:ASP87 4.6 5.6 1.0
F3 D:BEF1602 4.6 3.6 1.0
CB D:ASP398 4.8 9.7 1.0
O1B D:ADP1600 4.8 5.3 1.0
CG D:ASP398 4.8 9.7 1.0
C D:ASP87 4.9 5.6 1.0
O D:HOH2002 4.9 8.8 1.0
CA D:GLY88 5.0 5.3 1.0

Magnesium binding site 5 out of 7 in 8p4n

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Magnesium binding site 5 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1601

b:4.1
occ:1.00
 OD1 E:ASP87 1.9 5.5 1.0
O E:HOH2001 1.9 4.6 1.0
O E:HOH2003 1.9 5.1 1.0
O2B E:ADP1600 2.1 4.2 1.0
F1 E:BEF1602 2.3 2.3 1.0
CG E:ASP87 2.5 5.5 1.0
OD2 E:ASP87 2.5 5.5 1.0
O2A E:ADP1600 3.1 4.2 1.0
PB E:ADP1600 3.5 4.2 1.0
BE E:BEF1602 3.6 2.3 1.0
CB E:ASP87 3.9 5.5 1.0
OG E:SER151 4.0 8.1 1.0
O3B E:ADP1600 4.0 4.2 1.0
N E:GLY88 4.0 4.2 1.0
OD1 E:ASP398 4.1 8.3 1.0
PA E:ADP1600 4.3 4.2 1.0
O3A E:ADP1600 4.3 4.2 1.0
F2 E:BEF1602 4.4 2.3 1.0
O E:SER151 4.5 8.1 1.0
CA E:ASP87 4.5 5.5 1.0
O1B E:ADP1600 4.5 4.2 1.0
F3 E:BEF1602 4.7 2.3 1.0
CG E:ASP398 4.7 8.3 1.0
C E:ASP87 4.7 5.5 1.0
CA E:GLY88 4.8 4.2 1.0
CA E:SER151 5.0 8.1 1.0
CB E:ASP398 5.0 8.3 1.0
CB E:SER151 5.0 8.1 1.0

Magnesium binding site 6 out of 7 in 8p4n

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Magnesium binding site 6 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1601

b:5.4
occ:1.00
 O F:HOH2001 1.9 5.9 1.0
O F:HOH2003 1.9 3.6 1.0
OD1 F:ASP87 2.0 6.2 1.0
F1 F:BEF1602 2.0 4.1 1.0
O2B F:ADP1600 2.1 6.3 1.0
CG F:ASP87 2.9 6.2 1.0
O2A F:ADP1600 3.1 6.3 1.0
OD2 F:ASP87 3.2 6.2 1.0
PB F:ADP1600 3.4 6.3 1.0
BE F:BEF1602 3.4 4.1 1.0
O3B F:ADP1600 3.6 6.3 1.0
OD1 F:ASP398 3.8 8.9 1.0
F2 F:BEF1602 3.9 4.1 1.0
O3A F:ADP1600 4.2 6.3 1.0
O F:HOH2017 4.2 8.2 1.0
N F:GLY88 4.2 5.7 1.0
PA F:ADP1600 4.2 6.3 1.0
CB F:ASP87 4.2 6.2 1.0
O F:SER151 4.4 7.5 1.0
F3 F:BEF1602 4.5 4.1 1.0
O1B F:ADP1600 4.6 6.3 1.0
CA F:ASP87 4.6 6.2 1.0
CG F:ASP398 4.7 8.9 1.0
CB F:ASP398 4.7 8.9 1.0
O F:HOH2019 4.8 12.2 1.0
O F:HOH2004 4.9 7.0 1.0
O F:HOH2006 4.9 7.9 1.0
C F:ASP87 4.9 6.2 1.0

Magnesium binding site 7 out of 7 in 8p4n

Go back to Magnesium Binding Sites List in 8p4n
Magnesium binding site 7 out of 7 in the Cryoem Structure of A GROEL7-GROES7 Cage with Encapsulated Disordered 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 Disordered Substrate Metk in the Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1601

b:5.3
occ:1.00
 O G:HOH2001 1.9 4.7 1.0
O G:HOH2004 1.9 5.5 1.0
OD1 G:ASP87 2.0 6.8 1.0
O2B G:ADP1600 2.1 8.5 1.0
OD2 G:ASP87 2.3 6.8 1.0
CG G:ASP87 2.4 6.8 1.0
F1 G:BEF1602 2.5 6.9 1.0
PB G:ADP1600 3.4 8.5 1.0
O2A G:ADP1600 3.5 8.5 1.0
CB G:ASP87 3.8 6.8 1.0
O3B G:ADP1600 3.8 8.5 1.0
BE G:BEF1602 3.9 6.9 1.0
N G:GLY88 4.0 6.3 1.0
CA G:ASP87 4.3 6.8 1.0
O3A G:ADP1600 4.4 8.5 1.0
F2 G:BEF1602 4.4 6.9 1.0
O1B G:ADP1600 4.5 8.5 1.0
PA G:ADP1600 4.5 8.5 1.0
O G:SER151 4.6 8.3 1.0
C G:ASP87 4.7 6.8 1.0
O G:HOH2019 4.7 9.7 1.0
CB G:ASP398 4.7 9.1 1.0
CG G:ASP398 4.7 9.1 1.0
CA G:GLY88 4.9 6.3 1.0
OD2 G:ASP398 4.9 9.1 1.0
F3 G:BEF1602 5.0 6.9 1.0
O G:HOH2014 5.0 13.5 1.0
CB G:SER151 5.0 8.3 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 15:47:33 2024

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