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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

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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

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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

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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

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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

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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

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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

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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

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