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Potassium in PDB 8p4m: Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx

Enzymatic activity of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx

All present enzymatic activity of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx:
5.6.1.7;

Other elements in 8p4m:

The structure of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Fluorine (F) 21 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx (pdb code 8p4m). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx, PDB code: 8p4m:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 8p4m

Go back to Potassium Binding Sites List in 8p4m
Potassium binding site 1 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1603

b:24.2
occ:1.00
 O A:LYS51 2.8 26.5 1.0
F3 A:BEF1602 2.8 34.0 1.0
OG1 A:THR90 2.9 27.9 1.0
O A:THR30 2.9 25.7 1.0
O2A A:ADP1600 3.0 43.1 1.0
OG1 A:THR30 3.1 25.7 1.0
O3A A:ADP1600 3.2 43.1 1.0
O A:HOH1724 3.4 30.2 1.0
PA A:ADP1600 3.6 43.1 1.0
C A:THR30 3.6 25.7 1.0
CB A:THR30 3.7 25.7 1.0
CB A:THR90 3.8 27.9 1.0
BE A:BEF1602 4.0 34.0 1.0
C A:LYS51 4.1 26.5 1.0
O3B A:ADP1600 4.1 43.1 1.0
CG2 A:THR90 4.2 27.9 1.0
NZ A:LYS51 4.2 26.5 1.0
N A:GLY53 4.2 28.7 1.0
N A:LEU31 4.3 25.1 1.0
CA A:LEU31 4.3 25.1 1.0
F1 A:BEF1602 4.3 34.0 1.0
CA A:THR30 4.3 25.7 1.0
O1A A:ADP1600 4.4 43.1 1.0
PB A:ADP1600 4.4 43.1 1.0
CG A:LYS51 4.5 26.5 1.0
CA A:ASP52 4.7 30.7 1.0
C A:ASP52 4.7 30.7 1.0
N A:ASP52 4.8 30.7 1.0
CA A:GLY53 4.9 28.7 1.0
O5' A:ADP1600 4.9 43.1 1.0

Potassium binding site 2 out of 7 in 8p4m

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Potassium binding site 2 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K1603

b:24.3
occ:1.00
 O B:LYS51 2.8 25.8 1.0
O2A B:ADP1600 2.9 43.1 1.0
F3 B:BEF1602 2.9 34.7 1.0
O B:THR30 2.9 26.8 1.0
OG1 B:THR90 2.9 27.9 1.0
OG1 B:THR30 3.0 26.8 1.0
O B:HOH1718 3.3 29.7 1.0
O3A B:ADP1600 3.4 43.1 1.0
C B:THR30 3.6 26.8 1.0
PA B:ADP1600 3.7 43.1 1.0
CB B:THR30 3.7 26.8 1.0
CB B:THR90 3.9 27.9 1.0
C B:LYS51 4.0 25.8 1.0
BE B:BEF1602 4.1 34.7 1.0
O3B B:ADP1600 4.2 43.1 1.0
NZ B:LYS51 4.2 25.8 1.0
CG2 B:THR90 4.2 27.9 1.0
N B:GLY53 4.2 26.7 1.0
N B:LEU31 4.3 24.7 1.0
CA B:THR30 4.3 26.8 1.0
F1 B:BEF1602 4.3 34.7 1.0
CA B:LEU31 4.3 24.7 1.0
CG B:LYS51 4.4 25.8 1.0
O1A B:ADP1600 4.5 43.1 1.0
CA B:ASP52 4.5 29.5 1.0
PB B:ADP1600 4.6 43.1 1.0
C B:ASP52 4.7 29.5 1.0
N B:ASP52 4.7 29.5 1.0
CA B:GLY53 4.9 26.7 1.0
CA B:LYS51 5.0 25.8 1.0
O5' B:ADP1600 5.0 43.1 1.0

Potassium binding site 3 out of 7 in 8p4m

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Potassium binding site 3 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K1603

b:25.2
occ:1.00
 O C:LYS51 2.7 26.1 1.0
F3 C:BEF1602 2.9 33.1 1.0
O C:THR30 2.9 23.2 1.0
O2A C:ADP1600 2.9 43.1 1.0
OG1 C:THR30 3.0 23.2 1.0
OG1 C:THR90 3.0 27.6 1.0
O C:HOH1727 3.3 27.5 1.0
O3A C:ADP1600 3.4 43.1 1.0
C C:THR30 3.6 23.2 1.0
PA C:ADP1600 3.7 43.1 1.0
CB C:THR30 3.7 23.2 1.0
CB C:THR90 3.9 27.6 1.0
C C:LYS51 4.0 26.1 1.0
BE C:BEF1602 4.1 33.1 1.0
NZ C:LYS51 4.2 26.1 1.0
O3B C:ADP1600 4.2 43.1 1.0
N C:GLY53 4.3 27.6 1.0
CG2 C:THR90 4.3 27.6 1.0
N C:LEU31 4.3 25.4 1.0
CA C:THR30 4.3 23.2 1.0
CA C:LEU31 4.3 25.4 1.0
F1 C:BEF1602 4.3 33.1 1.0
CG C:LYS51 4.4 26.1 1.0
O1A C:ADP1600 4.5 43.1 1.0
PB C:ADP1600 4.5 43.1 1.0
CA C:ASP52 4.6 29.7 1.0
C C:ASP52 4.7 29.7 1.0
N C:ASP52 4.7 29.7 1.0
CA C:GLY53 4.9 27.6 1.0
CA C:LYS51 5.0 26.1 1.0

Potassium binding site 4 out of 7 in 8p4m

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Potassium binding site 4 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K1603

b:24.5
occ:1.00
 O D:LYS51 2.8 26.5 1.0
F3 D:BEF1602 2.9 33.3 1.0
O D:THR30 2.9 25.5 1.0
OG1 D:THR90 3.0 26.9 1.0
OG1 D:THR30 3.0 25.5 1.0
O2A D:ADP1600 3.1 43.1 1.0
O D:HOH1724 3.3 29.4 1.0
O3A D:ADP1600 3.4 43.1 1.0
C D:THR30 3.6 25.5 1.0
CB D:THR30 3.7 25.5 1.0
PA D:ADP1600 3.7 43.1 1.0
CB D:THR90 3.9 26.9 1.0
BE D:BEF1602 4.0 33.3 1.0
C D:LYS51 4.0 26.5 1.0
NZ D:LYS51 4.1 26.5 1.0
O3B D:ADP1600 4.1 43.1 1.0
CG2 D:THR90 4.2 26.9 1.0
N D:GLY53 4.2 28.1 1.0
F1 D:BEF1602 4.3 33.3 1.0
N D:LEU31 4.3 25.0 1.0
CA D:THR30 4.3 25.5 1.0
CA D:LEU31 4.3 25.0 1.0
CG D:LYS51 4.4 26.5 1.0
O1A D:ADP1600 4.5 43.1 1.0
PB D:ADP1600 4.5 43.1 1.0
CA D:ASP52 4.6 29.9 1.0
C D:ASP52 4.7 29.9 1.0
N D:ASP52 4.8 29.9 1.0
CA D:GLY53 4.9 28.1 1.0

Potassium binding site 5 out of 7 in 8p4m

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Potassium binding site 5 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K1603

b:24.1
occ:1.00
 O E:LYS51 2.8 25.8 1.0
F3 E:BEF1602 2.9 32.9 1.0
O2A E:ADP1600 2.9 43.1 1.0
O E:THR30 2.9 26.7 1.0
OG1 E:THR90 3.0 26.9 1.0
OG1 E:THR30 3.0 26.7 1.0
O E:HOH1724 3.3 30.3 1.0
O3A E:ADP1600 3.5 43.1 1.0
C E:THR30 3.6 26.7 1.0
CB E:THR30 3.6 26.7 1.0
PA E:ADP1600 3.7 43.1 1.0
CB E:THR90 3.9 26.9 1.0
C E:LYS51 4.0 25.8 1.0
BE E:BEF1602 4.0 32.9 1.0
NZ E:LYS51 4.1 25.8 1.0
O3B E:ADP1600 4.2 43.1 1.0
N E:GLY53 4.2 27.5 1.0
F1 E:BEF1602 4.2 32.9 1.0
CA E:THR30 4.3 26.7 1.0
CG2 E:THR90 4.3 26.9 1.0
N E:LEU31 4.3 25.5 1.0
CA E:LEU31 4.4 25.5 1.0
CG E:LYS51 4.4 25.8 1.0
O1A E:ADP1600 4.5 43.1 1.0
PB E:ADP1600 4.6 43.1 1.0
CA E:ASP52 4.6 29.9 1.0
C E:ASP52 4.7 29.9 1.0
N E:ASP52 4.8 29.9 1.0
CA E:GLY53 4.9 27.5 1.0
CG2 E:THR30 5.0 26.7 1.0
CA E:LYS51 5.0 25.8 1.0

Potassium binding site 6 out of 7 in 8p4m

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Potassium binding site 6 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
F:K1603

b:24.1
occ:1.00
 O F:LYS51 2.8 26.2 1.0
O F:THR30 2.9 24.3 1.0
F3 F:BEF1602 3.0 33.9 1.0
OG1 F:THR90 3.0 26.9 1.0
OG1 F:THR30 3.0 24.3 1.0
O2A F:ADP1600 3.0 43.1 1.0
O F:HOH1724 3.3 30.0 1.0
O3A F:ADP1600 3.4 43.1 1.0
C F:THR30 3.6 24.3 1.0
CB F:THR30 3.7 24.3 1.0
PA F:ADP1600 3.7 43.1 1.0
CB F:THR90 4.0 26.9 1.0
C F:LYS51 4.0 26.2 1.0
BE F:BEF1602 4.0 33.9 1.0
NZ F:LYS51 4.1 26.2 1.0
F1 F:BEF1602 4.2 33.9 1.0
N F:GLY53 4.3 26.8 1.0
CG2 F:THR90 4.3 26.9 1.0
O3B F:ADP1600 4.3 43.1 1.0
N F:LEU31 4.3 27.9 1.0
CA F:THR30 4.3 24.3 1.0
CA F:LEU31 4.3 27.9 1.0
CG F:LYS51 4.3 26.2 1.0
O1A F:ADP1600 4.4 43.1 1.0
PB F:ADP1600 4.6 43.1 1.0
CA F:ASP52 4.7 29.7 1.0
C F:ASP52 4.7 29.7 1.0
N F:ASP52 4.8 29.7 1.0
CA F:GLY53 4.9 26.8 1.0
CA F:LYS51 5.0 26.2 1.0
CB F:LYS51 5.0 26.2 1.0

Potassium binding site 7 out of 7 in 8p4m

Go back to Potassium Binding Sites List in 8p4m
Potassium binding site 7 out of 7 in the Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Cryoem Structure of A C7-Symmetrical GROEL7-GROES7 Cage in Presence of Adp-Befx within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K1603

b:24.9
occ:1.00
 O G:LYS51 2.8 25.7 1.0
F3 G:BEF1602 2.9 32.7 1.0
O G:THR30 2.9 25.1 1.0
O2A G:ADP1600 2.9 43.1 1.0
OG1 G:THR30 3.0 25.1 1.0
OG1 G:THR90 3.0 27.4 1.0
O G:HOH1725 3.3 28.2 1.0
O3A G:ADP1600 3.4 43.1 1.0
C G:THR30 3.6 25.1 1.0
PA G:ADP1600 3.7 43.1 1.0
CB G:THR30 3.7 25.1 1.0
CB G:THR90 3.9 27.4 1.0
C G:LYS51 4.0 25.7 1.0
BE G:BEF1602 4.0 32.7 1.0
NZ G:LYS51 4.1 25.7 1.0
O3B G:ADP1600 4.1 43.1 1.0
N G:GLY53 4.3 27.3 1.0
N G:LEU31 4.3 24.6 1.0
CA G:THR30 4.3 25.1 1.0
CG2 G:THR90 4.3 27.4 1.0
F1 G:BEF1602 4.3 32.7 1.0
CA G:LEU31 4.3 24.6 1.0
CG G:LYS51 4.3 25.7 1.0
O1A G:ADP1600 4.5 43.1 1.0
PB G:ADP1600 4.5 43.1 1.0
CA G:ASP52 4.7 29.5 1.0
C G:ASP52 4.7 29.5 1.0
N G:ASP52 4.8 29.5 1.0
CA G:GLY53 4.9 27.3 1.0
O5' G:ADP1600 5.0 43.1 1.0
CE G:LYS51 5.0 25.7 1.0
CB G:LYS51 5.0 25.7 1.0
CA G:LYS51 5.0 25.7 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: Tue Aug 13 00:21:42 2024

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