Potassium 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:
Potassium Binding Sites:
The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium 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 Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
Potassium binding site 1 out
of 7 in 8p4n
Go back to
Potassium Binding Sites List in 8p4n
Potassium 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 Potassium with other atoms in the K 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:K1603
b:5.8
occ:1.00
|
O
|
A:LYS51
|
2.7
|
2.5
|
1.0
|
F3
|
A:BEF1602
|
2.8
|
4.0
|
1.0
|
O
|
A:THR30
|
2.8
|
22.0
|
1.0
|
OG1
|
A:THR90
|
2.9
|
4.8
|
1.0
|
O1A
|
A:ADP1600
|
3.1
|
5.9
|
1.0
|
OG1
|
A:THR30
|
3.2
|
22.0
|
1.0
|
O3A
|
A:ADP1600
|
3.5
|
5.9
|
1.0
|
O3B
|
A:ADP1600
|
3.8
|
5.9
|
1.0
|
C
|
A:THR30
|
3.8
|
22.0
|
1.0
|
O
|
A:HOH2017
|
3.9
|
7.3
|
1.0
|
CB
|
A:THR90
|
3.9
|
4.8
|
1.0
|
CB
|
A:THR30
|
3.9
|
22.0
|
1.0
|
C
|
A:LYS51
|
3.9
|
2.5
|
1.0
|
PA
|
A:ADP1600
|
3.9
|
5.9
|
1.0
|
N
|
A:GLY53
|
3.9
|
5.2
|
1.0
|
BE
|
A:BEF1602
|
4.2
|
4.0
|
1.0
|
CA
|
A:ASP52
|
4.3
|
5.8
|
1.0
|
CG2
|
A:THR90
|
4.3
|
4.8
|
1.0
|
PB
|
A:ADP1600
|
4.4
|
5.9
|
1.0
|
C
|
A:ASP52
|
4.4
|
5.8
|
1.0
|
F1
|
A:BEF1602
|
4.5
|
4.0
|
1.0
|
CA
|
A:THR30
|
4.5
|
22.0
|
1.0
|
N
|
A:ASP52
|
4.5
|
5.8
|
1.0
|
CA
|
A:GLY53
|
4.6
|
5.2
|
1.0
|
NZ
|
A:LYS51
|
4.7
|
2.5
|
1.0
|
N
|
A:LEU31
|
4.7
|
22.0
|
1.0
|
CG
|
A:LYS51
|
4.7
|
2.5
|
1.0
|
CA
|
A:LEU31
|
4.7
|
22.0
|
1.0
|
O2A
|
A:ADP1600
|
4.8
|
5.9
|
1.0
|
|
Potassium binding site 2 out
of 7 in 8p4n
Go back to
Potassium Binding Sites List in 8p4n
Potassium 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 Potassium with other atoms in the K 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:K1603
b:5.2
occ:1.00
|
O
|
B:THR30
|
2.7
|
2.2
|
1.0
|
O1A
|
B:ADP1600
|
2.8
|
22.0
|
1.0
|
O
|
B:LYS51
|
2.8
|
3.1
|
1.0
|
F3
|
B:BEF1602
|
2.8
|
10.8
|
1.0
|
OG1
|
B:THR90
|
3.0
|
4.5
|
1.0
|
O3A
|
B:ADP1600
|
3.3
|
22.0
|
1.0
|
OG1
|
B:THR30
|
3.4
|
2.2
|
1.0
|
PA
|
B:ADP1600
|
3.5
|
22.0
|
1.0
|
C
|
B:THR30
|
3.7
|
2.2
|
1.0
|
O3B
|
B:ADP1600
|
3.9
|
22.0
|
1.0
|
O
|
B:HOH1717
|
3.9
|
8.3
|
1.0
|
C
|
B:LYS51
|
4.0
|
3.1
|
1.0
|
CB
|
B:THR90
|
4.0
|
4.5
|
1.0
|
CB
|
B:THR30
|
4.0
|
2.2
|
1.0
|
BE
|
B:BEF1602
|
4.1
|
10.8
|
1.0
|
F1
|
B:BEF1602
|
4.1
|
10.8
|
1.0
|
N
|
B:GLY53
|
4.2
|
5.7
|
1.0
|
O2A
|
B:ADP1600
|
4.3
|
22.0
|
1.0
|
PB
|
B:ADP1600
|
4.4
|
22.0
|
1.0
|
CA
|
B:ASP52
|
4.5
|
6.3
|
1.0
|
NZ
|
B:LYS51
|
4.5
|
3.1
|
1.0
|
CG2
|
B:THR90
|
4.5
|
4.5
|
1.0
|
CG
|
B:LYS51
|
4.5
|
3.1
|
1.0
|
CA
|
B:THR30
|
4.6
|
2.2
|
1.0
|
CA
|
B:LEU31
|
4.6
|
22.0
|
1.0
|
N
|
B:LEU31
|
4.6
|
22.0
|
1.0
|
C
|
B:ASP52
|
4.6
|
6.3
|
1.0
|
N
|
B:ASP52
|
4.7
|
6.3
|
1.0
|
CA
|
B:GLY53
|
4.8
|
5.7
|
1.0
|
O5'
|
B:ADP1600
|
4.9
|
22.0
|
1.0
|
O
|
B:HOH1715
|
4.9
|
17.3
|
1.0
|
|
Potassium binding site 3 out
of 7 in 8p4n
Go back to
Potassium Binding Sites List in 8p4n
Potassium 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 Potassium with other atoms in the K 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:K1603
b:6.2
occ:1.00
|
O
|
C:LYS51
|
2.7
|
5.0
|
1.0
|
O
|
C:THR30
|
2.7
|
3.7
|
1.0
|
O1A
|
C:ADP1600
|
3.0
|
22.0
|
1.0
|
F3
|
C:BEF1602
|
3.0
|
11.0
|
1.0
|
OG1
|
C:THR90
|
3.2
|
5.3
|
1.0
|
O3A
|
C:ADP1600
|
3.3
|
22.0
|
1.0
|
O
|
C:HOH2017
|
3.5
|
9.1
|
1.0
|
PA
|
C:ADP1600
|
3.6
|
22.0
|
1.0
|
OG1
|
C:THR30
|
3.7
|
3.7
|
1.0
|
C
|
C:THR30
|
3.9
|
3.7
|
1.0
|
O3B
|
C:ADP1600
|
3.9
|
22.0
|
1.0
|
C
|
C:LYS51
|
3.9
|
5.0
|
1.0
|
CB
|
C:THR30
|
4.1
|
3.7
|
1.0
|
F1
|
C:BEF1602
|
4.1
|
11.0
|
1.0
|
BE
|
C:BEF1602
|
4.2
|
11.0
|
1.0
|
CB
|
C:THR90
|
4.2
|
5.3
|
1.0
|
NZ
|
C:LYS51
|
4.3
|
5.0
|
1.0
|
N
|
C:GLY53
|
4.3
|
6.5
|
1.0
|
PB
|
C:ADP1600
|
4.3
|
22.0
|
1.0
|
O2A
|
C:ADP1600
|
4.4
|
22.0
|
1.0
|
CA
|
C:ASP52
|
4.4
|
7.0
|
1.0
|
O
|
C:HOH2013
|
4.5
|
17.2
|
1.0
|
CG
|
C:LYS51
|
4.5
|
5.0
|
1.0
|
N
|
C:ASP52
|
4.7
|
7.0
|
1.0
|
CA
|
C:THR30
|
4.7
|
3.7
|
1.0
|
C
|
C:ASP52
|
4.7
|
7.0
|
1.0
|
CG2
|
C:THR90
|
4.7
|
5.3
|
1.0
|
CA
|
C:LEU31
|
4.7
|
6.0
|
1.0
|
N
|
C:LEU31
|
4.7
|
6.0
|
1.0
|
F2
|
C:BEF1602
|
4.9
|
11.0
|
1.0
|
CA
|
C:GLY53
|
5.0
|
6.5
|
1.0
|
|
Potassium binding site 4 out
of 7 in 8p4n
Go back to
Potassium Binding Sites List in 8p4n
Potassium 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 Potassium with other atoms in the K 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:K1603
b:3.3
occ:1.00
|
O
|
D:LYS51
|
2.8
|
3.5
|
1.0
|
O
|
D:THR30
|
2.8
|
4.5
|
1.0
|
O1A
|
D:ADP1600
|
2.8
|
5.3
|
1.0
|
F3
|
D:BEF1602
|
2.8
|
3.6
|
1.0
|
OG1
|
D:THR90
|
3.0
|
5.4
|
1.0
|
O
|
D:HOH2016
|
3.4
|
5.8
|
1.0
|
OG1
|
D:THR30
|
3.5
|
4.5
|
1.0
|
O3A
|
D:ADP1600
|
3.5
|
5.3
|
1.0
|
PA
|
D:ADP1600
|
3.7
|
5.3
|
1.0
|
O3B
|
D:ADP1600
|
3.7
|
5.3
|
1.0
|
C
|
D:THR30
|
3.8
|
4.5
|
1.0
|
C
|
D:LYS51
|
4.0
|
3.5
|
1.0
|
CB
|
D:THR30
|
4.0
|
4.5
|
1.0
|
CB
|
D:THR90
|
4.0
|
5.4
|
1.0
|
BE
|
D:BEF1602
|
4.0
|
3.6
|
1.0
|
F1
|
D:BEF1602
|
4.0
|
3.6
|
1.0
|
NZ
|
D:LYS51
|
4.2
|
3.5
|
1.0
|
N
|
D:GLY53
|
4.2
|
5.0
|
1.0
|
PB
|
D:ADP1600
|
4.3
|
5.3
|
1.0
|
O2A
|
D:ADP1600
|
4.5
|
5.3
|
1.0
|
CG
|
D:LYS51
|
4.5
|
3.5
|
1.0
|
CG2
|
D:THR90
|
4.5
|
5.4
|
1.0
|
CA
|
D:THR30
|
4.6
|
4.5
|
1.0
|
CA
|
D:ASP52
|
4.6
|
4.5
|
1.0
|
N
|
D:LEU31
|
4.7
|
4.2
|
1.0
|
CA
|
D:LEU31
|
4.7
|
4.2
|
1.0
|
C
|
D:ASP52
|
4.7
|
4.5
|
1.0
|
N
|
D:ASP52
|
4.7
|
4.5
|
1.0
|
CA
|
D:GLY53
|
4.9
|
5.0
|
1.0
|
O5'
|
D:ADP1600
|
5.0
|
5.3
|
1.0
|
CA
|
D:LYS51
|
5.0
|
3.5
|
1.0
|
|
Potassium binding site 5 out
of 7 in 8p4n
Go back to
Potassium Binding Sites List in 8p4n
Potassium 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 Potassium with other atoms in the K 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:K1603
b:3.0
occ:1.00
|
O
|
E:LYS51
|
2.7
|
3.4
|
1.0
|
O
|
E:THR30
|
2.8
|
1.9
|
1.0
|
O1A
|
E:ADP1600
|
2.9
|
4.2
|
1.0
|
OG1
|
E:THR90
|
3.0
|
2.4
|
1.0
|
F3
|
E:BEF1602
|
3.2
|
2.3
|
1.0
|
OG1
|
E:THR30
|
3.2
|
1.9
|
1.0
|
O3A
|
E:ADP1600
|
3.5
|
4.2
|
1.0
|
C
|
E:THR30
|
3.6
|
1.9
|
1.0
|
PA
|
E:ADP1600
|
3.7
|
4.2
|
1.0
|
CB
|
E:THR30
|
3.8
|
1.9
|
1.0
|
C
|
E:LYS51
|
3.9
|
3.4
|
1.0
|
CB
|
E:THR90
|
4.0
|
2.4
|
1.0
|
O3B
|
E:ADP1600
|
4.1
|
4.2
|
1.0
|
N
|
E:GLY53
|
4.1
|
4.5
|
1.0
|
O
|
E:HOH2018
|
4.2
|
6.4
|
1.0
|
CG2
|
E:THR90
|
4.4
|
2.4
|
1.0
|
CA
|
E:THR30
|
4.4
|
1.9
|
1.0
|
N
|
E:LEU31
|
4.4
|
2.4
|
1.0
|
BE
|
E:BEF1602
|
4.4
|
2.3
|
1.0
|
NZ
|
E:LYS51
|
4.5
|
3.4
|
1.0
|
CA
|
E:LEU31
|
4.5
|
2.4
|
1.0
|
CA
|
E:ASP52
|
4.5
|
4.6
|
1.0
|
CG
|
E:LYS51
|
4.5
|
3.4
|
1.0
|
PB
|
E:ADP1600
|
4.5
|
4.2
|
1.0
|
F1
|
E:BEF1602
|
4.6
|
2.3
|
1.0
|
C
|
E:ASP52
|
4.6
|
4.6
|
1.0
|
N
|
E:ASP52
|
4.7
|
4.6
|
1.0
|
O2A
|
E:ADP1600
|
4.7
|
4.2
|
1.0
|
CA
|
E:GLY53
|
4.8
|
4.5
|
1.0
|
CA
|
E:LYS51
|
4.9
|
3.4
|
1.0
|
O5'
|
E:ADP1600
|
5.0
|
4.2
|
1.0
|
|
Potassium binding site 6 out
of 7 in 8p4n
Go back to
Potassium Binding Sites List in 8p4n
Potassium 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 Potassium with other atoms in the K 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:K1603
b:4.9
occ:1.00
|
O
|
F:THR30
|
2.7
|
3.7
|
1.0
|
O
|
F:LYS51
|
2.7
|
3.0
|
1.0
|
O1A
|
F:ADP1600
|
2.9
|
6.3
|
1.0
|
F3
|
F:BEF1602
|
2.9
|
4.1
|
1.0
|
OG1
|
F:THR90
|
3.0
|
5.9
|
1.0
|
OG1
|
F:THR30
|
3.3
|
3.7
|
1.0
|
O3A
|
F:ADP1600
|
3.4
|
6.3
|
1.0
|
PA
|
F:ADP1600
|
3.6
|
6.3
|
1.0
|
O
|
F:HOH2017
|
3.7
|
8.2
|
1.0
|
C
|
F:THR30
|
3.8
|
3.7
|
1.0
|
O3B
|
F:ADP1600
|
3.9
|
6.3
|
1.0
|
CB
|
F:THR90
|
3.9
|
5.9
|
1.0
|
C
|
F:LYS51
|
4.0
|
3.0
|
1.0
|
CB
|
F:THR30
|
4.0
|
3.7
|
1.0
|
F1
|
F:BEF1602
|
4.1
|
4.1
|
1.0
|
BE
|
F:BEF1602
|
4.1
|
4.1
|
1.0
|
N
|
F:GLY53
|
4.2
|
4.7
|
1.0
|
PB
|
F:ADP1600
|
4.4
|
6.3
|
1.0
|
O2A
|
F:ADP1600
|
4.4
|
6.3
|
1.0
|
CG2
|
F:THR90
|
4.4
|
5.9
|
1.0
|
NZ
|
F:LYS51
|
4.5
|
3.0
|
1.0
|
CG
|
F:LYS51
|
4.5
|
3.0
|
1.0
|
CA
|
F:ASP52
|
4.5
|
5.2
|
1.0
|
CA
|
F:THR30
|
4.6
|
3.7
|
1.0
|
C
|
F:ASP52
|
4.6
|
5.2
|
1.0
|
N
|
F:LEU31
|
4.7
|
22.0
|
1.0
|
CA
|
F:LEU31
|
4.7
|
22.0
|
1.0
|
N
|
F:ASP52
|
4.7
|
5.2
|
1.0
|
O
|
F:HOH2019
|
4.7
|
12.2
|
1.0
|
CA
|
F:GLY53
|
4.9
|
4.7
|
1.0
|
CA
|
F:LYS51
|
5.0
|
3.0
|
1.0
|
O5'
|
F:ADP1600
|
5.0
|
6.3
|
1.0
|
|
Potassium binding site 7 out
of 7 in 8p4n
Go back to
Potassium Binding Sites List in 8p4n
Potassium 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 Potassium with other atoms in the K 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:K1603
b:5.3
occ:1.00
|
F3
|
G:BEF1602
|
2.7
|
6.9
|
1.0
|
O
|
G:THR30
|
2.7
|
22.0
|
1.0
|
O
|
G:LYS51
|
2.8
|
4.2
|
1.0
|
OG1
|
G:THR90
|
2.8
|
4.9
|
1.0
|
O1A
|
G:ADP1600
|
2.9
|
8.5
|
1.0
|
OG1
|
G:THR30
|
3.2
|
22.0
|
1.0
|
O3A
|
G:ADP1600
|
3.4
|
8.5
|
1.0
|
PA
|
G:ADP1600
|
3.7
|
8.5
|
1.0
|
C
|
G:THR30
|
3.8
|
22.0
|
1.0
|
CB
|
G:THR90
|
3.8
|
4.9
|
1.0
|
O
|
G:HOH2019
|
3.9
|
9.7
|
1.0
|
CB
|
G:THR30
|
3.9
|
22.0
|
1.0
|
C
|
G:LYS51
|
4.0
|
4.2
|
1.0
|
O3B
|
G:ADP1600
|
4.0
|
8.5
|
1.0
|
N
|
G:GLY53
|
4.1
|
6.8
|
1.0
|
BE
|
G:BEF1602
|
4.1
|
6.9
|
1.0
|
F1
|
G:BEF1602
|
4.3
|
6.9
|
1.0
|
CG2
|
G:THR90
|
4.3
|
4.9
|
1.0
|
CA
|
G:ASP52
|
4.4
|
8.8
|
1.0
|
O2A
|
G:ADP1600
|
4.5
|
8.5
|
1.0
|
PB
|
G:ADP1600
|
4.5
|
8.5
|
1.0
|
CA
|
G:THR30
|
4.5
|
22.0
|
1.0
|
NZ
|
G:LYS51
|
4.6
|
4.2
|
1.0
|
C
|
G:ASP52
|
4.6
|
8.8
|
1.0
|
CG
|
G:LYS51
|
4.6
|
4.2
|
1.0
|
N
|
G:LEU31
|
4.6
|
22.0
|
1.0
|
N
|
G:ASP52
|
4.7
|
8.8
|
1.0
|
CA
|
G:LEU31
|
4.7
|
22.0
|
1.0
|
CA
|
G:GLY53
|
4.7
|
6.8
|
1.0
|
F2
|
G:BEF1602
|
5.0
|
6.9
|
1.0
|
O5'
|
G:ADP1600
|
5.0
|
8.5
|
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: Tue Aug 13 00:21:52 2024
|