Potassium 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:
Potassium Binding Sites:
The binding sites of Potassium 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 Potassium atom.
In total 7 binding sites of Potassium 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 Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
Potassium binding site 1 out
of 7 in 8p4o
Go back to
Potassium Binding Sites List in 8p4o
Potassium 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 Potassium with other atoms in the K 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:K1603
b:29.4
occ:1.00
|
O
|
A:THR30
|
2.8
|
21.7
|
1.0
|
O
|
A:LYS51
|
2.8
|
24.2
|
1.0
|
F3
|
A:BEF1602
|
2.9
|
30.4
|
1.0
|
O1A
|
A:ADP1600
|
2.9
|
21.7
|
1.0
|
O3A
|
A:ADP1600
|
3.0
|
21.7
|
1.0
|
PA
|
A:ADP1600
|
3.3
|
21.7
|
1.0
|
O2A
|
A:ADP1600
|
3.7
|
21.7
|
1.0
|
OG1
|
A:THR90
|
3.8
|
22.7
|
1.0
|
OG1
|
A:THR30
|
3.9
|
21.7
|
1.0
|
NZ
|
A:LYS51
|
4.0
|
24.2
|
1.0
|
BE
|
A:BEF1602
|
4.0
|
30.4
|
1.0
|
C
|
A:LYS51
|
4.0
|
24.2
|
1.0
|
C
|
A:THR30
|
4.0
|
21.7
|
1.0
|
F1
|
A:BEF1602
|
4.1
|
30.4
|
1.0
|
O3B
|
A:ADP1600
|
4.1
|
21.7
|
1.0
|
PB
|
A:ADP1600
|
4.2
|
21.7
|
1.0
|
CB
|
A:THR30
|
4.4
|
21.7
|
1.0
|
CG
|
A:LYS51
|
4.4
|
24.2
|
1.0
|
F2
|
A:BEF1602
|
4.5
|
30.4
|
1.0
|
N
|
A:GLY53
|
4.5
|
25.9
|
1.0
|
CA
|
A:ASP52
|
4.6
|
29.2
|
1.0
|
CB
|
A:THR90
|
4.7
|
22.7
|
1.0
|
O
|
A:HOH1703
|
4.7
|
24.7
|
1.0
|
N
|
A:ASP52
|
4.8
|
29.2
|
1.0
|
CB
|
A:LYS51
|
4.8
|
24.2
|
1.0
|
O5'
|
A:ADP1600
|
4.8
|
21.7
|
1.0
|
O2B
|
A:ADP1600
|
4.9
|
21.7
|
1.0
|
CA
|
A:THR30
|
4.9
|
21.7
|
1.0
|
C
|
A:ASP52
|
4.9
|
29.2
|
1.0
|
N
|
A:LEU31
|
5.0
|
23.3
|
1.0
|
CA
|
A:LYS51
|
5.0
|
24.2
|
1.0
|
|
Potassium binding site 2 out
of 7 in 8p4o
Go back to
Potassium Binding Sites List in 8p4o
Potassium 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 Potassium with other atoms in the K 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:K1603
b:36.5
occ:1.00
|
O
|
B:THR30
|
2.8
|
22.4
|
1.0
|
F3
|
B:BEF1602
|
2.8
|
29.9
|
1.0
|
O
|
B:LYS51
|
2.9
|
23.2
|
1.0
|
O3A
|
B:ADP1600
|
3.0
|
23.0
|
1.0
|
O1A
|
B:ADP1600
|
3.1
|
23.0
|
1.0
|
OG1
|
B:THR90
|
3.4
|
23.5
|
1.0
|
PA
|
B:ADP1600
|
3.5
|
23.0
|
1.0
|
OG1
|
B:THR30
|
3.5
|
22.4
|
1.0
|
F1
|
B:BEF1602
|
3.9
|
29.9
|
1.0
|
O3B
|
B:ADP1600
|
3.9
|
23.0
|
1.0
|
BE
|
B:BEF1602
|
3.9
|
29.9
|
1.0
|
C
|
B:THR30
|
4.0
|
22.4
|
1.0
|
O2A
|
B:ADP1600
|
4.0
|
23.0
|
1.0
|
C
|
B:LYS51
|
4.1
|
23.2
|
1.0
|
N
|
B:GLY53
|
4.2
|
27.2
|
1.0
|
PB
|
B:ADP1600
|
4.2
|
23.0
|
1.0
|
CB
|
B:THR30
|
4.2
|
22.4
|
1.0
|
CB
|
B:THR90
|
4.3
|
23.5
|
1.0
|
CA
|
B:ASP52
|
4.5
|
30.9
|
1.0
|
C
|
B:ASP52
|
4.6
|
30.9
|
1.0
|
MG
|
B:MG1601
|
4.7
|
30.2
|
1.0
|
CE
|
B:LYS51
|
4.7
|
23.2
|
1.0
|
CA
|
B:THR30
|
4.8
|
22.4
|
1.0
|
N
|
B:ASP52
|
4.8
|
30.9
|
1.0
|
CG
|
B:LYS51
|
4.8
|
23.2
|
1.0
|
CD
|
B:LYS51
|
4.9
|
23.2
|
1.0
|
N
|
B:LEU31
|
4.9
|
23.3
|
1.0
|
CG2
|
B:THR90
|
4.9
|
23.5
|
1.0
|
O5'
|
B:ADP1600
|
5.0
|
23.0
|
1.0
|
CA
|
B:LEU31
|
5.0
|
23.3
|
1.0
|
O2B
|
B:ADP1600
|
5.0
|
23.0
|
1.0
|
|
Potassium binding site 3 out
of 7 in 8p4o
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Potassium Binding Sites List in 8p4o
Potassium 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 Potassium with other atoms in the K 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:K1603
b:33.6
occ:1.00
|
F3
|
C:BEF1602
|
2.8
|
38.4
|
1.0
|
O
|
C:THR30
|
2.8
|
23.9
|
1.0
|
O
|
C:LYS51
|
2.8
|
25.9
|
1.0
|
OG1
|
C:THR90
|
2.9
|
27.5
|
1.0
|
OG1
|
C:THR30
|
3.1
|
23.9
|
1.0
|
O3A
|
C:ADP1600
|
3.3
|
51.5
|
1.0
|
O1A
|
C:ADP1600
|
3.4
|
51.5
|
1.0
|
N
|
C:GLY53
|
3.8
|
27.8
|
1.0
|
C
|
C:THR30
|
3.8
|
23.9
|
1.0
|
O3B
|
C:ADP1600
|
3.9
|
51.5
|
1.0
|
CB
|
C:THR90
|
3.9
|
27.5
|
1.0
|
PA
|
C:ADP1600
|
3.9
|
51.5
|
1.0
|
CB
|
C:THR30
|
3.9
|
23.9
|
1.0
|
C
|
C:LYS51
|
4.0
|
25.9
|
1.0
|
BE
|
C:BEF1602
|
4.1
|
38.4
|
1.0
|
CA
|
C:ASP52
|
4.3
|
29.2
|
1.0
|
C
|
C:ASP52
|
4.3
|
29.2
|
1.0
|
PB
|
C:ADP1600
|
4.3
|
51.5
|
1.0
|
F1
|
C:BEF1602
|
4.4
|
38.4
|
1.0
|
CG
|
C:LYS51
|
4.5
|
25.9
|
1.0
|
CG2
|
C:THR90
|
4.5
|
27.5
|
1.0
|
CA
|
C:GLY53
|
4.5
|
27.8
|
1.0
|
CA
|
C:THR30
|
4.5
|
23.9
|
1.0
|
O2A
|
C:ADP1600
|
4.6
|
51.5
|
1.0
|
N
|
C:ASP52
|
4.6
|
29.2
|
1.0
|
N
|
C:LEU31
|
4.7
|
27.9
|
1.0
|
CA
|
C:LEU31
|
4.9
|
27.9
|
1.0
|
|
Potassium binding site 4 out
of 7 in 8p4o
Go back to
Potassium Binding Sites List in 8p4o
Potassium 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 Potassium with other atoms in the K 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:K1603
b:37.0
occ:1.00
|
O
|
D:LYS51
|
2.8
|
27.1
|
1.0
|
O
|
D:THR30
|
2.8
|
25.4
|
1.0
|
F3
|
D:BEF1602
|
2.8
|
41.0
|
1.0
|
O3A
|
D:ADP1600
|
3.3
|
51.5
|
1.0
|
O1A
|
D:ADP1600
|
3.3
|
51.5
|
1.0
|
OG1
|
D:THR90
|
3.4
|
27.9
|
1.0
|
OG1
|
D:THR30
|
3.5
|
25.4
|
1.0
|
PA
|
D:ADP1600
|
3.8
|
51.5
|
1.0
|
C
|
D:LYS51
|
3.9
|
27.1
|
1.0
|
C
|
D:THR30
|
4.0
|
25.4
|
1.0
|
N
|
D:GLY53
|
4.0
|
30.1
|
1.0
|
BE
|
D:BEF1602
|
4.0
|
41.0
|
1.0
|
F1
|
D:BEF1602
|
4.1
|
41.0
|
1.0
|
O3B
|
D:ADP1600
|
4.1
|
51.5
|
1.0
|
CB
|
D:THR30
|
4.2
|
25.4
|
1.0
|
CA
|
D:ASP52
|
4.2
|
33.5
|
1.0
|
O2A
|
D:ADP1600
|
4.3
|
51.5
|
1.0
|
CG
|
D:LYS51
|
4.4
|
27.1
|
1.0
|
CB
|
D:THR90
|
4.4
|
27.9
|
1.0
|
C
|
D:ASP52
|
4.4
|
33.5
|
1.0
|
PB
|
D:ADP1600
|
4.4
|
51.5
|
1.0
|
N
|
D:ASP52
|
4.5
|
33.5
|
1.0
|
CE
|
D:LYS51
|
4.7
|
27.1
|
1.0
|
F2
|
D:BEF1602
|
4.8
|
41.0
|
1.0
|
CA
|
D:THR30
|
4.8
|
25.4
|
1.0
|
CD
|
D:LYS51
|
4.8
|
27.1
|
1.0
|
CA
|
D:GLY53
|
4.8
|
30.1
|
1.0
|
CB
|
D:LYS51
|
4.9
|
27.1
|
1.0
|
CA
|
D:LYS51
|
5.0
|
27.1
|
1.0
|
CG2
|
D:THR90
|
5.0
|
27.9
|
1.0
|
N
|
D:LEU31
|
5.0
|
28.2
|
1.0
|
OD1
|
D:ASP52
|
5.0
|
33.5
|
1.0
|
|
Potassium binding site 5 out
of 7 in 8p4o
Go back to
Potassium Binding Sites List in 8p4o
Potassium 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 Potassium with other atoms in the K 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:K1603
b:39.3
occ:1.00
|
O
|
E:LYS51
|
2.8
|
27.4
|
1.0
|
O
|
E:THR30
|
2.8
|
24.1
|
1.0
|
F3
|
E:BEF1602
|
2.8
|
39.7
|
1.0
|
O1A
|
E:ADP1600
|
3.1
|
51.5
|
1.0
|
O3A
|
E:ADP1600
|
3.1
|
51.5
|
1.0
|
OG1
|
E:THR90
|
3.2
|
27.3
|
1.0
|
PA
|
E:ADP1600
|
3.6
|
51.5
|
1.0
|
OG1
|
E:THR30
|
3.7
|
24.1
|
1.0
|
C
|
E:LYS51
|
4.0
|
27.4
|
1.0
|
C
|
E:THR30
|
4.0
|
24.1
|
1.0
|
BE
|
E:BEF1602
|
4.0
|
39.7
|
1.0
|
O3B
|
E:ADP1600
|
4.0
|
51.5
|
1.0
|
F1
|
E:BEF1602
|
4.1
|
39.7
|
1.0
|
N
|
E:GLY53
|
4.2
|
28.2
|
1.0
|
CB
|
E:THR90
|
4.2
|
27.3
|
1.0
|
O2A
|
E:ADP1600
|
4.3
|
51.5
|
1.0
|
CA
|
E:ASP52
|
4.3
|
32.0
|
1.0
|
CB
|
E:THR30
|
4.3
|
24.1
|
1.0
|
PB
|
E:ADP1600
|
4.3
|
51.5
|
1.0
|
C
|
E:ASP52
|
4.4
|
32.0
|
1.0
|
NZ
|
E:LYS51
|
4.5
|
27.4
|
1.0
|
N
|
E:ASP52
|
4.6
|
32.0
|
1.0
|
F2
|
E:BEF1602
|
4.7
|
39.7
|
1.0
|
CG
|
E:LYS51
|
4.8
|
27.4
|
1.0
|
CG2
|
E:THR90
|
4.8
|
27.3
|
1.0
|
CA
|
E:THR30
|
4.8
|
24.1
|
1.0
|
N
|
E:LEU31
|
4.9
|
26.9
|
1.0
|
CA
|
E:GLY53
|
4.9
|
28.2
|
1.0
|
CA
|
E:LEU31
|
5.0
|
26.9
|
1.0
|
|
Potassium binding site 6 out
of 7 in 8p4o
Go back to
Potassium Binding Sites List in 8p4o
Potassium 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 Potassium with other atoms in the K 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:K1603
b:39.2
occ:1.00
|
O
|
F:THR30
|
2.8
|
22.5
|
1.0
|
F3
|
F:BEF1602
|
2.8
|
40.8
|
1.0
|
O
|
F:LYS51
|
2.9
|
24.4
|
1.0
|
O3A
|
F:ADP1600
|
3.0
|
51.5
|
1.0
|
O1A
|
F:ADP1600
|
3.1
|
51.5
|
1.0
|
OG1
|
F:THR90
|
3.3
|
28.1
|
1.0
|
PA
|
F:ADP1600
|
3.4
|
51.5
|
1.0
|
OG1
|
F:THR30
|
3.8
|
22.5
|
1.0
|
C
|
F:THR30
|
3.9
|
22.5
|
1.0
|
O2A
|
F:ADP1600
|
4.0
|
51.5
|
1.0
|
O3B
|
F:ADP1600
|
4.0
|
51.5
|
1.0
|
F1
|
F:BEF1602
|
4.0
|
40.8
|
1.0
|
BE
|
F:BEF1602
|
4.0
|
40.8
|
1.0
|
C
|
F:LYS51
|
4.0
|
24.4
|
1.0
|
CB
|
F:THR90
|
4.2
|
28.1
|
1.0
|
PB
|
F:ADP1600
|
4.2
|
51.5
|
1.0
|
CB
|
F:THR30
|
4.2
|
22.5
|
1.0
|
N
|
F:GLY53
|
4.3
|
28.0
|
1.0
|
CA
|
F:ASP52
|
4.4
|
32.2
|
1.0
|
CG
|
F:LYS51
|
4.6
|
24.4
|
1.0
|
N
|
F:ASP52
|
4.7
|
32.2
|
1.0
|
C
|
F:ASP52
|
4.7
|
32.2
|
1.0
|
MG
|
F:MG1601
|
4.7
|
42.8
|
1.0
|
CA
|
F:THR30
|
4.8
|
22.5
|
1.0
|
CG2
|
F:THR90
|
4.8
|
28.1
|
1.0
|
F2
|
F:BEF1602
|
4.8
|
40.8
|
1.0
|
N
|
F:LEU31
|
4.8
|
27.5
|
1.0
|
CA
|
F:LEU31
|
4.9
|
27.5
|
1.0
|
O5'
|
F:ADP1600
|
4.9
|
51.5
|
1.0
|
O2B
|
F:ADP1600
|
5.0
|
51.5
|
1.0
|
|
Potassium binding site 7 out
of 7 in 8p4o
Go back to
Potassium Binding Sites List in 8p4o
Potassium 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 Potassium with other atoms in the K 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:K1603
b:39.3
occ:1.00
|
O
|
G:THR30
|
2.8
|
25.3
|
1.0
|
O
|
G:LYS51
|
2.9
|
25.2
|
1.0
|
O1A
|
G:ADP1600
|
3.0
|
51.5
|
1.0
|
F3
|
G:BEF1602
|
3.0
|
41.0
|
1.0
|
O3A
|
G:ADP1600
|
3.0
|
51.5
|
1.0
|
OG1
|
G:THR90
|
3.4
|
27.2
|
1.0
|
PA
|
G:ADP1600
|
3.4
|
51.5
|
1.0
|
OG1
|
G:THR30
|
3.8
|
25.3
|
1.0
|
O3B
|
G:ADP1600
|
3.9
|
51.5
|
1.0
|
F1
|
G:BEF1602
|
3.9
|
41.0
|
1.0
|
C
|
G:THR30
|
3.9
|
25.3
|
1.0
|
BE
|
G:BEF1602
|
4.0
|
41.0
|
1.0
|
O2A
|
G:ADP1600
|
4.0
|
51.5
|
1.0
|
C
|
G:LYS51
|
4.1
|
25.2
|
1.0
|
PB
|
G:ADP1600
|
4.2
|
51.5
|
1.0
|
CB
|
G:THR30
|
4.2
|
25.3
|
1.0
|
N
|
G:GLY53
|
4.3
|
27.2
|
1.0
|
CB
|
G:THR90
|
4.3
|
27.2
|
1.0
|
NZ
|
G:LYS51
|
4.3
|
25.2
|
1.0
|
CA
|
G:ASP52
|
4.5
|
31.7
|
1.0
|
CG
|
G:LYS51
|
4.5
|
25.2
|
1.0
|
F2
|
G:BEF1602
|
4.6
|
41.0
|
1.0
|
C
|
G:ASP52
|
4.7
|
31.7
|
1.0
|
CA
|
G:THR30
|
4.8
|
25.3
|
1.0
|
N
|
G:ASP52
|
4.8
|
31.7
|
1.0
|
N
|
G:LEU31
|
4.8
|
23.2
|
1.0
|
CA
|
G:LEU31
|
4.8
|
23.2
|
1.0
|
CG2
|
G:THR90
|
4.9
|
27.2
|
1.0
|
O5'
|
G:ADP1600
|
4.9
|
51.5
|
1.0
|
O2B
|
G:ADP1600
|
5.0
|
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: Tue Aug 13 00:22:25 2024
|