Potassium in PDB 7zre: Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
Enzymatic activity of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
All present enzymatic activity of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions:
7.2.2.6;
Potassium Binding Sites:
The binding sites of Potassium atom in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
(pdb code 7zre). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the
Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions, PDB code: 7zre:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Potassium binding site 1 out
of 9 in 7zre
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Potassium Binding Sites List in 7zre
Potassium binding site 1 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K601
b:23.7
occ:1.00
|
OG1
|
A:THR542
|
3.3
|
19.0
|
1.0
|
CG1
|
A:VAL538
|
3.4
|
20.7
|
1.0
|
CG
|
A:PRO425
|
3.5
|
15.8
|
1.0
|
CB
|
A:THR542
|
4.0
|
19.0
|
1.0
|
O
|
A:ILE368
|
4.1
|
16.9
|
1.0
|
O
|
A:VAL538
|
4.1
|
20.7
|
1.0
|
CG2
|
A:THR542
|
4.3
|
19.0
|
1.0
|
K
|
A:K602
|
4.3
|
35.3
|
1.0
|
C
|
A:VAL538
|
4.4
|
20.7
|
1.0
|
CB
|
A:PRO425
|
4.5
|
15.8
|
1.0
|
CZ
|
A:PHE386
|
4.6
|
18.7
|
1.0
|
CA
|
A:GLY539
|
4.6
|
19.7
|
1.0
|
N
|
A:GLY539
|
4.6
|
19.7
|
1.0
|
CD
|
A:PRO425
|
4.6
|
15.8
|
1.0
|
O
|
A:GLN367
|
4.7
|
15.4
|
1.0
|
C
|
A:ILE368
|
4.7
|
16.9
|
1.0
|
CB
|
A:VAL538
|
4.7
|
20.7
|
1.0
|
O
|
A:ILE421
|
4.7
|
16.5
|
1.0
|
CG2
|
A:ILE421
|
4.7
|
16.5
|
1.0
|
CE2
|
A:PHE543
|
4.8
|
17.5
|
1.0
|
CA
|
A:ILE368
|
5.0
|
16.9
|
1.0
|
|
Potassium binding site 2 out
of 9 in 7zre
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Potassium Binding Sites List in 7zre
Potassium binding site 2 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K602
b:35.3
occ:1.00
|
OG1
|
A:THR424
|
3.2
|
16.1
|
1.0
|
O
|
A:ILE421
|
3.6
|
16.5
|
1.0
|
CA
|
A:GLY369
|
3.8
|
17.4
|
1.0
|
O
|
A:ILE368
|
4.0
|
16.9
|
1.0
|
CA
|
A:ILE421
|
4.0
|
16.5
|
1.0
|
CD
|
A:PRO425
|
4.0
|
15.8
|
1.0
|
C
|
A:ILE421
|
4.2
|
16.5
|
1.0
|
CG2
|
A:ILE421
|
4.2
|
16.5
|
1.0
|
K
|
A:K601
|
4.3
|
23.7
|
1.0
|
CG
|
A:PRO425
|
4.4
|
15.8
|
1.0
|
CE2
|
A:PHE386
|
4.4
|
18.7
|
1.0
|
CZ
|
A:PHE386
|
4.4
|
18.7
|
1.0
|
CB
|
A:ILE421
|
4.6
|
16.5
|
1.0
|
O
|
A:ALA420
|
4.6
|
16.6
|
1.0
|
N
|
A:GLY369
|
4.6
|
17.4
|
1.0
|
C
|
A:ILE368
|
4.7
|
16.9
|
1.0
|
CB
|
A:THR424
|
4.7
|
16.1
|
1.0
|
CG1
|
A:ILE421
|
4.8
|
16.5
|
1.0
|
K
|
A:K603
|
4.8
|
37.9
|
1.0
|
C
|
A:GLY369
|
5.0
|
17.4
|
1.0
|
|
Potassium binding site 3 out
of 9 in 7zre
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Potassium Binding Sites List in 7zre
Potassium binding site 3 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K603
b:37.9
occ:1.00
|
O
|
A:GLY369
|
3.0
|
17.4
|
1.0
|
K
|
A:K604
|
3.1
|
21.4
|
1.0
|
C
|
A:GLY369
|
4.1
|
17.4
|
1.0
|
CG1
|
A:VAL496
|
4.1
|
13.8
|
1.0
|
CG2
|
A:VAL496
|
4.4
|
13.8
|
1.0
|
CA
|
A:GLY369
|
4.5
|
17.4
|
1.0
|
OG1
|
A:THR424
|
4.6
|
16.1
|
1.0
|
CG2
|
A:THR424
|
4.6
|
16.1
|
1.0
|
ND2
|
A:ASN465
|
4.7
|
13.6
|
1.0
|
CB
|
A:VAL496
|
4.7
|
13.8
|
1.0
|
K
|
A:K602
|
4.8
|
35.3
|
1.0
|
K
|
A:K605
|
4.8
|
33.7
|
1.0
|
O
|
A:SER378
|
4.9
|
17.3
|
1.0
|
CA
|
A:GLY382
|
4.9
|
17.4
|
1.0
|
|
Potassium binding site 4 out
of 9 in 7zre
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Potassium Binding Sites List in 7zre
Potassium binding site 4 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K604
b:21.4
occ:1.00
|
K
|
A:K603
|
3.1
|
37.9
|
1.0
|
OD1
|
A:ASN466
|
3.4
|
14.3
|
1.0
|
K
|
A:K605
|
3.4
|
33.7
|
1.0
|
CG
|
A:ASN466
|
4.0
|
14.3
|
1.0
|
O
|
A:ASN465
|
4.2
|
13.6
|
1.0
|
CG2
|
A:THR424
|
4.3
|
16.1
|
1.0
|
C
|
A:ASN465
|
4.3
|
13.6
|
1.0
|
CB
|
A:ASN466
|
4.4
|
14.3
|
1.0
|
CG2
|
A:VAL496
|
4.5
|
13.8
|
1.0
|
O
|
A:ALA464
|
4.5
|
12.9
|
1.0
|
CA
|
A:ASN465
|
4.5
|
13.6
|
1.0
|
CB
|
A:VAL496
|
4.7
|
13.8
|
1.0
|
O
|
A:GLY492
|
4.7
|
13.2
|
1.0
|
ND2
|
A:ASN465
|
4.8
|
13.6
|
1.0
|
CG1
|
A:VAL496
|
4.8
|
13.8
|
1.0
|
N
|
A:ASN466
|
4.9
|
14.3
|
1.0
|
O
|
A:GLY369
|
4.9
|
17.4
|
1.0
|
C
|
A:GLY492
|
4.9
|
13.2
|
1.0
|
CA
|
A:ARG493
|
4.9
|
13.5
|
1.0
|
ND2
|
A:ASN466
|
5.0
|
14.3
|
1.0
|
|
Potassium binding site 5 out
of 9 in 7zre
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Potassium Binding Sites List in 7zre
Potassium binding site 5 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_05.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K605
b:33.7
occ:1.00
|
OG
|
A:SER343
|
3.2
|
15.4
|
1.0
|
CB
|
A:SER378
|
3.3
|
17.3
|
1.0
|
K
|
A:K604
|
3.4
|
21.4
|
1.0
|
O
|
A:ASN465
|
3.6
|
13.6
|
1.0
|
CB
|
A:ASN466
|
3.8
|
14.3
|
1.0
|
CB
|
A:SER343
|
3.9
|
15.4
|
1.0
|
OG
|
A:SER378
|
4.0
|
17.3
|
1.0
|
CB
|
A:GLU370
|
4.3
|
15.9
|
1.0
|
OD1
|
A:ASN466
|
4.3
|
14.3
|
1.0
|
CA
|
A:GLY375
|
4.3
|
15.4
|
1.0
|
C
|
A:ASN465
|
4.5
|
13.6
|
1.0
|
CG
|
A:ASN466
|
4.6
|
14.3
|
1.0
|
CA
|
A:SER378
|
4.6
|
17.3
|
1.0
|
O
|
A:ASN466
|
4.6
|
14.3
|
1.0
|
N
|
A:GLY375
|
4.6
|
15.4
|
1.0
|
O
|
A:GLU370
|
4.6
|
15.9
|
1.0
|
C
|
A:SER378
|
4.6
|
17.3
|
1.0
|
N
|
A:GLY379
|
4.8
|
16.6
|
1.0
|
CA
|
A:ASN466
|
4.8
|
14.3
|
1.0
|
K
|
A:K603
|
4.8
|
37.9
|
1.0
|
CG
|
A:GLU370
|
4.9
|
15.9
|
1.0
|
C
|
A:ASN466
|
5.0
|
14.3
|
1.0
|
|
Potassium binding site 6 out
of 9 in 7zre
Go back to
Potassium Binding Sites List in 7zre
Potassium binding site 6 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_06.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K606
b:14.3
occ:1.00
|
O
|
A:ASN231
|
2.8
|
14.6
|
1.0
|
O
|
A:ASN112
|
2.8
|
14.6
|
1.0
|
O
|
A:ASN467
|
2.9
|
14.4
|
1.0
|
O
|
A:SER343
|
2.9
|
15.4
|
1.0
|
O
|
A:ASN466
|
2.9
|
14.3
|
1.0
|
O
|
A:THR113
|
3.0
|
13.8
|
1.0
|
CA
|
A:THR113
|
3.5
|
13.8
|
1.0
|
C
|
A:THR113
|
3.5
|
13.8
|
1.0
|
C
|
A:ASN467
|
3.6
|
14.4
|
1.0
|
C
|
A:SER343
|
3.6
|
15.4
|
1.0
|
O
|
A:THR230
|
3.6
|
15.1
|
1.0
|
C
|
A:ASN112
|
3.6
|
14.6
|
1.0
|
C
|
A:ASN466
|
3.8
|
14.3
|
1.0
|
C
|
A:ASN231
|
3.8
|
14.6
|
1.0
|
CA
|
A:ASN467
|
3.9
|
14.4
|
1.0
|
N
|
A:THR113
|
3.9
|
13.8
|
1.0
|
OD1
|
A:ASN112
|
4.1
|
14.6
|
1.0
|
CA
|
A:CYS344
|
4.1
|
15.5
|
1.0
|
N
|
A:CYS344
|
4.2
|
15.5
|
1.0
|
OD1
|
A:ASN114
|
4.2
|
14.7
|
1.0
|
N
|
A:GLY345
|
4.2
|
15.4
|
1.0
|
N
|
A:ASN467
|
4.2
|
14.4
|
1.0
|
CA
|
A:ASN231
|
4.3
|
14.6
|
1.0
|
CB
|
A:SER343
|
4.5
|
15.4
|
1.0
|
CA
|
A:SER343
|
4.5
|
15.4
|
1.0
|
C
|
A:CYS344
|
4.5
|
15.5
|
1.0
|
C
|
A:THR230
|
4.6
|
15.1
|
1.0
|
N
|
A:ASN114
|
4.6
|
14.7
|
1.0
|
N
|
A:GLY468
|
4.6
|
14.7
|
1.0
|
CB
|
A:ASN114
|
4.8
|
14.7
|
1.0
|
CB
|
A:THR113
|
4.8
|
13.8
|
1.0
|
CG
|
A:ASN112
|
4.9
|
14.6
|
1.0
|
N
|
A:ASN231
|
4.9
|
14.6
|
1.0
|
CA
|
A:ASN112
|
4.9
|
14.6
|
1.0
|
OD1
|
A:ASN467
|
4.9
|
14.4
|
1.0
|
CG
|
A:ASN114
|
4.9
|
14.7
|
1.0
|
N
|
A:GLY232
|
4.9
|
15.2
|
1.0
|
CA
|
A:ASN466
|
5.0
|
14.3
|
1.0
|
CG2
|
A:THR113
|
5.0
|
13.8
|
1.0
|
|
Potassium binding site 7 out
of 9 in 7zre
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Potassium Binding Sites List in 7zre
Potassium binding site 7 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_07.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 7 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K607
b:17.1
occ:1.00
|
O
|
A:ASN114
|
3.0
|
14.7
|
1.0
|
ND2
|
A:ASN239
|
3.1
|
16.7
|
1.0
|
O
|
A:GLY232
|
3.2
|
15.2
|
1.0
|
OE1
|
A:GLN116
|
3.3
|
16.7
|
1.0
|
OD1
|
A:ASN239
|
3.4
|
16.7
|
1.0
|
CG
|
A:ASN239
|
3.4
|
16.7
|
1.0
|
O
|
A:GLY468
|
3.5
|
14.7
|
1.0
|
CD
|
A:GLN116
|
3.8
|
16.7
|
1.0
|
CG
|
A:GLN116
|
3.8
|
16.7
|
1.0
|
CB
|
A:GLN116
|
3.9
|
16.7
|
1.0
|
N
|
A:GLN116
|
3.9
|
16.7
|
1.0
|
O
|
A:GLY345
|
4.0
|
15.4
|
1.0
|
C
|
A:ASN114
|
4.2
|
14.7
|
1.0
|
C
|
A:GLY232
|
4.3
|
15.2
|
1.0
|
C
|
A:TRP115
|
4.4
|
14.8
|
1.0
|
CA
|
A:TRP115
|
4.4
|
14.8
|
1.0
|
C
|
A:GLY468
|
4.5
|
14.7
|
1.0
|
C
|
A:GLY345
|
4.5
|
15.4
|
1.0
|
CA
|
A:GLN116
|
4.5
|
16.7
|
1.0
|
CB
|
A:ASN239
|
4.6
|
16.7
|
1.0
|
CA
|
A:GLY345
|
4.6
|
15.4
|
1.0
|
CA
|
A:GLY233
|
4.7
|
15.4
|
1.0
|
N
|
A:TRP115
|
4.7
|
14.8
|
1.0
|
N
|
A:GLY234
|
4.8
|
16.4
|
1.0
|
NE2
|
A:GLN116
|
4.9
|
16.7
|
1.0
|
|
Potassium binding site 8 out
of 9 in 7zre
Go back to
Potassium Binding Sites List in 7zre
Potassium binding site 8 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_08.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K701
b:32.2
occ:1.00
|
CB
|
B:ALA227
|
3.7
|
19.8
|
1.0
|
CD2
|
B:LEU228
|
4.1
|
20.5
|
1.0
|
CD1
|
A:LEU389
|
4.3
|
21.1
|
1.0
|
CD2
|
A:LEU389
|
4.4
|
21.1
|
1.0
|
N
|
B:LEU228
|
4.4
|
20.5
|
1.0
|
CG
|
B:LEU228
|
4.4
|
20.5
|
1.0
|
C
|
B:ALA227
|
4.5
|
19.8
|
1.0
|
CG2
|
A:ILE421
|
4.5
|
16.5
|
1.0
|
O
|
B:LEU224
|
4.5
|
22.0
|
1.0
|
CA
|
B:ALA227
|
4.7
|
19.8
|
1.0
|
CG
|
B:LEU224
|
4.9
|
22.0
|
1.0
|
O
|
B:ALA227
|
4.9
|
19.8
|
1.0
|
CA
|
B:LEU228
|
4.9
|
20.5
|
1.0
|
CG
|
A:LEU389
|
5.0
|
21.1
|
1.0
|
|
Potassium binding site 9 out
of 9 in 7zre
Go back to
Potassium Binding Sites List in 7zre
Potassium binding site 9 out
of 9 in the Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions
![](/pictures/K/pdb/zr/7zre-K-sphere_09.jpg) Mono view
![](/pictures/K/pdb/zr/7zre-K-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Cryo-Em Map of the Wt Kdpfabc Complex in the E1-P Tight Conformation, Under Turnover Conditions within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K702
b:27.7
occ:1.00
|
O
|
B:ILE263
|
3.0
|
21.3
|
1.0
|
ND2
|
B:ASN624
|
3.0
|
26.9
|
1.0
|
O
|
B:CYS261
|
3.3
|
22.8
|
1.0
|
NZ
|
B:LYS586
|
3.7
|
24.2
|
1.0
|
OD1
|
B:ASP583
|
3.9
|
25.8
|
1.0
|
OG1
|
B:THR265
|
3.9
|
23.8
|
1.0
|
N
|
B:THR265
|
3.9
|
23.8
|
1.0
|
C
|
B:ILE263
|
4.0
|
21.3
|
1.0
|
C
|
B:CYS261
|
4.1
|
22.8
|
1.0
|
CG
|
B:ASN624
|
4.1
|
26.9
|
1.0
|
CA
|
B:PRO264
|
4.2
|
22.2
|
1.0
|
O
|
B:LEU262
|
4.3
|
21.2
|
1.0
|
C
|
B:LEU262
|
4.4
|
21.2
|
1.0
|
O
|
B:VAL260
|
4.5
|
22.1
|
1.0
|
O
|
B:SER579
|
4.5
|
26.0
|
1.0
|
N
|
B:PRO264
|
4.5
|
22.2
|
1.0
|
C
|
B:PRO264
|
4.6
|
22.2
|
1.0
|
N
|
B:LEU262
|
4.7
|
21.2
|
1.0
|
N
|
B:ILE263
|
4.8
|
21.3
|
1.0
|
CB
|
B:THR265
|
4.8
|
23.8
|
1.0
|
CA
|
B:CYS261
|
4.8
|
22.8
|
1.0
|
CG2
|
B:THR265
|
4.8
|
23.8
|
1.0
|
CA
|
B:LEU262
|
4.8
|
21.2
|
1.0
|
OD1
|
B:ASN624
|
4.9
|
26.9
|
1.0
|
CA
|
B:THR265
|
4.9
|
23.8
|
1.0
|
OG1
|
B:THR266
|
4.9
|
25.4
|
1.0
|
CB
|
B:ASN624
|
4.9
|
26.9
|
1.0
|
CG
|
B:ASP583
|
5.0
|
25.8
|
1.0
|
N
|
B:THR266
|
5.0
|
25.4
|
1.0
|
|
Reference:
J.M.Silberberg,
C.Stock,
L.Hielkema,
R.A.Corey,
J.Rheinberger,
D.Wunnicke,
V.R.A.Dubach,
P.J.Stansfeld,
I.Hanelt,
C.Paulino.
Inhibited Kdpfabc Transitions Into An E1 Off-Cycle State. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36255052
DOI: 10.7554/ELIFE.80988
Page generated: Mon Aug 12 21:52:38 2024
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