Potassium in PDB 7zrh: Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
Enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
All present enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+:
7.2.2.6;
Potassium Binding Sites:
The binding sites of Potassium atom in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
(pdb code 7zrh). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the
Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+, PDB code: 7zrh:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
Potassium binding site 1 out
of 7 in 7zrh
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Potassium Binding Sites List in 7zrh
Potassium binding site 1 out
of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
![](/pictures/K/pdb/zr/7zrh-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/zr/7zrh-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 Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K601
b:17.1
occ:1.00
|
CG2
|
A:ILE421
|
3.4
|
9.6
|
1.0
|
CD1
|
A:LEU389
|
3.8
|
11.9
|
1.0
|
CB
|
B:ALA227
|
4.2
|
6.8
|
1.0
|
CB
|
A:ILE421
|
4.4
|
9.6
|
1.0
|
CG1
|
A:VAL538
|
4.6
|
13.3
|
1.0
|
CD2
|
B:LEU228
|
4.6
|
7.9
|
1.0
|
CG
|
B:LEU228
|
4.8
|
7.9
|
1.0
|
CG1
|
A:ILE421
|
4.8
|
9.6
|
1.0
|
CG2
|
A:VAL538
|
4.9
|
13.3
|
1.0
|
N
|
B:LEU228
|
5.0
|
7.9
|
1.0
|
|
Potassium binding site 2 out
of 7 in 7zrh
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Potassium Binding Sites List in 7zrh
Potassium binding site 2 out
of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
![](/pictures/K/pdb/zr/7zrh-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/zr/7zrh-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 Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K602
b:34.5
occ:1.00
|
O
|
A:GLY468
|
2.9
|
10.9
|
1.0
|
O
|
A:GLY345
|
3.4
|
8.2
|
1.0
|
O
|
A:ASN114
|
3.5
|
13.6
|
1.0
|
ND2
|
A:ASN239
|
3.5
|
8.8
|
1.0
|
O
|
A:GLY232
|
3.6
|
7.3
|
1.0
|
CG
|
A:ASN239
|
3.8
|
8.8
|
1.0
|
C
|
A:GLY468
|
3.9
|
10.9
|
1.0
|
OD1
|
A:ASN239
|
4.2
|
8.8
|
1.0
|
C
|
A:GLY345
|
4.3
|
8.2
|
1.0
|
N
|
A:GLN116
|
4.4
|
10.8
|
1.0
|
CB
|
A:ASN239
|
4.4
|
8.8
|
1.0
|
CB
|
A:GLN116
|
4.4
|
10.8
|
1.0
|
CG
|
A:GLN116
|
4.4
|
10.8
|
1.0
|
CA
|
A:GLY345
|
4.5
|
8.2
|
1.0
|
C
|
A:ASN114
|
4.6
|
13.6
|
1.0
|
NE2
|
A:GLN116
|
4.7
|
10.8
|
1.0
|
N
|
A:SER469
|
4.7
|
10.5
|
1.0
|
CA
|
A:GLY468
|
4.7
|
10.9
|
1.0
|
C
|
A:GLY232
|
4.8
|
7.3
|
1.0
|
CA
|
A:TRP115
|
4.8
|
10.6
|
1.0
|
CA
|
A:SER469
|
4.8
|
10.5
|
1.0
|
C
|
A:TRP115
|
5.0
|
10.6
|
1.0
|
|
Potassium binding site 3 out
of 7 in 7zrh
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Potassium Binding Sites List in 7zrh
Potassium binding site 3 out
of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
![](/pictures/K/pdb/zr/7zrh-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/zr/7zrh-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 Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K603
b:55.1
occ:1.00
|
OD1
|
A:ASN466
|
3.9
|
17.9
|
1.0
|
O
|
A:GLY492
|
4.1
|
20.1
|
1.0
|
CB
|
A:SER378
|
4.2
|
12.2
|
1.0
|
CG2
|
A:VAL496
|
4.2
|
20.1
|
1.0
|
NH1
|
A:ARG493
|
4.2
|
20.1
|
1.0
|
CB
|
A:VAL496
|
4.3
|
20.1
|
1.0
|
CG1
|
A:VAL496
|
4.3
|
20.1
|
1.0
|
OG
|
A:SER378
|
4.6
|
12.2
|
1.0
|
O
|
A:ASN465
|
4.7
|
17.9
|
1.0
|
CB
|
A:ASN466
|
4.7
|
17.9
|
1.0
|
CG
|
A:ASN466
|
4.7
|
17.9
|
1.0
|
CA
|
A:ARG493
|
4.8
|
20.1
|
1.0
|
|
Potassium binding site 4 out
of 7 in 7zrh
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Potassium Binding Sites List in 7zrh
Potassium binding site 4 out
of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
![](/pictures/K/pdb/zr/7zrh-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/zr/7zrh-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 Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K604
b:25.2
occ:1.00
|
CG
|
A:PRO425
|
3.4
|
17.4
|
1.0
|
CG1
|
A:VAL538
|
3.5
|
13.3
|
1.0
|
O
|
A:VAL538
|
4.2
|
13.3
|
1.0
|
O
|
A:ILE421
|
4.3
|
9.6
|
1.0
|
CG2
|
A:ILE421
|
4.3
|
9.6
|
1.0
|
CD
|
A:PRO425
|
4.3
|
17.4
|
1.0
|
CZ
|
A:PHE386
|
4.4
|
9.6
|
1.0
|
OG1
|
A:THR542
|
4.4
|
11.3
|
1.0
|
CB
|
A:PRO425
|
4.5
|
17.4
|
1.0
|
C
|
A:VAL538
|
4.5
|
13.3
|
1.0
|
CE1
|
A:PHE386
|
4.6
|
9.6
|
1.0
|
CA
|
A:GLY539
|
4.7
|
12.6
|
1.0
|
N
|
A:GLY539
|
4.8
|
12.6
|
1.0
|
CG2
|
A:THR542
|
4.8
|
11.3
|
1.0
|
CB
|
A:VAL538
|
4.8
|
13.3
|
1.0
|
O
|
A:ILE368
|
4.8
|
12.1
|
1.0
|
|
Potassium binding site 5 out
of 7 in 7zrh
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Potassium Binding Sites List in 7zrh
Potassium binding site 5 out
of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
![](/pictures/K/pdb/zr/7zrh-K-sphere_05.jpg) Mono view
![](/pictures/K/pdb/zr/7zrh-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 Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K605
b:15.1
occ:1.00
|
O
|
A:ASN231
|
2.8
|
9.4
|
1.0
|
O
|
A:ASN112
|
2.8
|
17.6
|
1.0
|
O
|
A:SER343
|
2.8
|
11.6
|
1.0
|
O
|
A:ASN467
|
2.9
|
12.3
|
1.0
|
O
|
A:THR113
|
3.0
|
15.2
|
1.0
|
O
|
A:THR230
|
3.1
|
7.0
|
1.0
|
C
|
A:THR113
|
3.6
|
15.2
|
1.0
|
C
|
A:ASN231
|
3.6
|
9.4
|
1.0
|
CA
|
A:THR113
|
3.7
|
15.2
|
1.0
|
C
|
A:ASN467
|
3.8
|
12.3
|
1.0
|
C
|
A:ASN112
|
3.8
|
17.6
|
1.0
|
O
|
A:ASN466
|
3.8
|
17.9
|
1.0
|
C
|
A:SER343
|
3.8
|
11.6
|
1.0
|
N
|
A:GLY345
|
3.8
|
8.2
|
1.0
|
CA
|
A:ASN231
|
3.9
|
9.4
|
1.0
|
CA
|
A:CYS344
|
4.0
|
10.0
|
1.0
|
C
|
A:THR230
|
4.1
|
7.0
|
1.0
|
N
|
A:THR113
|
4.2
|
15.2
|
1.0
|
OG
|
A:SER343
|
4.2
|
11.6
|
1.0
|
C
|
A:CYS344
|
4.3
|
10.0
|
1.0
|
N
|
A:CYS344
|
4.3
|
10.0
|
1.0
|
CA
|
A:ASN467
|
4.3
|
12.3
|
1.0
|
N
|
A:ASN231
|
4.5
|
9.4
|
1.0
|
C
|
A:ASN466
|
4.5
|
17.9
|
1.0
|
ND2
|
A:ASN114
|
4.6
|
13.6
|
1.0
|
N
|
A:ASN114
|
4.7
|
13.6
|
1.0
|
CA
|
A:GLY345
|
4.7
|
8.2
|
1.0
|
OD1
|
A:ASN112
|
4.7
|
17.6
|
1.0
|
N
|
A:GLY468
|
4.7
|
10.9
|
1.0
|
N
|
A:GLY232
|
4.8
|
7.3
|
1.0
|
N
|
A:ASN467
|
4.8
|
12.3
|
1.0
|
CB
|
A:ASN114
|
4.9
|
13.6
|
1.0
|
CA
|
A:SER343
|
5.0
|
11.6
|
1.0
|
CA
|
A:ASN112
|
5.0
|
17.6
|
1.0
|
|
Potassium binding site 6 out
of 7 in 7zrh
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Potassium Binding Sites List in 7zrh
Potassium binding site 6 out
of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
![](/pictures/K/pdb/zr/7zrh-K-sphere_06.jpg) Mono view
![](/pictures/K/pdb/zr/7zrh-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 Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K606
b:41.1
occ:1.00
|
OG1
|
A:THR424
|
3.0
|
16.7
|
1.0
|
O
|
A:ALA420
|
3.9
|
9.3
|
1.0
|
CB
|
A:THR424
|
4.1
|
16.7
|
1.0
|
CG2
|
A:THR424
|
4.1
|
16.7
|
1.0
|
CA
|
A:GLY369
|
4.2
|
12.0
|
1.0
|
O
|
A:ILE421
|
4.5
|
9.6
|
1.0
|
CD1
|
A:ILE421
|
4.7
|
9.6
|
1.0
|
CA
|
A:ILE421
|
4.7
|
9.6
|
1.0
|
C
|
A:ALA420
|
5.0
|
9.3
|
1.0
|
|
Potassium binding site 7 out
of 7 in 7zrh
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Potassium Binding Sites List in 7zrh
Potassium binding site 7 out
of 7 in the Cryo-Em Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+
![](/pictures/K/pdb/zr/7zrh-K-sphere_07.jpg) Mono view
![](/pictures/K/pdb/zr/7zrh-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 Structure of the Kdpfabc Complex in A Nucleotide-Free E1 Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K802
b:21.8
occ:1.00
|
NZ
|
B:LYS586
|
3.1
|
10.8
|
1.0
|
OD1
|
B:ASP583
|
3.3
|
12.8
|
1.0
|
O
|
B:CYS261
|
3.5
|
8.3
|
1.0
|
O
|
B:SER579
|
3.5
|
14.7
|
1.0
|
OD1
|
B:ASN624
|
3.7
|
11.6
|
1.0
|
O
|
B:ILE263
|
3.8
|
7.5
|
1.0
|
CB
|
B:ASN582
|
3.9
|
15.1
|
1.0
|
ND2
|
B:ASN582
|
4.4
|
15.1
|
1.0
|
CE
|
B:LYS586
|
4.4
|
10.8
|
1.0
|
C
|
B:SER579
|
4.5
|
14.7
|
1.0
|
C
|
B:CYS261
|
4.5
|
8.3
|
1.0
|
CG
|
B:ASP583
|
4.6
|
12.8
|
1.0
|
CA
|
B:SER579
|
4.6
|
14.7
|
1.0
|
O
|
B:LEU262
|
4.6
|
7.9
|
1.0
|
N
|
B:THR265
|
4.7
|
9.0
|
1.0
|
C
|
B:ILE263
|
4.7
|
7.5
|
1.0
|
CA
|
B:PRO264
|
4.7
|
7.8
|
1.0
|
CG
|
B:ASN582
|
4.7
|
15.1
|
1.0
|
CG
|
B:LYS586
|
4.7
|
10.8
|
1.0
|
CB
|
B:SER579
|
4.8
|
14.7
|
1.0
|
CG
|
B:ASN624
|
4.9
|
11.6
|
1.0
|
C
|
B:LEU262
|
4.9
|
7.9
|
1.0
|
N
|
B:ASP583
|
4.9
|
12.8
|
1.0
|
C
|
B:ASN582
|
5.0
|
15.1
|
1.0
|
CA
|
B:ASN582
|
5.0
|
15.1
|
1.0
|
OG1
|
B:THR266
|
5.0
|
9.5
|
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 21:54:09 2024
|