Potassium in PDB 7nnl: Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
All present enzymatic activity of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp 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 An E1-Atp Conformation Loaded with K+
(pdb code 7nnl). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the
Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+, PDB code: 7nnl:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Potassium binding site 1 out
of 10 in 7nnl
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Potassium Binding Sites List in 7nnl
Potassium binding site 1 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
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 An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K601
b:47.6
occ:1.00
|
CG1
|
A:VAL538
|
3.4
|
38.9
|
1.0
|
K
|
A:K602
|
3.6
|
44.8
|
1.0
|
O
|
A:ILE421
|
3.8
|
33.9
|
1.0
|
K
|
B:K701
|
3.9
|
42.3
|
1.0
|
CG1
|
B:VAL231
|
3.9
|
33.7
|
1.0
|
CG
|
A:PRO425
|
4.1
|
30.3
|
1.0
|
OG1
|
A:THR542
|
4.1
|
35.5
|
1.0
|
CG1
|
A:ILE421
|
4.3
|
33.9
|
1.0
|
CG2
|
A:ILE421
|
4.5
|
33.9
|
1.0
|
O
|
A:VAL538
|
4.6
|
38.9
|
1.0
|
CG2
|
B:VAL231
|
4.6
|
33.7
|
1.0
|
CB
|
B:VAL231
|
4.6
|
33.7
|
1.0
|
C
|
A:ILE421
|
4.7
|
33.9
|
1.0
|
CD1
|
A:ILE421
|
4.8
|
33.9
|
1.0
|
CB
|
A:VAL538
|
4.8
|
38.9
|
1.0
|
CB
|
A:ILE421
|
5.0
|
33.9
|
1.0
|
CB
|
A:PRO425
|
5.0
|
30.3
|
1.0
|
|
Potassium binding site 2 out
of 10 in 7nnl
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Potassium Binding Sites List in 7nnl
Potassium binding site 2 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
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 An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K602
b:44.8
occ:1.00
|
CG
|
A:PRO425
|
3.4
|
30.3
|
1.0
|
K
|
A:K601
|
3.6
|
47.6
|
1.0
|
O
|
A:GLN367
|
3.8
|
31.9
|
1.0
|
O
|
A:ILE368
|
4.0
|
33.5
|
1.0
|
CD
|
A:PRO425
|
4.0
|
30.3
|
1.0
|
C
|
A:ILE368
|
4.2
|
33.5
|
1.0
|
O
|
A:ILE421
|
4.2
|
33.9
|
1.0
|
CZ
|
A:PHE386
|
4.3
|
36.2
|
1.0
|
CA
|
A:ILE368
|
4.4
|
33.5
|
1.0
|
CB
|
A:PRO425
|
4.5
|
30.3
|
1.0
|
CE2
|
A:PHE543
|
4.6
|
32.4
|
1.0
|
CG1
|
A:ILE421
|
4.7
|
33.9
|
1.0
|
CG1
|
A:VAL538
|
4.7
|
38.9
|
1.0
|
N
|
A:GLY369
|
4.8
|
34.9
|
1.0
|
C
|
A:GLN367
|
4.8
|
31.9
|
1.0
|
CA
|
A:GLY539
|
4.8
|
37.2
|
1.0
|
|
Potassium binding site 3 out
of 10 in 7nnl
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Potassium Binding Sites List in 7nnl
Potassium binding site 3 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
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 An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K603
b:45.2
occ:1.00
|
OG1
|
A:THR424
|
2.9
|
31.4
|
1.0
|
O
|
A:ALA420
|
3.0
|
32.0
|
1.0
|
CG2
|
A:THR424
|
3.5
|
31.4
|
1.0
|
CB
|
A:THR424
|
3.8
|
31.4
|
1.0
|
CG2
|
A:VAL496
|
4.0
|
30.1
|
1.0
|
C
|
A:ALA420
|
4.1
|
32.0
|
1.0
|
CG1
|
A:VAL496
|
4.2
|
30.1
|
1.0
|
CA
|
A:ILE421
|
4.2
|
33.9
|
1.0
|
N
|
A:THR424
|
4.2
|
31.4
|
1.0
|
K
|
A:K604
|
4.3
|
50.4
|
1.0
|
C
|
A:ILE421
|
4.6
|
33.9
|
1.0
|
N
|
A:ILE421
|
4.6
|
33.9
|
1.0
|
O
|
A:ILE421
|
4.6
|
33.9
|
1.0
|
CA
|
A:THR424
|
4.7
|
31.4
|
1.0
|
CB
|
A:VAL496
|
4.8
|
30.1
|
1.0
|
CD1
|
A:LEU385
|
4.8
|
34.2
|
1.0
|
CD
|
A:PRO425
|
4.9
|
30.3
|
1.0
|
|
Potassium binding site 4 out
of 10 in 7nnl
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Potassium Binding Sites List in 7nnl
Potassium binding site 4 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
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 An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K604
b:50.4
occ:1.00
|
O
|
A:GLY369
|
2.9
|
34.9
|
1.0
|
O
|
A:SER378
|
3.3
|
32.8
|
1.0
|
CA
|
A:GLY382
|
3.5
|
33.1
|
1.0
|
C
|
A:GLY369
|
4.1
|
34.9
|
1.0
|
K
|
A:K605
|
4.2
|
46.4
|
1.0
|
N
|
A:GLY382
|
4.3
|
33.1
|
1.0
|
K
|
A:K603
|
4.3
|
45.2
|
1.0
|
C
|
A:SER378
|
4.4
|
32.8
|
1.0
|
CG1
|
A:VAL496
|
4.5
|
30.1
|
1.0
|
C
|
A:GLY382
|
4.6
|
33.1
|
1.0
|
CA
|
A:GLY369
|
4.7
|
34.9
|
1.0
|
CB
|
A:SER378
|
4.7
|
32.8
|
1.0
|
O
|
A:GLU370
|
4.7
|
33.2
|
1.0
|
CA
|
A:SER378
|
5.0
|
32.8
|
1.0
|
CG1
|
A:VAL371
|
5.0
|
34.0
|
1.0
|
O
|
A:GLY382
|
5.0
|
33.1
|
1.0
|
|
Potassium binding site 5 out
of 10 in 7nnl
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Potassium Binding Sites List in 7nnl
Potassium binding site 5 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
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 An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K605
b:46.4
occ:1.00
|
OH
|
A:TYR381
|
3.0
|
32.4
|
1.0
|
CB
|
A:SER378
|
3.5
|
32.8
|
1.0
|
CE1
|
A:TYR381
|
3.5
|
32.4
|
1.0
|
CZ
|
A:TYR381
|
3.6
|
32.4
|
1.0
|
CB
|
A:VAL496
|
4.0
|
30.1
|
1.0
|
O
|
A:GLY492
|
4.1
|
27.4
|
1.0
|
CG1
|
A:VAL496
|
4.2
|
30.1
|
1.0
|
K
|
A:K604
|
4.2
|
50.4
|
1.0
|
OD1
|
A:ASN466
|
4.2
|
29.1
|
1.0
|
OG
|
A:SER378
|
4.3
|
32.8
|
1.0
|
O
|
A:ARG493
|
4.4
|
28.4
|
1.0
|
NH1
|
A:ARG493
|
4.4
|
28.4
|
1.0
|
CA
|
A:ARG493
|
4.4
|
28.4
|
1.0
|
CA
|
A:SER378
|
4.5
|
32.8
|
1.0
|
CG
|
A:ARG493
|
4.5
|
28.4
|
1.0
|
CG2
|
A:VAL496
|
4.6
|
30.1
|
1.0
|
CD1
|
A:TYR381
|
4.7
|
32.4
|
1.0
|
C
|
A:ARG493
|
4.9
|
28.4
|
1.0
|
CE2
|
A:TYR381
|
4.9
|
32.4
|
1.0
|
CG1
|
A:ILE497
|
5.0
|
29.4
|
1.0
|
|
Potassium binding site 6 out
of 10 in 7nnl
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Potassium Binding Sites List in 7nnl
Potassium binding site 6 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
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 An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K606
b:37.9
occ:1.00
|
OG
|
A:SER343
|
3.0
|
30.9
|
1.0
|
ND2
|
A:ASN112
|
3.1
|
29.3
|
1.0
|
OG
|
A:SER378
|
3.2
|
32.8
|
1.0
|
NH1
|
A:ARG493
|
3.4
|
28.4
|
1.0
|
O
|
A:ASN466
|
3.6
|
29.1
|
1.0
|
O
|
A:ASN112
|
3.6
|
29.3
|
1.0
|
CB
|
A:ASN466
|
3.9
|
29.1
|
1.0
|
CG
|
A:ASN112
|
3.9
|
29.3
|
1.0
|
CB
|
A:SER343
|
3.9
|
30.9
|
1.0
|
CB
|
A:ASN112
|
3.9
|
29.3
|
1.0
|
CB
|
A:SER378
|
4.3
|
32.8
|
1.0
|
CA
|
A:GLY375
|
4.3
|
31.9
|
1.0
|
O
|
A:SER343
|
4.3
|
30.9
|
1.0
|
CZ
|
A:ARG493
|
4.5
|
28.4
|
1.0
|
C
|
A:ASN466
|
4.6
|
29.1
|
1.0
|
C
|
A:ASN112
|
4.6
|
29.3
|
1.0
|
NH2
|
A:ARG493
|
4.7
|
28.4
|
1.0
|
CA
|
A:ASN466
|
4.9
|
29.1
|
1.0
|
CG
|
A:ASN466
|
4.9
|
29.1
|
1.0
|
OG1
|
A:THR230
|
4.9
|
29.7
|
1.0
|
CA
|
A:ASN112
|
4.9
|
29.3
|
1.0
|
N
|
A:VAL376
|
5.0
|
30.7
|
1.0
|
O
|
A:THR111
|
5.0
|
28.9
|
1.0
|
C
|
A:GLY375
|
5.0
|
31.9
|
1.0
|
OD1
|
A:ASN112
|
5.0
|
29.3
|
1.0
|
OD1
|
A:ASN466
|
5.0
|
29.1
|
1.0
|
|
Potassium binding site 7 out
of 10 in 7nnl
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Potassium Binding Sites List in 7nnl
Potassium binding site 7 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
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 An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K607
b:30.2
occ:1.00
|
O
|
A:ASN112
|
2.8
|
29.3
|
1.0
|
O
|
A:ASN231
|
2.8
|
29.3
|
1.0
|
O
|
A:SER343
|
2.8
|
30.9
|
1.0
|
O
|
A:ASN467
|
2.8
|
29.7
|
1.0
|
O
|
A:CYS344
|
2.9
|
29.6
|
1.0
|
O
|
A:THR113
|
2.9
|
29.9
|
1.0
|
O
|
A:ASN466
|
3.2
|
29.1
|
1.0
|
C
|
A:THR113
|
3.4
|
29.9
|
1.0
|
CA
|
A:THR113
|
3.5
|
29.9
|
1.0
|
C
|
A:ASN467
|
3.5
|
29.7
|
1.0
|
O
|
A:THR230
|
3.6
|
29.7
|
1.0
|
C
|
A:ASN112
|
3.6
|
29.3
|
1.0
|
C
|
A:CYS344
|
3.7
|
29.6
|
1.0
|
C
|
A:ASN231
|
3.8
|
29.3
|
1.0
|
CA
|
A:ASN467
|
3.8
|
29.7
|
1.0
|
C
|
A:SER343
|
3.8
|
30.9
|
1.0
|
C
|
A:ASN466
|
3.9
|
29.1
|
1.0
|
N
|
A:THR113
|
3.9
|
29.9
|
1.0
|
CA
|
A:CYS344
|
4.1
|
29.6
|
1.0
|
OG
|
A:SER343
|
4.2
|
30.9
|
1.0
|
N
|
A:ASN467
|
4.2
|
29.7
|
1.0
|
CA
|
A:ASN231
|
4.2
|
29.3
|
1.0
|
N
|
A:CYS344
|
4.4
|
29.6
|
1.0
|
C
|
A:THR230
|
4.5
|
29.7
|
1.0
|
N
|
A:GLY468
|
4.5
|
30.2
|
1.0
|
N
|
A:ASN114
|
4.5
|
30.9
|
1.0
|
N
|
A:GLY345
|
4.7
|
29.9
|
1.0
|
CB
|
A:ASN114
|
4.8
|
30.9
|
1.0
|
N
|
A:ASN231
|
4.8
|
29.3
|
1.0
|
CB
|
A:THR113
|
4.8
|
29.9
|
1.0
|
N
|
A:GLY232
|
4.8
|
30.6
|
1.0
|
CA
|
A:ASN112
|
4.9
|
29.3
|
1.0
|
OD1
|
A:ASN467
|
4.9
|
29.7
|
1.0
|
CA
|
A:SER343
|
5.0
|
30.9
|
1.0
|
|
Potassium binding site 8 out
of 10 in 7nnl
Go back to
Potassium Binding Sites List in 7nnl
Potassium binding site 8 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 8 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K608
b:35.9
occ:1.00
|
O
|
A:GLY468
|
2.9
|
30.2
|
1.0
|
O
|
A:GLY232
|
3.0
|
30.6
|
1.0
|
ND2
|
A:ASN239
|
3.0
|
33.7
|
1.0
|
O
|
A:ASN114
|
3.1
|
30.9
|
1.0
|
O
|
A:GLY345
|
3.1
|
29.9
|
1.0
|
C
|
A:GLY468
|
3.8
|
30.2
|
1.0
|
CG
|
A:ASN239
|
4.0
|
33.7
|
1.0
|
OD1
|
A:ASN239
|
4.1
|
33.7
|
1.0
|
C
|
A:ASN114
|
4.1
|
30.9
|
1.0
|
C
|
A:GLY232
|
4.1
|
30.6
|
1.0
|
C
|
A:GLY345
|
4.2
|
29.9
|
1.0
|
CA
|
A:TRP115
|
4.2
|
30.8
|
1.0
|
N
|
A:GLN116
|
4.4
|
33.0
|
1.0
|
N
|
A:SER469
|
4.5
|
30.9
|
1.0
|
CG
|
A:GLN116
|
4.5
|
33.0
|
1.0
|
CA
|
A:GLY468
|
4.5
|
30.2
|
1.0
|
N
|
A:TRP115
|
4.6
|
30.8
|
1.0
|
CA
|
A:SER469
|
4.6
|
30.9
|
1.0
|
C
|
A:TRP115
|
4.8
|
30.8
|
1.0
|
CA
|
A:GLY233
|
4.9
|
31.9
|
1.0
|
CA
|
A:GLY232
|
4.9
|
30.6
|
1.0
|
CA
|
A:GLY345
|
4.9
|
29.9
|
1.0
|
N
|
A:GLY233
|
4.9
|
31.9
|
1.0
|
|
Potassium binding site 9 out
of 10 in 7nnl
Go back to
Potassium Binding Sites List in 7nnl
Potassium binding site 9 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 9 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K701
b:42.3
occ:1.00
|
CG2
|
A:ILE421
|
3.8
|
33.9
|
1.0
|
CB
|
B:ALA227
|
3.9
|
33.9
|
1.0
|
K
|
A:K601
|
3.9
|
47.6
|
1.0
|
CD2
|
A:LEU389
|
4.0
|
37.6
|
1.0
|
CD2
|
B:LEU228
|
4.3
|
34.3
|
1.0
|
C
|
B:ALA227
|
4.4
|
33.9
|
1.0
|
N
|
B:LEU228
|
4.4
|
34.3
|
1.0
|
CG
|
B:LEU228
|
4.5
|
34.3
|
1.0
|
O
|
B:ALA227
|
4.7
|
33.9
|
1.0
|
CG1
|
A:VAL538
|
4.8
|
38.9
|
1.0
|
CA
|
B:ALA227
|
4.8
|
33.9
|
1.0
|
CA
|
B:LEU228
|
4.9
|
34.3
|
1.0
|
O
|
B:LEU224
|
4.9
|
35.7
|
1.0
|
CD1
|
A:ILE421
|
4.9
|
33.9
|
1.0
|
|
Potassium binding site 10 out
of 10 in 7nnl
Go back to
Potassium Binding Sites List in 7nnl
Potassium binding site 10 out
of 10 in the Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 10 of Cryo-Em Structure of the Kdpfabc Complex in An E1-Atp Conformation Loaded with K+ within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K703
b:52.0
occ:1.00
|
NZ
|
B:LYS586
|
3.2
|
36.9
|
1.0
|
O
|
B:CYS261
|
3.6
|
36.2
|
1.0
|
OD1
|
B:ASP583
|
3.7
|
37.9
|
1.0
|
O
|
B:ILE263
|
3.7
|
35.8
|
1.0
|
O
|
B:SER579
|
3.8
|
40.3
|
1.0
|
OG1
|
B:THR265
|
3.9
|
38.8
|
1.0
|
OG1
|
B:THR266
|
3.9
|
39.5
|
1.0
|
ND2
|
B:ASN624
|
4.0
|
38.5
|
1.0
|
CB
|
B:ASN582
|
4.2
|
40.0
|
1.0
|
N
|
B:THR265
|
4.3
|
38.8
|
1.0
|
CA
|
B:SER579
|
4.5
|
40.3
|
1.0
|
C
|
B:CYS261
|
4.5
|
36.2
|
1.0
|
ND2
|
B:ASN582
|
4.5
|
40.0
|
1.0
|
C
|
B:SER579
|
4.6
|
40.3
|
1.0
|
CG
|
B:ASN624
|
4.6
|
38.5
|
1.0
|
O
|
B:LEU262
|
4.6
|
35.0
|
1.0
|
CA
|
B:PRO264
|
4.6
|
36.3
|
1.0
|
N
|
B:THR266
|
4.7
|
39.5
|
1.0
|
CB
|
B:SER579
|
4.7
|
40.3
|
1.0
|
C
|
B:ILE263
|
4.7
|
35.8
|
1.0
|
CE
|
B:LYS586
|
4.7
|
36.9
|
1.0
|
OD1
|
B:ASN624
|
4.8
|
38.5
|
1.0
|
CG
|
B:ASP583
|
4.9
|
37.9
|
1.0
|
CG
|
B:ASN582
|
4.9
|
40.0
|
1.0
|
CB
|
B:THR266
|
4.9
|
39.5
|
1.0
|
C
|
B:LEU262
|
4.9
|
35.0
|
1.0
|
C
|
B:PRO264
|
5.0
|
36.3
|
1.0
|
|
Reference:
J.M.Silberberg,
R.A.Corey,
L.Hielkema,
C.Stock,
P.J.Stansfeld,
C.Paulino,
I.Hanelt.
Deciphering Ion Transport and Atpase Coupling in the Intersubunit Tunnel of Kdpfabc Biorxiv 2021.
DOI: 10.1101/2021.05.18.444724
Page generated: Mon Aug 12 19:32:59 2024
|