Potassium in PDB 8csr: Human Mitochondrial Small Subunit Assembly Intermediate (State C)
Enzymatic activity of Human Mitochondrial Small Subunit Assembly Intermediate (State C)
All present enzymatic activity of Human Mitochondrial Small Subunit Assembly Intermediate (State C):
2.3.1.39;
Other elements in 8csr:
The structure of Human Mitochondrial Small Subunit Assembly Intermediate (State C) also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Human Mitochondrial Small Subunit Assembly Intermediate (State C)
(pdb code 8csr). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the
Human Mitochondrial Small Subunit Assembly Intermediate (State C), PDB code: 8csr:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
Potassium binding site 1 out
of 5 in 8csr
Go back to
Potassium Binding Sites List in 8csr
Potassium binding site 1 out
of 5 in the Human Mitochondrial Small Subunit Assembly Intermediate (State C)
![](/pictures/K/pdb/cs/8csr-K-sphere_01.jpg) Mono view
![](/pictures/K/pdb/cs/8csr-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 Human Mitochondrial Small Subunit Assembly Intermediate (State C) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1701
b:32.9
occ:1.00
|
O2
|
A:C702
|
2.9
|
33.0
|
1.0
|
N3
|
A:C707
|
2.9
|
28.1
|
1.0
|
O2'
|
A:C842
|
3.1
|
33.6
|
1.0
|
O3'
|
A:C842
|
3.3
|
33.6
|
1.0
|
O2
|
A:C708
|
3.3
|
27.0
|
1.0
|
N4
|
A:C707
|
3.3
|
28.1
|
1.0
|
C4
|
A:C707
|
3.6
|
28.1
|
1.0
|
C2
|
A:C708
|
3.7
|
27.0
|
1.0
|
C2
|
A:C707
|
3.9
|
28.1
|
1.0
|
C3'
|
A:C842
|
4.0
|
33.6
|
1.0
|
O2
|
A:C707
|
4.0
|
28.1
|
1.0
|
C2
|
A:C702
|
4.1
|
33.0
|
1.0
|
N3
|
A:C708
|
4.1
|
27.0
|
1.0
|
C2'
|
A:C842
|
4.1
|
33.6
|
1.0
|
C4'
|
A:C842
|
4.1
|
33.6
|
1.0
|
C5'
|
A:G843
|
4.2
|
33.6
|
1.0
|
OP1
|
A:G843
|
4.3
|
33.6
|
1.0
|
N1
|
A:C708
|
4.4
|
27.0
|
1.0
|
P
|
A:G843
|
4.4
|
33.6
|
1.0
|
N4
|
A:C706
|
4.6
|
27.8
|
1.0
|
N2
|
A:G701
|
4.7
|
33.0
|
1.0
|
N3
|
A:C702
|
4.8
|
33.0
|
1.0
|
C1'
|
A:C708
|
4.8
|
27.0
|
1.0
|
O5'
|
A:G843
|
4.8
|
33.6
|
1.0
|
C1'
|
A:A703
|
4.8
|
29.9
|
1.0
|
O4'
|
A:A703
|
4.8
|
29.9
|
1.0
|
O2'
|
A:C702
|
4.9
|
33.0
|
1.0
|
C4
|
A:C708
|
5.0
|
27.0
|
1.0
|
|
Potassium binding site 2 out
of 5 in 8csr
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Potassium Binding Sites List in 8csr
Potassium binding site 2 out
of 5 in the Human Mitochondrial Small Subunit Assembly Intermediate (State C)
![](/pictures/K/pdb/cs/8csr-K-sphere_02.jpg) Mono view
![](/pictures/K/pdb/cs/8csr-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 Human Mitochondrial Small Subunit Assembly Intermediate (State C) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1702
b:24.5
occ:1.00
|
O4'
|
A:G791
|
2.9
|
28.7
|
1.0
|
O2'
|
A:G717
|
2.9
|
24.8
|
1.0
|
O6
|
A:G719
|
3.0
|
26.1
|
1.0
|
N7
|
A:G719
|
3.0
|
26.1
|
1.0
|
O3'
|
A:G717
|
3.1
|
24.8
|
1.0
|
N7
|
A:A718
|
3.4
|
26.4
|
1.0
|
O5'
|
A:G791
|
3.5
|
28.7
|
1.0
|
C1'
|
A:G717
|
3.5
|
24.8
|
1.0
|
C6
|
A:G719
|
3.6
|
26.1
|
1.0
|
C5
|
A:G719
|
3.6
|
26.1
|
1.0
|
C2'
|
A:G717
|
3.6
|
24.8
|
1.0
|
N3
|
A:G717
|
3.7
|
24.8
|
1.0
|
C4'
|
A:G791
|
3.9
|
28.7
|
1.0
|
C1'
|
A:G791
|
3.9
|
28.7
|
1.0
|
OP2
|
A:A718
|
3.9
|
26.4
|
1.0
|
C8
|
A:A718
|
4.0
|
26.4
|
1.0
|
MG
|
A:MG1709
|
4.0
|
32.6
|
1.0
|
C3'
|
A:G717
|
4.0
|
24.8
|
1.0
|
C5'
|
A:G791
|
4.0
|
28.7
|
1.0
|
C8
|
A:G719
|
4.2
|
26.1
|
1.0
|
P
|
A:A718
|
4.2
|
26.4
|
1.0
|
C5
|
A:A718
|
4.2
|
26.4
|
1.0
|
C8
|
A:G791
|
4.3
|
28.7
|
1.0
|
N9
|
A:G717
|
4.4
|
24.8
|
1.0
|
N9
|
A:G791
|
4.4
|
28.7
|
1.0
|
C4
|
A:G717
|
4.4
|
24.8
|
1.0
|
O4
|
A:U720
|
4.5
|
28.8
|
1.0
|
O4'
|
A:G717
|
4.5
|
24.8
|
1.0
|
N6
|
A:A718
|
4.6
|
26.4
|
1.0
|
C2
|
A:G717
|
4.6
|
24.8
|
1.0
|
N2
|
A:G717
|
4.7
|
24.8
|
1.0
|
P
|
A:G791
|
4.8
|
28.7
|
1.0
|
C4
|
A:U720
|
4.8
|
28.8
|
1.0
|
C6
|
A:A718
|
4.8
|
26.4
|
1.0
|
OP2
|
A:G791
|
4.8
|
28.7
|
1.0
|
C4'
|
A:G717
|
4.8
|
24.8
|
1.0
|
C4
|
A:G719
|
4.9
|
26.1
|
1.0
|
N9
|
A:A718
|
4.9
|
26.4
|
1.0
|
N1
|
A:G719
|
5.0
|
26.1
|
1.0
|
O5'
|
A:A718
|
5.0
|
26.4
|
1.0
|
|
Potassium binding site 3 out
of 5 in 8csr
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Potassium Binding Sites List in 8csr
Potassium binding site 3 out
of 5 in the Human Mitochondrial Small Subunit Assembly Intermediate (State C)
![](/pictures/K/pdb/cs/8csr-K-sphere_03.jpg) Mono view
![](/pictures/K/pdb/cs/8csr-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 Human Mitochondrial Small Subunit Assembly Intermediate (State C) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1703
b:34.5
occ:1.00
|
O2
|
A:C1105
|
2.7
|
29.6
|
1.0
|
OP2
|
A:U1107
|
2.8
|
34.0
|
1.0
|
O2'
|
A:C1105
|
3.0
|
29.6
|
1.0
|
O3'
|
A:U1592
|
3.0
|
33.6
|
1.0
|
O2'
|
A:U1592
|
3.3
|
33.6
|
1.0
|
C1'
|
A:C1105
|
3.6
|
29.6
|
1.0
|
C2
|
A:C1105
|
3.7
|
29.6
|
1.0
|
C4'
|
A:U1592
|
3.7
|
33.6
|
1.0
|
C3'
|
A:U1592
|
3.8
|
33.6
|
1.0
|
C2'
|
A:C1105
|
3.8
|
29.6
|
1.0
|
O5'
|
A:U1107
|
3.9
|
34.0
|
1.0
|
P
|
A:U1107
|
3.9
|
34.0
|
1.0
|
OP1
|
A:U1593
|
4.0
|
31.7
|
1.0
|
O3'
|
A:C1105
|
4.0
|
29.6
|
1.0
|
N1
|
A:C1105
|
4.0
|
29.6
|
1.0
|
C5'
|
A:U1593
|
4.1
|
31.7
|
1.0
|
N2
|
A:G1594
|
4.1
|
29.4
|
1.0
|
P
|
A:U1593
|
4.1
|
31.7
|
1.0
|
C2'
|
A:U1592
|
4.1
|
33.6
|
1.0
|
O5'
|
A:U1593
|
4.5
|
31.7
|
1.0
|
C5'
|
A:U1592
|
4.6
|
33.6
|
1.0
|
C3'
|
A:C1105
|
4.6
|
29.6
|
1.0
|
O4'
|
A:U1592
|
4.7
|
33.6
|
1.0
|
N3
|
A:C1105
|
4.7
|
29.6
|
1.0
|
O4'
|
A:C1105
|
4.8
|
29.6
|
1.0
|
OP1
|
A:U1107
|
4.9
|
34.0
|
1.0
|
OP2
|
A:A1104
|
4.9
|
28.5
|
1.0
|
C1'
|
A:U1592
|
5.0
|
33.6
|
1.0
|
|
Potassium binding site 4 out
of 5 in 8csr
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Potassium Binding Sites List in 8csr
Potassium binding site 4 out
of 5 in the Human Mitochondrial Small Subunit Assembly Intermediate (State C)
![](/pictures/K/pdb/cs/8csr-K-sphere_04.jpg) Mono view
![](/pictures/K/pdb/cs/8csr-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 Human Mitochondrial Small Subunit Assembly Intermediate (State C) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1704
b:36.5
occ:1.00
|
OP1
|
A:C806
|
2.9
|
49.8
|
1.0
|
O3'
|
A:C805
|
3.1
|
53.5
|
1.0
|
O
|
A:HOH1818
|
3.3
|
35.3
|
1.0
|
MG
|
A:MG1716
|
3.6
|
37.0
|
1.0
|
O3'
|
A:C800
|
3.6
|
25.3
|
1.0
|
P
|
A:C806
|
3.6
|
49.8
|
1.0
|
OP1
|
A:A801
|
3.7
|
27.1
|
1.0
|
OP2
|
A:C804
|
3.8
|
49.5
|
1.0
|
O2'
|
A:C805
|
4.1
|
53.5
|
1.0
|
P
|
A:A801
|
4.4
|
27.1
|
1.0
|
C3'
|
A:C805
|
4.4
|
53.5
|
1.0
|
OP2
|
A:C806
|
4.6
|
49.8
|
1.0
|
C4'
|
A:C800
|
4.6
|
25.3
|
1.0
|
C3'
|
A:C800
|
4.7
|
25.3
|
1.0
|
OP1
|
A:C803
|
4.7
|
48.2
|
1.0
|
O5'
|
A:C806
|
4.8
|
49.8
|
1.0
|
C4'
|
A:C805
|
4.8
|
53.5
|
1.0
|
C2'
|
A:C805
|
4.8
|
53.5
|
1.0
|
C5'
|
A:C806
|
4.8
|
49.8
|
1.0
|
O
|
A:HOH1807
|
4.9
|
35.1
|
1.0
|
O
|
A:HOH1815
|
5.0
|
38.2
|
1.0
|
C5'
|
A:C800
|
5.0
|
25.3
|
1.0
|
|
Potassium binding site 5 out
of 5 in 8csr
Go back to
Potassium Binding Sites List in 8csr
Potassium binding site 5 out
of 5 in the Human Mitochondrial Small Subunit Assembly Intermediate (State C)
![](/pictures/K/pdb/cs/8csr-K-sphere_05.jpg) Mono view
![](/pictures/K/pdb/cs/8csr-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 Human Mitochondrial Small Subunit Assembly Intermediate (State C) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K1705
b:34.5
occ:1.00
|
O2'
|
A:C835
|
2.7
|
31.4
|
1.0
|
O4
|
A:U838
|
2.7
|
33.6
|
1.0
|
O2
|
A:C835
|
2.8
|
31.4
|
1.0
|
N6
|
A:A839
|
3.1
|
33.6
|
1.0
|
O4
|
A:U850
|
3.1
|
33.6
|
1.0
|
C4
|
A:U838
|
3.7
|
33.6
|
1.0
|
C2
|
A:C835
|
3.9
|
31.4
|
1.0
|
C2'
|
A:C835
|
4.0
|
31.4
|
1.0
|
C5
|
A:U838
|
4.1
|
33.6
|
1.0
|
C4
|
A:U850
|
4.3
|
33.6
|
1.0
|
C6
|
A:A839
|
4.3
|
33.6
|
1.0
|
C1'
|
A:C835
|
4.4
|
31.4
|
1.0
|
N6
|
A:A852
|
4.4
|
33.6
|
1.0
|
OP2
|
A:A837
|
4.5
|
32.9
|
1.0
|
N7
|
A:A837
|
4.6
|
32.9
|
1.0
|
N1
|
A:C835
|
4.6
|
31.4
|
1.0
|
N3
|
A:C835
|
4.7
|
31.4
|
1.0
|
O3'
|
A:C835
|
4.7
|
31.4
|
1.0
|
N3
|
A:U838
|
4.9
|
33.6
|
1.0
|
C3'
|
A:C835
|
5.0
|
31.4
|
1.0
|
|
Reference:
N.J.Harper,
C.Burnside,
S.Klinge.
Principles of Mitoribosomal Small Subunit Assembly in Eukaryotes. Nature 2022.
ISSN: ESSN 1476-4687
PubMed: 36482135
DOI: 10.1038/S41586-022-05621-0
Page generated: Mon Aug 12 22:59:27 2024
|