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Potassium in PDB 8css: Human Mitochondrial Small Subunit Assembly Intermediate (State D)

Enzymatic activity of Human Mitochondrial Small Subunit Assembly Intermediate (State D)

All present enzymatic activity of Human Mitochondrial Small Subunit Assembly Intermediate (State D):
2.3.1.39;

Other elements in 8css:

The structure of Human Mitochondrial Small Subunit Assembly Intermediate (State D) also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Iron (Fe) 8 atoms
Magnesium (Mg) 32 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human Mitochondrial Small Subunit Assembly Intermediate (State D) (pdb code 8css). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Human Mitochondrial Small Subunit Assembly Intermediate (State D), PDB code: 8css:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 8css

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Potassium binding site 1 out of 7 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


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 D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1701

b:35.5
occ:1.00
 O2 A:C702 2.8 33.7 1.0
N3 A:C707 3.0 26.2 1.0
O2' A:C842 3.0 33.7 1.0
O3' A:C842 3.2 33.7 1.0
O2 A:C708 3.4 31.7 1.0
N4 A:C707 3.6 26.2 1.0
C2 A:C708 3.7 31.7 1.0
C4 A:C707 3.8 26.2 1.0
C3' A:C842 3.9 33.7 1.0
C2 A:C707 3.9 26.2 1.0
O2 A:C707 4.0 26.2 1.0
C4' A:C842 4.0 33.7 1.0
C2' A:C842 4.0 33.7 1.0
C2 A:C702 4.0 33.7 1.0
N3 A:C708 4.1 31.7 1.0
C5' A:G843 4.2 33.7 1.0
OP1 A:G843 4.3 33.7 1.0
N1 A:C708 4.3 31.7 1.0
P A:G843 4.3 33.7 1.0
N2 A:G701 4.6 33.7 1.0
N3 A:C702 4.6 33.7 1.0
C1' A:C708 4.7 31.7 1.0
N4 A:C706 4.7 24.1 1.0
O5' A:G843 4.7 33.7 1.0
O4' A:A703 4.8 28.5 1.0
C1' A:A703 4.9 28.5 1.0
C4 A:C708 4.9 31.7 1.0
O4' A:C842 5.0 33.7 1.0
C5' A:C842 5.0 33.7 1.0

Potassium binding site 2 out of 7 in 8css

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Potassium binding site 2 out of 7 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


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 D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1702

b:23.7
occ:1.00
 O2' A:G717 2.8 33.7 1.0
O4' A:G791 2.9 31.7 1.0
O3' A:G717 3.0 33.7 1.0
O A:HOH1838 3.0 31.5 1.0
N7 A:G719 3.1 24.6 1.0
O6 A:G719 3.2 24.6 1.0
O5' A:G791 3.2 31.7 1.0
C2' A:G717 3.5 33.7 1.0
C1' A:G717 3.6 33.7 1.0
N7 A:A718 3.6 25.9 1.0
OP2 A:A718 3.7 25.9 1.0
C4' A:G791 3.8 31.7 1.0
C5 A:G719 3.8 24.6 1.0
C5' A:G791 3.8 31.7 1.0
C6 A:G719 3.8 24.6 1.0
N3 A:G717 3.9 33.7 1.0
C3' A:G717 3.9 33.7 1.0
C1' A:G791 4.0 31.7 1.0
P A:A718 4.0 25.9 1.0
C8 A:A718 4.1 25.9 1.0
C8 A:G719 4.3 24.6 1.0
C8 A:G791 4.3 31.7 1.0
MG A:MG1711 4.4 28.1 1.0
C5 A:A718 4.4 25.9 1.0
P A:G791 4.5 31.7 1.0
N9 A:G717 4.5 33.7 1.0
N9 A:G791 4.5 31.7 1.0
O4' A:G717 4.5 33.7 1.0
O4 A:U720 4.5 23.8 1.0
OP2 A:G791 4.5 31.7 1.0
C4 A:G717 4.6 33.7 1.0
C4' A:G717 4.8 33.7 1.0
O5' A:A718 4.8 25.9 1.0
C2 A:G717 4.8 33.7 1.0
N2 A:G717 4.9 33.7 1.0
N6 A:A718 4.9 25.9 1.0
C4 A:U720 4.9 23.8 1.0

Potassium binding site 3 out of 7 in 8css

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Potassium binding site 3 out of 7 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


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 D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1703

b:48.9
occ:1.00
 OD1 J:ASN74 2.8 41.5 1.0
O J:PRO73 2.9 45.1 1.0
N7 A:G901 3.0 42.9 1.0
O6 A:G901 3.1 42.9 1.0
O2 A:C890 3.2 51.3 1.0
N3 A:C890 3.4 51.3 1.0
C2 A:C890 3.6 51.3 1.0
C5 A:G901 3.7 42.9 1.0
C6 A:G901 3.7 42.9 1.0
CG J:ASN74 3.8 41.5 1.0
CA J:ASN74 3.9 41.5 1.0
C J:PRO73 3.9 45.1 1.0
C8 A:G901 4.1 42.9 1.0
N J:ASN74 4.3 41.5 1.0
CB J:ASN74 4.4 41.5 1.0
C4 A:C890 4.4 51.3 1.0
C5 A:C900 4.7 38.5 1.0
N4 A:C900 4.7 38.5 1.0
N4 A:C890 4.8 51.3 1.0
C4 A:C900 4.8 38.5 1.0
N1 A:C890 4.9 51.3 1.0
C4 A:G901 4.9 42.9 1.0
ND2 J:ASN74 5.0 41.5 1.0

Potassium binding site 4 out of 7 in 8css

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Potassium binding site 4 out of 7 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


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 D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1704

b:34.0
occ:1.00
 O3' A:U1592 2.8 33.7 1.0
OP2 A:U1107 2.8 31.8 1.0
O2' A:C1105 3.0 32.6 1.0
O2 A:C1105 3.0 32.6 1.0
O2' A:U1592 3.3 33.7 1.0
C4' A:U1592 3.5 33.7 1.0
C3' A:U1592 3.6 33.7 1.0
C1' A:C1105 3.9 32.6 1.0
C2 A:C1105 3.9 32.6 1.0
C2' A:C1105 4.0 32.6 1.0
P A:U1107 4.0 31.8 1.0
O5' A:U1107 4.0 31.8 1.0
OP1 A:U1593 4.0 33.7 1.0
P A:U1593 4.0 33.7 1.0
C2' A:U1592 4.0 33.7 1.0
C5' A:U1593 4.1 33.7 1.0
N2 A:G1594 4.2 33.7 1.0
O3' A:C1105 4.2 32.6 1.0
C5' A:U1592 4.2 33.7 1.0
N1 A:C1105 4.3 32.6 1.0
O5' A:U1593 4.5 33.7 1.0
O4' A:U1592 4.5 33.7 1.0
C3' A:C1105 4.8 32.6 1.0
C1' A:U1592 4.8 33.7 1.0
OP1 A:U1107 4.9 31.8 1.0
N3 A:C1105 4.9 32.6 1.0

Potassium binding site 5 out of 7 in 8css

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Potassium binding site 5 out of 7 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


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 D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1705

b:35.4
occ:1.00
 O A:HOH1813 2.9 40.4 1.0
O A:HOH1862 3.0 27.9 1.0
OP1 A:C806 3.1 45.9 1.0
O3' A:C800 3.4 28.7 1.0
O3' A:C805 3.5 50.8 1.0
O A:HOH1845 3.6 29.2 1.0
OP1 A:A801 3.8 35.0 1.0
MG A:MG1718 3.8 33.8 1.0
P A:C806 3.9 45.9 1.0
O2' A:C805 4.0 50.8 1.0
C4' A:C800 4.1 28.7 1.0
OP2 A:C804 4.2 45.1 1.0
P A:A801 4.3 35.0 1.0
C3' A:C800 4.3 28.7 1.0
C5' A:C800 4.5 28.7 1.0
C3' A:C805 4.6 50.8 1.0
O2' A:C800 4.7 28.7 1.0
C5' A:C806 4.8 45.9 1.0
O5' A:C806 4.9 45.9 1.0
C2' A:C805 4.9 50.8 1.0
O A:HOH1804 5.0 29.2 1.0
OP1 A:C803 5.0 43.5 1.0

Potassium binding site 6 out of 7 in 8css

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Potassium binding site 6 out of 7 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1706

b:38.1
occ:1.00
 O2' A:C835 2.8 30.9 1.0
O2 A:C835 2.8 30.9 1.0
O4 A:U838 2.8 33.7 1.0
N6 A:A839 3.5 33.7 1.0
O4 A:U850 3.6 33.7 1.0
C4 A:U838 3.7 33.7 1.0
C2 A:C835 4.0 30.9 1.0
C5 A:U838 4.0 33.7 1.0
C2' A:C835 4.0 30.9 1.0
OP2 A:A837 4.0 33.4 1.0
N7 A:A837 4.2 33.4 1.0
C1' A:C835 4.4 30.9 1.0
O3' A:C835 4.6 30.9 1.0
C6 A:A839 4.7 33.7 1.0
N6 A:A852 4.7 33.7 1.0
N1 A:C835 4.7 30.9 1.0
C8 A:A837 4.8 33.4 1.0
C4 A:U850 4.8 33.7 1.0
N3 A:C835 4.9 30.9 1.0
C5 A:A837 4.9 33.4 1.0
C3' A:C835 5.0 30.9 1.0
N3 A:U838 5.0 33.7 1.0

Potassium binding site 7 out of 7 in 8css

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Potassium binding site 7 out of 7 in the Human Mitochondrial Small Subunit Assembly Intermediate (State D)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Human Mitochondrial Small Subunit Assembly Intermediate (State D) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1707

b:60.8
occ:1.00
 OP1 A:A905 2.8 50.0 1.0
O4 A:U888 3.0 59.0 1.0
O3' A:C904 3.8 81.2 1.0
O6 A:G889 3.8 60.6 1.0
P A:A905 3.9 50.0 1.0
C4 A:U888 4.0 59.0 1.0
N7 A:G887 4.4 58.6 1.0
O5' A:A905 4.5 50.0 1.0
C5 A:U888 4.5 59.0 1.0
C6 A:G889 4.6 60.6 1.0
N1 A:G889 4.7 60.6 1.0
O6 A:G887 4.7 58.6 1.0
OP2 A:G887 4.7 58.6 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 23:00:27 2024

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