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Potassium in PDB 4x65: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

Protein crystallography data

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4x65 was solved by H.Demirci, J.Chen, J.Choi, M.Soltis, J.D.Puglisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.96 / 3.35
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 401.440, 401.440, 175.924, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 21

Other elements in 4x65:

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus also contains other interesting chemical elements:

Magnesium (Mg) 317 atoms
Zinc (Zn) 2 atoms

Potassium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 46;

Binding sites:

The binding sites of Potassium atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 4x65). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 46 binding sites of Potassium where determined in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4x65:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 46 in 4x65

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Potassium binding site 1 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1900

b:0.1
occ:1.00
O4 A:U229 3.3 67.9 1.0
O4 A:U133 3.6 56.8 1.0
O6 A:G230 4.0 53.7 1.0
C4 A:U229 4.1 61.8 1.0
C5 A:U229 4.3 62.0 1.0
C4 A:U133 4.6 53.7 1.0
N3 A:U133 4.6 52.1 1.0
N4 A:C132 4.7 51.0 1.0

Potassium binding site 2 out of 46 in 4x65

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Potassium binding site 2 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1901

b:0.6
occ:1.00
O4 A:U863 3.1 58.3 1.0
OP2 A:C866 3.8 46.9 1.0
O6 A:G867 3.8 48.8 1.0
C4 A:U863 4.0 52.0 1.0
N3 A:U863 4.1 48.4 1.0
C6 A:G867 4.6 47.2 1.0
MG A:MG1848 4.7 59.9 1.0
N7 A:G867 5.0 48.8 1.0

Potassium binding site 3 out of 46 in 4x65

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Potassium binding site 3 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1902

b:0.6
occ:1.00
OP1 A:G577 3.8 47.3 1.0
OP1 A:U813 3.8 40.7 1.0
N7 A:G577 4.4 41.0 1.0
P A:U813 4.8 41.0 1.0
OP2 A:U813 4.8 41.2 1.0

Potassium binding site 4 out of 46 in 4x65

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Potassium binding site 4 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1903

b:98.4
occ:1.00
MG A:MG1644 3.0 76.5 1.0
OP1 A:C291 3.6 42.6 1.0
O A:HOH2205 3.7 0.2 1.0
O6 A:G305 3.7 46.9 1.0
OP2 A:C291 4.3 42.8 1.0
K A:K1932 4.3 0.5 1.0
N7 A:G305 4.4 50.7 1.0
O4 A:U304 4.4 51.4 1.0
P A:C291 4.4 42.8 1.0
MG A:MG1806 4.5 0.5 1.0
C6 A:G305 4.6 43.3 1.0
C4 A:U304 4.8 50.7 1.0
C5 A:G305 4.8 48.1 1.0

Potassium binding site 5 out of 46 in 4x65

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Potassium binding site 5 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1904

b:0.5
occ:1.00
OP1 A:G576 3.3 40.1 1.0
OP2 A:G577 3.6 43.8 1.0
OP2 A:A815 4.2 40.4 1.0
OP1 A:A815 4.3 40.3 1.0
P A:G576 4.3 40.3 1.0
MG A:MG1776 4.4 53.6 1.0
OP2 A:G576 4.4 40.4 1.0
OP1 A:G575 4.5 39.9 1.0
C5' A:G577 4.7 42.4 1.0
P A:A815 4.8 40.4 1.0
O5' A:G576 5.0 40.2 1.0

Potassium binding site 6 out of 46 in 4x65

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Potassium binding site 6 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1905

b:0.0
occ:1.00
O6 A:G297 3.4 68.8 1.0
MG A:MG1729 4.0 71.4 1.0
O4 A:U296 4.3 44.9 1.0
C6 A:G297 4.7 60.7 1.0

Potassium binding site 7 out of 46 in 4x65

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Potassium binding site 7 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1906

b:0.8
occ:1.00
O6 A:G1089 3.6 81.9 1.0
O6 A:G1088 3.8 70.9 1.0
N7 A:G1088 3.8 68.7 1.0
O4 A:U1090 4.1 70.8 1.0
N7 A:G1089 4.2 78.2 1.0
C6 A:G1088 4.3 70.9 1.0
C5 A:G1088 4.4 69.9 1.0
OP2 A:G1087 4.4 67.2 1.0
C6 A:G1089 4.6 80.7 1.0
MG A:MG1780 4.6 47.0 1.0
C5 A:G1089 4.8 79.5 1.0
OP2 A:G1088 4.8 80.0 1.0
C8 A:G1088 4.8 68.8 1.0
N7 A:G1087 4.9 67.4 1.0

Potassium binding site 8 out of 46 in 4x65

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Potassium binding site 8 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1907

b:0.3
occ:1.00
O2 A:C840 3.6 0.9 1.0
O6 A:G838 3.7 88.8 1.0
N3 A:C840 3.8 0.9 1.0
C2 A:C840 4.0 0.9 1.0
N7 A:G838 4.6 88.6 1.0
C6 A:G838 4.7 91.1 1.0
C4 A:C840 4.8 0.3 1.0
N7 A:G837 4.9 73.5 1.0

Potassium binding site 9 out of 46 in 4x65

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Potassium binding site 9 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1908

b:0.7
occ:1.00
O4 A:U14 3.0 56.3 1.0
OP2 A:U17 3.7 49.4 1.0
OP1 A:U17 4.0 50.4 1.0
C4 A:U14 4.1 52.5 1.0
P A:U17 4.4 49.9 1.0
N3 A:U14 4.6 50.6 1.0

Potassium binding site 10 out of 46 in 4x65

Go back to Potassium Binding Sites List in 4x65
Potassium binding site 10 out of 46 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1909

b:98.0
occ:1.00
MG A:MG1752 3.2 66.5 1.0
OP2 A:C536 3.5 59.5 1.0
O6 A:G538 4.1 65.8 1.0
N7 A:G537 4.3 73.2 1.0
N7 A:G538 4.4 65.6 1.0
P A:C536 4.8 58.5 1.0
OP2 A:G537 4.8 64.2 1.0
C5 A:G537 4.8 71.4 1.0
O6 A:G537 4.9 73.8 1.0
C8 A:G537 4.9 71.7 1.0
C6 A:G538 4.9 66.7 1.0

Reference:

J.Choi, K.W.Ieong, H.Demirci, J.Chen, A.Petrov, A.Prabhakar, S.E.O'leary, D.Dominissini, G.Rechavi, S.M.Soltis, M.Ehrenberg, J.D.Puglisi. N(6)-Methyladenosine in Mrna Disrupts Trna Selection and Translation-Elongation Dynamics. Nat.Struct.Mol.Biol. V. 23 110 2016.
ISSN: ESSN 1545-9985
PubMed: 26751643
DOI: 10.1038/NSMB.3148
Page generated: Sun Dec 13 23:51:06 2020

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