Potassium in PDB 2f4v: 30S Ribosome + Designer Antibiotic

The structure of 30S Ribosome + Designer Antibiotic, PDB code: 2f4v was solved by J.B.Murray, S.O.Meroueh, R.J.Russell, G.Lentzen, J.Haddad, S.Mobashery, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	403.323, 403.323, 176.685, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 31.5

The structure of 30S Ribosome + Designer Antibiotic also contains other interesting chemical elements:

Magnesium	(Mg)	101 atoms
Chlorine	(Cl)	1 atom
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Potassium atom in the 30S Ribosome + Designer Antibiotic (pdb code 2f4v). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 12 binding sites of Potassium where determined in the 30S Ribosome + Designer Antibiotic, PDB code: 2f4v:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1539 b:27.7 occ:1.00 OP2 A:A766 2.0 46.4 1.0 O2 A:C812 3.5 48.5 1.0 P A:A766 3.5 46.4 1.0 N3 A:C812 3.9 48.3 1.0 N3 A:C811 4.0 33.3 1.0 C2 A:C812 4.1 47.5 1.0 N4 A:C811 4.3 35.2 1.0 O3' A:G765 4.3 45.6 1.0 O5' A:A766 4.4 44.7 1.0 OP1 A:A766 4.4 45.5 1.0 C3' A:G765 4.4 45.9 1.0 C4 A:C811 4.5 34.5 1.0 O4 A:U813 4.6 30.7 1.0 C2' A:G765 4.7 45.4 1.0 N6 A:A768 4.8 30.3 1.0 N7 A:A767 4.9 37.9 1.0 C2 A:C811 4.9 32.1 1.0 C4 A:U813 4.9 30.4 1.0 O2 A:C811 5.0 31.8 1.0

Potassium binding site 2 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1540 b:25.7 occ:1.00 OP2 A:A768 2.5 34.6 1.0 P A:A768 3.8 34.7 1.0 N7 A:G769 4.0 31.4 1.0 N7 A:A768 4.0 26.6 1.0 OP2 A:A767 4.2 47.2 1.0 O5' A:A768 4.2 30.7 1.0 OP1 A:U804 4.3 46.5 1.0 C8 A:A768 4.3 26.1 1.0 C3' A:A767 4.7 36.9 1.0 O3' A:A767 4.7 36.3 1.0 O6 A:G769 4.8 31.3 1.0 C8 A:G769 4.9 31.7 1.0 OP1 A:A768 4.9 33.7 1.0 OP2 A:C805 5.0 43.9 1.0

Potassium binding site 3 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1548 b:24.3 occ:1.00 OP1 A:G21 2.1 33.0 1.0 P A:G21 3.5 33.5 1.0 N2 A:G567 3.9 46.1 1.0 N1 A:A573 4.0 48.8 1.0 N3 A:G567 4.0 43.3 1.0 N6 A:A563 4.1 42.9 1.0 N6 A:A573 4.2 48.9 1.0 OP2 A:G21 4.3 35.3 1.0 O3' A:U20 4.3 34.0 1.0 O2' A:G567 4.4 42.5 1.0 C2 A:G567 4.5 44.5 1.0 C6 A:A573 4.6 48.1 1.0 O5' A:G21 4.6 31.4 1.0 O2' A:G568 4.7 43.5 1.0 O4' A:G568 4.9 45.7 1.0 C5' A:G21 4.9 30.3 1.0 C2 A:A573 5.0 48.6 1.0

Potassium binding site 4 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1550 b:25.4 occ:1.00 N7 A:G869 2.5 51.0 1.0 O6 A:G858 2.6 49.5 1.0 N7 A:G858 2.6 52.7 1.0 C6 A:G858 3.2 50.6 1.0 C5 A:G858 3.2 51.9 1.0 O6 A:G869 3.3 51.4 1.0 C5 A:G869 3.4 51.2 1.0 C8 A:G869 3.5 50.8 1.0 C6 A:G869 3.7 52.0 1.0 OP2 A:G869 3.7 42.4 1.0 C8 A:G858 3.8 53.7 1.0 OP2 A:C868 3.8 44.7 1.0 C4 A:G858 4.6 52.2 1.0 N1 A:G858 4.6 50.2 1.0 OP2 A:G858 4.6 59.0 1.0 C4 A:G869 4.6 50.3 1.0 N9 A:G869 4.7 49.5 1.0 O5' A:C868 4.8 44.2 1.0 P A:C868 4.8 43.4 1.0 C5 A:C857 4.8 58.4 1.0 N9 A:G858 4.8 53.6 1.0 C5 A:C868 4.8 44.6 1.0 C6 A:C857 5.0 58.0 1.0

Potassium binding site 5 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1553 b:34.9 occ:1.00 OP2 A:A937 2.6 56.3 1.0 N6 A:A938 3.5 41.4 1.0 O5' A:A937 3.6 54.0 1.0 P A:A937 3.7 56.3 1.0 O6 A:G939 3.9 52.9 1.0 N7 A:A938 3.9 42.5 1.0 N7 A:A937 4.1 57.3 1.0 C8 A:A937 4.1 57.9 1.0 N7 A:G939 4.4 53.2 1.0 C6 A:A938 4.4 41.8 1.0 C5 A:A938 4.5 41.9 1.0 C5' A:A937 4.6 54.2 1.0 C6 A:G939 4.7 52.5 1.0 OP1 A:A937 4.7 58.0 1.0 O3' A:C936 4.8 53.6 1.0 OP2 A:A938 4.8 55.2 1.0 C5 A:G939 4.9 52.8 1.0 C3' A:C936 4.9 50.5 1.0

Potassium binding site 6 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1559 b:35.6 occ:1.00 N3 A:C980 3.1 87.6 1.0 OP1 A:A1360 3.4 84.0 1.0 N4 A:C980 3.6 90.1 1.0 C4 A:C980 3.8 88.8 1.0 C2 A:C980 4.0 87.1 1.0 O2 A:C980 4.0 86.7 1.0 O N:VAL18 4.2 0.7 1.0 N7 A:A1360 4.4 75.0 1.0 O N:ALA20 4.5 0.1 1.0 O3' A:C1359 4.5 83.4 1.0 P A:A1360 4.6 84.6 1.0 N4 A:C979 4.7 89.4 1.0 C N:ALA20 4.8 0.4 1.0 CA N:TYR21 4.9 97.4 1.0 N N:ALA20 4.9 0.1 1.0 CB N:TYR21 5.0 97.3 1.0

Potassium binding site 7 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1560 b:61.2 occ:1.00 OP2 A:G1197 2.1 77.5 1.0 OP2 A:C1054 2.5 76.6 1.0 P A:G1197 3.6 77.7 1.0 P A:C1054 3.6 77.0 1.0 O2' A:G1053 3.8 78.2 1.0 N7 A:G1198 4.0 67.2 1.0 OP1 A:C1054 4.0 77.1 1.0 O5' A:G1197 4.1 74.6 1.0 O3' A:U1196 4.2 79.9 1.0 O4 A:U1199 4.3 56.7 1.0 O5' A:C1054 4.4 77.2 1.0 C8 A:G1197 4.6 66.7 1.0 MG A:MG1580 4.6 18.0 1.0 N7 A:G1197 4.6 66.7 1.0 C8 A:G1198 4.7 66.8 1.0 OP1 A:G1197 4.7 76.7 1.0 OP2 A:G1198 4.9 67.6 1.0 O3' A:G1053 5.0 77.6 1.0

Potassium binding site 8 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1578 b:22.6 occ:1.00 O6 A:G799 3.8 45.7 1.0 O6 A:G800 3.9 52.3 1.0 N7 A:G799 4.2 45.8 1.0 OP1 A:A781 4.4 40.7 1.0 C6 A:G800 4.5 51.5 1.0 N7 A:G798 4.5 41.8 1.0 C6 A:G799 4.7 44.8 1.0 N1 A:G800 4.7 50.4 1.0 O6 A:G798 4.7 41.7 1.0 C5 A:G799 4.9 45.1 1.0

Potassium binding site 9 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1602 b:0.2 occ:1.00 OP1 A:U182 3.1 82.3 1.0 N7 A:G183 3.6 72.6 1.0 O2' A:G181 3.8 78.8 1.0 P A:U182 3.8 82.2 1.0 OP2 A:U182 3.9 82.8 1.0 OP2 A:G183 4.0 77.5 1.0 O3' A:G181 4.1 81.5 1.0 C8 A:G183 4.1 72.9 1.0 C5 A:G183 4.9 71.8 1.0

Potassium binding site 10 out of 12 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ A:K1605 b:32.7 occ:1.00 N7 A:G581 2.7 60.3 1.0 N7 A:G758 3.0 32.3 1.0 O6 A:G581 3.4 59.5 1.0 C5 A:G581 3.6 60.3 1.0 O6 A:G758 3.6 34.9 1.0 C8 A:G581 3.8 61.3 1.0 C6 A:G581 3.9 59.9 1.0 C5 A:G758 3.9 32.3 1.0 C8 A:G758 4.0 33.4 1.0 OP2 A:G581 4.1 62.5 1.0 C6 A:G758 4.1 33.0 1.0 OP2 A:U757 4.4 39.3 1.0 OP2 A:G758 4.5 36.0 1.0 OP2 A:U580 4.7 61.3 1.0 C4 A:G581 4.9 60.3 1.0 N9 A:G581 4.9 61.5 1.0

J.B.Murray, S.O.Meroueh, R.J.Russell, G.Lentzen, J.Haddad, S.Mobashery. Interactions of Designer Antibiotics and the Bacterial Ribosome Aminoacyl-Trna Site Chem.Biol. V. 13 129 2006.
ISSN: ISSN 1074-5521
PubMed: 16492561
DOI: 10.1016/J.CHEMBIOL.2005.11.004