Potassium in PDB 8cgu: Gentamicin Bound to the 30S Body

The structure of Gentamicin Bound to the 30S Body also contains other interesting chemical elements:

Magnesium

(Mg)

58 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Potassium atom in the Gentamicin Bound to the 30S Body (pdb code 8cgu). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 24 binding sites of Potassium where determined in the Gentamicin Bound to the 30S Body, PDB code: 8cgu:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1601 b:41.0 occ:1.00 O6 A:G645 2.7 34.8 1.0 O A:HOH2217 2.8 32.5 1.0 O A:HOH2790 2.8 40.0 1.0 O4 A:U644 2.9 37.6 1.0 O A:HOH2835 2.9 39.3 1.0 O4 A:U594 2.9 39.6 1.0 C4 A:U644 3.7 33.4 1.0 C6 A:G645 3.7 35.2 1.0 O A:HOH3322 3.7 43.0 1.0 C4 A:U594 3.8 40.7 1.0 MG A:MG1623 3.8 39.1 1.0 C2 A:A595 3.9 39.6 1.0 N3 A:U594 3.9 36.9 1.0 N1 A:A595 4.0 41.4 1.0 N7 A:G645 4.1 36.3 1.0 C5 A:U644 4.1 36.1 1.0 C5 A:G645 4.2 35.8 1.0 O4 A:U593 4.3 42.1 1.0 O A:HOH2575 4.3 53.2 1.0 O A:HOH2539 4.4 40.5 1.0 N6 A:A596 4.5 33.2 1.0 N4 A:C643 4.5 32.2 1.0 C5 A:C643 4.8 32.3 1.0 N3 A:A595 4.9 41.5 1.0 N3 A:U644 4.9 34.2 1.0 O A:HOH2881 4.9 35.3 1.0 O6 A:G646 4.9 35.4 1.0 N1 A:G645 4.9 34.4 1.0 C4 A:C643 5.0 31.9 1.0

Potassium binding site 2 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1602 b:42.6 occ:1.00 O A:HOH1716 2.6 41.7 1.0 O A:HOH2236 2.8 37.1 1.0 O2 A:C758 2.9 27.1 1.0 O6 A:G584 2.9 25.5 1.0 N3 A:C758 3.0 25.6 1.0 N7 A:A583 3.0 30.7 1.0 C2 A:C758 3.3 25.4 1.0 C5 A:C582 3.4 29.7 1.0 N7 A:G584 3.5 26.9 1.0 C6 A:G584 3.5 24.5 1.0 OP2 A:C582 3.6 33.9 1.0 OP2 A:A583 3.6 45.6 1.0 C8 A:A583 3.6 29.3 1.0 C5 A:G584 3.7 26.8 1.0 C6 A:C582 3.9 30.0 1.0 C4 A:C758 4.1 24.7 1.0 C4 A:C582 4.1 27.7 1.0 C5 A:A583 4.1 29.4 1.0 O5' A:C582 4.3 35.5 1.0 N4 A:C758 4.4 23.6 1.0 N4 A:C582 4.4 27.6 1.0 N6 A:A583 4.5 26.8 1.0 O4 A:U757 4.5 26.7 1.0 C8 A:G584 4.5 27.9 1.0 P A:C582 4.6 32.6 1.0 N1 A:C758 4.6 24.7 1.0 N1 A:G584 4.7 22.4 1.0 N3 A:U757 4.7 22.1 1.0 C6 A:A583 4.8 27.3 1.0 N1 A:C582 4.8 31.2 1.0 O A:HOH1954 4.8 43.8 1.0 C4 A:G584 4.9 25.5 1.0 P A:A583 4.9 42.7 1.0 C3' A:C582 4.9 37.8 1.0 N3 A:C582 5.0 31.4 1.0 N9 A:A583 5.0 31.0 1.0 O5' A:A583 5.0 42.2 1.0

Potassium binding site 3 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1647 b:30.2 occ:1.00 OP1 A:C1521 2.7 33.6 1.0 OP1 A:A1508 2.7 27.2 1.0 OP1 A:A1500 2.7 27.1 1.0 O A:HOH3108 2.9 48.3 1.0 O A:HOH2913 2.9 24.0 1.0 O3' A:A1499 3.1 30.1 1.0 O A:HOH3265 3.3 46.8 1.0 P A:A1500 3.5 25.8 1.0 MG A:MG1646 3.6 23.3 1.0 P A:C1521 3.7 31.5 1.0 P A:A1508 3.8 27.2 1.0 OP2 A:C1521 4.0 33.8 1.0 O A:HOH1880 4.0 44.1 1.0 C5' A:A1500 4.2 30.4 1.0 OP2 A:A1508 4.3 29.4 1.0 O5' A:A1508 4.3 28.4 1.0 C3' A:A1499 4.3 30.1 1.0 O5' A:A1500 4.4 28.4 1.0 O2' A:A1499 4.4 32.7 1.0 O A:HOH2281 4.5 34.7 1.0 O3' A:C1520 4.5 34.1 1.0 C4' A:A1499 4.6 31.7 1.0 C5' A:A1508 4.7 28.8 1.0 OP2 A:A1500 4.8 27.8 1.0 OP1 A:G1505 4.9 26.4 1.0 O A:HOH2271 4.9 58.5 1.0 C2' A:A1499 5.0 29.8 1.0

Potassium binding site 4 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1648 b:37.5 occ:1.00 O A:HOH3127 2.6 37.1 1.0 O6 A:G326 2.7 23.9 1.0 OP2 A:G107 2.8 27.8 1.0 N7 A:A325 3.0 25.2 1.0 O2' A:G324 3.0 31.3 1.0 OP1 A:G107 3.3 27.9 1.0 P A:G107 3.6 23.3 1.0 C6 A:G326 3.6 21.1 1.0 C8 A:A325 3.6 25.1 1.0 O A:HOH2566 3.8 33.7 1.0 K A:K1649 4.1 39.2 1.0 C5 A:A325 4.1 24.9 1.0 C5 A:G326 4.2 22.5 1.0 N7 A:G326 4.2 23.5 1.0 O3' A:G324 4.2 35.8 1.0 C2' A:G324 4.3 28.7 1.0 N6 A:A325 4.5 24.1 1.0 N1 A:G326 4.6 20.8 1.0 O3' A:C106 4.6 25.8 1.0 C6 A:A325 4.7 25.2 1.0 C3' A:G324 4.8 29.5 1.0 O5' A:G107 4.8 25.3 1.0 N9 A:A325 4.9 26.3 1.0 O A:HOH1930 4.9 60.3 1.0 C4' A:G324 4.9 27.9 1.0

Potassium binding site 5 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1649 b:39.2 occ:1.00 OP2 A:G108 2.8 26.4 1.0 OP2 A:G107 2.8 27.8 1.0 O6 A:G326 2.9 23.9 1.0 N7 A:G108 2.9 23.4 1.0 O5' A:G107 3.3 25.3 1.0 C8 A:G108 3.6 23.6 1.0 N1 A:A109 3.6 19.4 1.0 O A:HOH3127 3.6 37.1 1.0 P A:G107 3.6 23.3 1.0 C2 A:A109 3.8 19.5 1.0 C6 A:G326 3.8 21.1 1.0 C8 A:G107 3.9 22.8 1.0 NH2 T:ARG10 3.9 28.2 1.0 N7 A:G107 4.0 22.5 1.0 N1 A:G326 4.0 20.8 1.0 K A:K1648 4.1 37.5 1.0 P A:G108 4.1 22.9 1.0 O A:HOH2566 4.2 33.7 1.0 C5 A:G108 4.2 23.4 1.0 C3' A:G107 4.2 23.8 1.0 OP1 A:G107 4.3 27.9 1.0 O5' A:G108 4.5 24.9 1.0 CZ T:ARG10 4.6 28.8 1.0 C5' A:G107 4.6 23.8 1.0 O6 A:G108 4.6 24.9 1.0 C6 A:A109 4.6 18.7 1.0 O3' A:G107 4.7 23.7 1.0 N9 A:G107 4.8 23.0 1.0 C6 A:G108 4.8 23.6 1.0 N3 A:A109 4.9 19.7 1.0 N9 A:G108 4.9 23.9 1.0 C4' A:G107 4.9 23.1 1.0 C5 A:G107 4.9 23.5 1.0

Potassium binding site 6 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1650 b:47.8 occ:1.00 N1 A:A780 2.8 27.8 1.0 OP2 A:A802 2.8 38.9 1.0 O A:HOH3287 2.9 42.2 1.0 O6 A:G803 3.0 28.2 1.0 OP2 A:U801 3.3 43.1 1.0 N2 A:G776 3.4 28.9 1.0 C2 A:A780 3.4 25.5 1.0 N4 A:C779 3.7 26.3 1.0 O5' A:U801 3.7 40.0 1.0 C6 A:A780 3.8 26.5 1.0 C6 A:G803 3.9 24.5 1.0 N6 A:A780 4.0 29.5 1.0 P A:U801 4.0 37.6 1.0 P A:A802 4.2 38.3 1.0 O A:HOH2004 4.2 52.3 1.0 C3' A:U801 4.2 36.5 1.0 C2 A:G776 4.3 30.5 1.0 O3' A:U801 4.5 36.0 1.0 C5 A:G803 4.6 24.0 1.0 O A:HOH2705 4.7 31.9 1.0 C6 A:U801 4.7 30.0 1.0 N3 A:A780 4.7 24.9 1.0 C5' A:U801 4.7 37.9 1.0 OP1 A:U801 4.7 45.8 1.0 N7 A:G803 4.7 23.6 1.0 N1 A:G803 4.8 23.7 1.0 N1 A:G776 4.9 30.2 1.0 C4 A:C779 4.9 26.2 1.0 N3 A:G776 5.0 28.4 1.0 N7 A:A802 5.0 24.7 1.0 O A:HOH3093 5.0 46.5 1.0

Potassium binding site 7 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1651 b:40.3 occ:1.00 OP2 A:C564 2.6 34.6 1.0 OP2 A:G567 2.6 36.0 1.0 OP2 A:U565 2.8 39.8 1.0 O A:HOH2351 2.8 46.6 1.0 O2' A:A563 2.8 29.0 1.0 O A:HOH1778 3.0 46.3 1.0 O3' A:A563 3.5 29.9 1.0 P A:C564 3.6 29.7 1.0 C2' A:A563 3.8 27.9 1.0 P A:G567 3.8 32.7 1.0 O3' A:G566 3.9 33.6 1.0 O2' A:G566 3.9 30.1 1.0 P A:U565 4.0 36.1 1.0 O5' A:C564 4.1 34.6 1.0 C3' A:A563 4.2 28.7 1.0 C5' A:C564 4.3 39.2 1.0 N7 A:G567 4.4 25.2 1.0 OP1 A:U565 4.4 43.5 1.0 C8 A:G567 4.4 26.6 1.0 O5' A:G567 4.4 31.5 1.0 NH2 L:ARG12 4.5 30.6 1.0 C3' A:G566 4.5 33.2 1.0 O3' A:C564 4.7 36.7 1.0 C2' A:G566 4.8 30.1 1.0 OP1 A:C564 4.9 32.4 1.0

Potassium binding site 8 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1652 b:34.1 occ:1.00 O A:HOH1872 2.6 47.6 1.0 O4 A:U12 2.7 28.8 1.0 O6 A:G22 2.8 26.1 1.0 O A:HOH2037 2.8 32.7 1.0 O6 A:G11 3.0 28.1 1.0 O6 A:G21 3.0 30.9 1.0 O A:HOH3224 3.0 45.4 1.0 C6 A:G21 3.5 24.6 1.0 N4 A:C23 3.6 25.4 1.0 C4 A:U12 3.6 26.9 1.0 N3 A:U12 3.8 26.3 1.0 C6 A:G22 3.8 23.3 1.0 N1 A:G21 3.9 24.3 1.0 C6 A:G11 4.0 26.5 1.0 N7 A:G22 4.1 23.8 1.0 C5 A:G22 4.4 23.5 1.0 C5 A:G21 4.5 26.0 1.0 C4 A:C23 4.6 24.7 1.0 C2 A:G21 4.9 24.3 1.0 C5 A:G11 4.9 27.2 1.0 N1 A:G11 4.9 26.7 1.0 C5 A:U12 5.0 27.9 1.0

Potassium binding site 9 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1653 b:29.9 occ:1.00 O4 A:U375 2.6 25.5 1.0 O2' A:C372 2.7 32.1 1.0 O2 A:C372 2.8 30.0 1.0 O4 A:U387 2.9 32.7 1.0 O A:HOH2485 2.9 33.4 1.0 O6 A:G376 2.9 27.8 1.0 O A:HOH2903 3.0 38.0 1.0 O A:HOH1743 3.5 43.5 1.0 C2 A:C372 3.7 27.6 1.0 C4 A:U375 3.7 25.9 1.0 C4 A:U387 3.8 29.3 1.0 C2' A:C372 3.9 33.2 1.0 C6 A:G376 3.9 25.9 1.0 N6 A:A389 3.9 24.6 1.0 N3 A:U387 3.9 28.8 1.0 O A:HOH2734 4.2 46.8 1.0 C5 A:U375 4.3 27.2 1.0 N3 A:C372 4.4 28.3 1.0 C1' A:C372 4.4 32.0 1.0 N1 A:C372 4.4 30.0 1.0 N7 A:G376 4.4 29.4 1.0 O A:HOH2176 4.5 36.4 1.0 C5 A:G376 4.5 28.3 1.0 N6 A:A374 4.7 25.8 1.0 N7 A:A374 4.7 30.1 1.0 N3 A:U375 4.8 23.7 1.0 O A:HOH1933 5.0 45.9 1.0

Potassium binding site 10 out of 24 in the Gentamicin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Gentamicin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:K1654 b:44.1 occ:1.00 O6 A:G925 2.6 36.2 1.0 O4 A:U1390 2.8 37.1 1.0 O A:HOH2023 2.9 47.5 1.0 O A:HOH2905 2.9 48.9 1.0 O4 A:U1391 3.0 39.9 1.0 O6 A:G927 3.0 40.0 1.0 N4 A:C924 3.4 30.7 1.0 C6 A:G925 3.6 33.6 1.0 C4 A:U1391 3.6 38.5 1.0 O A:HOH2302 3.7 51.4 1.0 N3 A:U1391 3.7 38.0 1.0 C4 A:U1390 3.7 39.0 1.0 N3 A:U1390 3.9 38.4 1.0 C6 A:G927 4.0 36.0 1.0 N7 A:G925 4.2 32.9 1.0 C4 A:C924 4.2 30.7 1.0 C5 A:G925 4.3 33.2 1.0 N7 A:G927 4.6 35.9 1.0 C5 A:C924 4.6 31.0 1.0 C5 A:G927 4.7 37.5 1.0 N1 A:G925 4.8 33.5 1.0 O6 A:G1392 4.9 33.9 1.0 C2 A:U1391 4.9 36.6 1.0 O6 A:G928 4.9 39.3 1.0 C5 A:U1391 4.9 38.5 1.0

H.Paternoga, C.Crowe-Mcauliffe, L.V.Bock, T.O.Koller, M.Morici, B.Beckert, A.G.Myasnikov, H.Grubmueller, J.Novacek, D.N.Wilson. Structural Conservation of Antibiotic Interaction with Ribosomes To Be Published.