Potassium in PDB 8cgd: Clindamycin Bound to the 50S Subunit

The structure of Clindamycin Bound to the 50S Subunit also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	254 atoms
Zinc	(Zn)	2 atoms

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 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 85;

Binding sites:

The binding sites of Potassium atom in the Clindamycin Bound to the 50S Subunit (pdb code 8cgd). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 85 binding sites of Potassium where determined in the Clindamycin Bound to the 50S Subunit, PDB code: 8cgd:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3191 b:29.2 occ:1.00 O a:HOH7265 2.6 25.7 1.0 OP1 a:C2427 2.7 22.5 1.0 OP2 a:U827 2.9 22.8 1.0 O a:HOH6872 2.9 46.3 1.0 O a:HOH3440 2.9 20.6 1.0 O3' a:A2426 3.0 24.0 1.0 OP1 a:G2429 3.2 22.4 1.0 OP2 a:G2429 3.2 23.5 1.0 O a:HOH9998 3.3 42.6 1.0 O2' a:A2426 3.5 25.2 1.0 P a:C2427 3.5 20.7 1.0 OP1 a:U827 3.5 24.0 1.0 P a:G2429 3.7 19.4 1.0 MG a:MG3067 3.7 19.1 1.0 P a:U827 3.7 19.8 1.0 OP2 a:A2430 3.9 38.2 1.0 C5' a:G2429 4.0 23.8 1.0 C3' a:A2426 4.2 24.5 1.0 C2' a:A2426 4.2 24.5 1.0 MG a:MG3014 4.3 23.9 1.0 O5' a:G2429 4.4 22.3 1.0 C1' a:A2426 4.4 24.2 1.0 C5' a:C2427 4.4 21.4 1.0 O a:HOH9836 4.5 37.6 1.0 O5' a:C2427 4.5 21.4 1.0 OP2 a:C2427 4.6 24.4 1.0 O a:HOH7271 4.7 36.4 1.0 O3' a:U826 4.7 20.9 1.0 O4 a:U828 4.8 26.6 1.0 O5' a:U827 5.0 22.8 1.0

Potassium binding site 2 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3192 b:41.7 occ:1.00 O a:HOH8353 2.6 42.8 1.0 O6 a:G2371 2.6 30.1 1.0 O a:HOH4087 2.6 41.0 1.0 O6 a:G2370 2.7 32.9 1.0 O6 a:G2345 2.9 30.2 1.0 O a:HOH8066 3.3 37.3 1.0 C6 a:G2371 3.5 27.4 1.0 O a:HOH8129 3.5 46.5 1.0 C6 a:G2370 3.8 29.2 1.0 C6 a:G2345 3.8 25.9 1.0 N4 a:C2347 3.9 26.6 1.0 N1 a:G2371 3.9 26.8 1.0 N1 a:G2345 4.2 25.2 1.0 N7 a:G2370 4.4 31.6 1.0 N6 a:A2369 4.4 30.4 1.0 C5 a:G2370 4.5 29.4 1.0 C5 a:G2371 4.6 28.9 1.0 O4 a:U2372 4.9 33.7 1.0 O6 a:G2382 4.9 28.2 1.0 N1 a:G2370 5.0 29.2 1.0

Potassium binding site 3 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3193 b:31.8 occ:1.00 O6 a:G649 2.6 27.1 1.0 O6 a:G638 2.7 30.6 1.0 O a:HOH5329 2.8 29.7 1.0 O4 a:U639 2.8 32.1 1.0 O a:HOH9872 2.9 46.3 1.0 O6 a:G648 2.9 31.7 1.0 C6 a:G648 3.7 30.2 1.0 C4 a:U639 3.7 27.8 1.0 C6 a:G649 3.7 26.6 1.0 N4 a:C650 3.7 25.1 1.0 C6 a:G638 3.8 29.3 1.0 N3 a:U639 3.8 27.4 1.0 O a:HOH7633 3.8 52.5 1.0 O a:HOH7978 4.0 55.9 1.0 N7 a:G649 4.1 28.7 1.0 C5 a:G649 4.3 28.3 1.0 C5 a:G648 4.3 31.8 1.0 N7 a:G648 4.4 32.6 1.0 N4 a:C640 4.4 26.4 1.0 O a:HOH6151 4.6 58.1 1.0 C5 a:G638 4.6 31.6 1.0 N1 a:G648 4.6 29.2 1.0 N1 a:G638 4.6 30.0 1.0 C4 a:C650 4.7 25.7 1.0 N7 a:G638 4.8 32.6 1.0 N1 a:G649 4.9 25.6 1.0

Potassium binding site 4 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3194 b:29.2 occ:1.00 O6 a:G1288 2.5 26.7 1.0 O2 a:U1326 2.6 24.7 1.0 O m:GLY105 2.6 29.5 1.0 O a:HOH190 2.7 33.7 1.0 O a:HOH8298 2.8 29.1 1.0 O a:HOH9958 2.9 46.8 1.0 O4' a:A1327 3.0 25.3 1.0 N6 a:A1287 3.2 24.3 1.0 O2' a:U1326 3.4 25.4 1.0 C1' a:A1327 3.6 25.2 1.0 C m:GLY105 3.6 28.7 1.0 C6 a:G1288 3.8 24.3 1.0 C2 a:U1326 3.8 22.5 1.0 C2' a:U1326 3.9 24.3 1.0 O a:HOH8297 3.9 39.7 1.0 CA m:GLY105 3.9 28.9 1.0 N9 a:A1327 4.1 22.9 1.0 C4' a:A1327 4.2 26.2 1.0 C6 a:A1287 4.3 23.3 1.0 C1' a:U1326 4.3 23.6 1.0 C8 a:A1327 4.5 23.0 1.0 N1 a:G1288 4.5 22.7 1.0 N1 a:U1326 4.6 23.1 1.0 C5' a:A1327 4.7 26.1 1.0 N3 a:U1326 4.7 22.4 1.0 C5 a:G1288 4.8 23.2 1.0 N m:ASP106 4.9 26.9 1.0 C5 a:A1287 4.9 23.4 1.0 C4 a:A1327 4.9 22.3 1.0 N7 a:A1287 4.9 24.6 1.0 C2' a:A1327 5.0 26.1 1.0

Potassium binding site 5 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3195 b:48.7 occ:1.00 OP1 a:U2477 2.6 49.0 1.0 O6 a:G2529 2.6 38.8 1.0 O2 a:C2475 2.8 44.8 1.0 O a:HOH6060 2.9 60.6 1.0 O2' a:C2475 3.0 48.9 1.0 O 3:HOH206 3.5 70.9 1.0 C6 a:G2529 3.6 36.6 1.0 C2' a:C2475 3.7 51.8 1.0 P a:U2477 3.7 44.2 1.0 C1' a:C2475 3.7 47.1 1.0 N2 a:G2472 3.9 33.6 1.0 N1 a:G2529 3.9 37.0 1.0 C2 a:C2475 3.9 40.3 1.0 OP2 a:U2477 4.0 46.7 1.0 N1 a:C2475 4.3 43.5 1.0 N1 a:G2472 4.3 33.7 1.0 NZ 3:LYS32 4.4 37.6 1.0 C2 a:G2472 4.5 32.5 1.0 O5' a:U2477 4.7 43.2 1.0 OP1 a:A2478 4.7 43.2 1.0 O3' a:A2476 4.9 43.8 1.0 O4' a:C2475 4.9 51.8 1.0 C5 a:G2529 4.9 38.0 1.0

Potassium binding site 6 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3196 b:31.0 occ:1.00 O4 a:U2240 2.7 28.6 1.0 O5' a:G2238 2.8 33.1 1.0 O a:HOH5661 2.8 27.7 1.0 O4' a:G2238 2.8 27.6 1.0 O6 a:G2239 2.9 26.2 1.0 N7 a:G2239 3.0 27.8 1.0 O3' a:G2237 3.1 35.5 1.0 C4 a:U2240 3.4 24.9 1.0 C6 a:G2239 3.5 24.6 1.0 C5 a:G2239 3.6 26.4 1.0 C4' a:G2238 3.6 28.7 1.0 P a:G2238 3.6 33.5 1.0 N6 a:A2080 3.7 21.4 1.0 C5' a:G2238 3.8 29.7 1.0 C3' a:G2237 3.8 33.4 1.0 C2' a:G2237 3.9 32.9 1.0 C5 a:U2240 3.9 26.2 1.0 C1' a:G2238 4.0 24.8 1.0 O2' a:G2237 4.1 33.9 1.0 OP2 a:G2238 4.1 39.2 1.0 N9 a:G2238 4.2 22.8 1.0 C8 a:G2239 4.2 28.5 1.0 N3 a:U2240 4.5 25.0 1.0 C4 a:G2238 4.6 22.2 1.0 C8 a:G2238 4.6 22.0 1.0 N1 a:G2239 4.8 23.9 1.0 C4 a:G2239 4.8 26.3 1.0 N3 a:G2238 4.9 21.4 1.0 OP1 a:G2238 4.9 36.0 1.0 O4 a:U2081 4.9 24.2 1.0 C6 a:A2080 4.9 22.3 1.0 C3' a:G2238 5.0 27.9 1.0

Potassium binding site 7 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3197 b:39.9 occ:1.00 O6 a:G1471 2.6 34.0 1.0 O6 a:G1519 2.7 39.5 1.0 O4 a:U1520 2.8 37.5 1.0 O a:HOH4328 2.9 37.8 1.0 O a:HOH4820 2.9 40.9 1.0 O a:HOH9116 2.9 46.5 1.0 C4 a:U1520 3.6 37.0 1.0 N4 a:C1472 3.7 34.6 1.0 N3 a:U1520 3.7 36.2 1.0 C6 a:G1519 3.8 39.6 1.0 C6 a:G1471 3.8 33.3 1.0 N2 a:G1521 3.8 33.8 1.0 N1 a:G1521 3.9 33.8 1.0 C2 a:G1521 4.0 32.5 1.0 OP2 a:A1470 4.2 40.5 1.0 N7 a:G1471 4.4 35.1 1.0 C5 a:G1471 4.5 33.5 1.0 C5 a:G1519 4.6 41.8 1.0 O a:HOH6589 4.6 61.6 1.0 C4 a:C1472 4.6 34.7 1.0 N1 a:G1519 4.7 38.5 1.0 N3 a:G1521 4.7 34.9 1.0 C6 a:G1521 4.7 33.0 1.0 N7 a:G1519 4.7 42.2 1.0 N4 a:C1518 4.8 41.9 1.0 N1 a:G1471 4.9 33.2 1.0 C2 a:U1520 4.9 36.5 1.0 C5 a:U1520 4.9 37.5 1.0 N3 a:C1472 5.0 36.7 1.0

Potassium binding site 8 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3198 b:37.3 occ:1.00 O4 a:U588 2.6 27.3 1.0 O a:HOH77 2.7 48.4 1.0 O2' a:A670 2.8 22.2 1.0 O a:HOH358 2.8 42.9 1.0 O a:HOH5999 2.9 36.6 1.0 O3' a:A670 2.9 21.2 1.0 O a:HOH7683 2.9 42.3 1.0 OP2 a:C671 3.2 21.7 1.0 C4 a:U588 3.7 23.2 1.0 P a:C671 3.7 19.4 1.0 O a:HOH5544 3.7 37.0 1.0 C2' a:A670 3.8 21.1 1.0 N6 a:A668 3.9 20.8 1.0 C3' a:A670 3.9 21.5 1.0 C5 a:U588 4.2 23.9 1.0 C1' a:A670 4.2 20.6 1.0 O a:HOH8400 4.2 48.4 1.0 O4 a:U589 4.3 29.8 1.0 C5' a:C671 4.6 19.2 1.0 O5' a:C671 4.7 20.2 1.0 OP1 a:C671 4.8 23.3 1.0 N3 a:U588 4.8 22.0 1.0 O4' a:A670 5.0 20.9 1.0

Potassium binding site 9 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3199 b:28.1 occ:1.00 N1 a:A2614 2.8 20.1 1.0 N7 a:G2053 2.8 18.9 1.0 O a:HOH3663 2.9 30.9 1.0 O2' a:A2051 3.1 21.3 1.0 O6 a:G2053 3.1 20.5 1.0 N3 a:A2051 3.1 21.8 1.0 N6 a:A2052 3.2 19.3 1.0 C2 a:A2614 3.4 18.9 1.0 N7 a:A2052 3.4 18.2 1.0 C6 a:A2052 3.5 18.6 1.0 C5 a:A2052 3.5 18.1 1.0 C5 a:G2053 3.6 18.3 1.0 C6 a:G2053 3.7 17.6 1.0 C6 a:A2614 3.8 18.5 1.0 C2 a:A2051 3.8 20.4 1.0 N6 a:A2577 3.8 18.0 1.0 C8 a:G2053 3.9 17.8 1.0 N6 a:A2614 4.0 18.2 1.0 C6 a:A2577 4.0 18.1 1.0 C4 a:A2051 4.0 20.2 1.0 C2' a:A2051 4.2 19.9 1.0 C1' a:A2051 4.2 19.1 1.0 C8 a:A2052 4.3 17.4 1.0 C5 a:A2577 4.3 20.4 1.0 N9 a:A2051 4.4 19.8 1.0 N1 a:A2052 4.4 18.5 1.0 C4 a:A2052 4.5 17.7 1.0 N1 a:A2577 4.5 19.7 1.0 N7 a:A2577 4.6 21.4 1.0 N3 a:A2614 4.6 18.3 1.0 C4 a:G2053 4.8 17.9 1.0 N9 a:A2052 4.9 17.8 1.0 C5 a:A2614 5.0 18.7 1.0 N1 a:A2051 5.0 20.2 1.0 O3' a:A2051 5.0 20.1 1.0

Potassium binding site 10 out of 85 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:K3200 b:43.4 occ:1.00 O a:HOH5854 2.7 41.0 1.0 O2' a:G2464 2.7 34.0 1.0 OP1 a:A1126 2.8 30.5 1.0 OP2 a:A1126 2.8 32.5 1.0 O a:HOH9778 2.9 33.7 1.0 O a:HOH8758 2.9 33.4 1.0 N3 a:G2464 3.0 26.9 1.0 P a:A1126 3.3 27.7 1.0 C2' a:G2464 3.4 32.9 1.0 O a:HOH6757 3.5 51.0 1.0 O4' a:C2465 3.6 29.1 1.0 C1' a:G2464 3.6 32.2 1.0 O a:HOH7870 3.7 37.6 1.0 N2 a:G2464 3.8 23.3 1.0 C2 a:G2464 3.9 23.7 1.0 C4 a:G2464 4.0 25.9 1.0 C1' a:C2465 4.2 26.3 1.0 O3' a:G1125 4.2 27.5 1.0 N9 a:G2464 4.3 26.7 1.0 C4' a:C2465 4.5 30.6 1.0 N2 a:G2487 4.5 23.0 1.0 N6 a:A1028 4.6 23.6 1.0 N1 a:A1028 4.6 25.7 1.0 O5' a:A1126 4.6 30.0 1.0 O2' a:G1125 4.7 27.2 1.0 N3 a:G2487 4.8 24.3 1.0 O4' a:G2464 4.8 34.5 1.0 C3' a:G2464 4.9 33.9 1.0 C5' a:A1126 5.0 29.7 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.