Potassium in PDB 1k8a: Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k8a was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.5

The structure of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	119 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	23 atoms
Sodium	(Na)	83 atoms

The binding sites of Potassium atom in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1k8a). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k8a:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8601 b:62.8 occ:1.00 OP2 A:C2487 3.6 45.2 1.0 N7 A:A2488 3.6 48.2 1.0 O A:HOH9977 3.9 78.9 1.0 N7 A:G2489 4.2 45.3 1.0 O6 A:G2489 4.3 43.0 1.0 N6 A:A2488 4.3 54.4 1.0 OP2 A:A2486 4.4 36.7 1.0 C5 A:A2488 4.4 50.4 1.0 C8 A:A2488 4.5 46.4 1.0 N6 A:A2490 4.6 39.2 1.0 C6 A:A2488 4.7 52.1 1.0 N1 A:A2532 4.8 37.0 1.0 O4 A:U2531 4.8 40.7 1.0 OP2 A:A2488 4.8 38.6 1.0 C2 A:A2532 4.8 37.4 1.0 P A:C2487 4.9 45.1 1.0 O A:HOH9425 5.0 33.8 1.0 C6 A:G2489 5.0 43.8 1.0 C5 A:G2489 5.0 44.0 1.0

Potassium binding site 2 out of 3 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8602 b:69.7 occ:1.00 O A:HOH8711 2.6 43.6 1.0 O4 A:U172 2.8 43.0 1.0 O A:HOH8617 2.9 53.1 1.0 O A:HOH8745 3.1 38.0 1.0 O4 A:U163 3.2 40.8 1.0 CD N:ARG82 3.3 0.3 1.0 O A:HOH7372 3.4 62.0 1.0 O A:HOH4508 3.6 73.9 1.0 OP2 A:C162 3.7 33.5 1.0 C4 A:U172 3.7 43.2 1.0 N3 A:U172 3.9 43.0 1.0 O A:HOH7371 4.1 56.4 1.0 NE N:ARG82 4.1 0.2 1.0 C4 A:U163 4.2 40.3 1.0 N4 A:C171 4.2 49.0 1.0 O A:HOH8917 4.3 52.7 1.0 OP2 A:A169 4.5 38.4 1.0 CG N:ARG82 4.6 1.0 1.0 CB N:ARG82 4.7 0.4 1.0 O6 A:G164 4.7 39.6 1.0 C5 A:U163 4.8 40.0 1.0 OP1 A:A169 4.8 38.1 1.0 P A:C162 4.8 32.8 1.0 MG A:MG8054 4.9 42.1 1.0 N4 A:C173 4.9 37.4 1.0 OP2 A:U170 4.9 39.4 1.0 N3 A:C173 4.9 37.4 1.0

Potassium binding site 3 out of 3 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8603 b:67.0 occ:1.00 O A:HOH5671 3.2 83.0 1.0 OP1 A:C2476 4.2 31.6 1.0 N3 A:A2103 4.5 39.2 1.0 OP1 A:C2477 4.5 33.8 1.0 OP2 A:C2476 4.7 31.0 1.0 C1' A:A2103 4.8 42.5 1.0 O3' A:C2476 4.8 35.2 1.0 C5' A:C2476 4.9 33.8 1.0 P A:C2476 4.9 31.4 1.0 P A:C2477 4.9 35.0 1.0 OP2 A:C2477 5.0 32.5 1.0

J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz. The Structures of Four Macrolide Antibiotics Bound to the Large Ribosomal Subunit. Mol.Cell V. 10 117 2002.
ISSN: ISSN 1097-2765
PubMed: 12150912
DOI: 10.1016/S1097-2765(02)00570-1