Potassium in PDB 1yjn: Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yjn was solved by D.Tu, G.Blaha, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.97 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.512, 300.125, 573.849, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.8

The structure of Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	116 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	23 atoms
Sodium	(Na)	86 atoms

The binding sites of Potassium atom in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1yjn). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yjn:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8401 b:99.6 occ:1.00 O6 0:G2482 2.6 40.2 1.0 O6 0:G2102 2.7 54.2 1.0 N7 0:G2482 3.1 41.0 1.0 O2 0:C2536 3.2 35.2 1.0 O4' 0:C2536 3.3 41.7 1.0 C6 0:G2482 3.4 39.8 1.0 C6 0:G2102 3.5 52.0 1.0 C5 0:G2482 3.5 40.9 1.0 N7 0:G2102 3.6 50.0 1.0 C1' 0:C2536 3.8 40.5 1.0 C2 0:C2536 3.8 36.9 1.0 C5 0:G2102 3.9 51.0 1.0 N6 0:A2486 4.0 55.3 1.0 O2 0:U2535 4.0 48.4 1.0 N1 0:C2536 4.1 39.4 1.0 C4' 0:C2536 4.1 41.1 1.0 C8 0:G2482 4.3 40.9 1.0 C2 0:U2535 4.3 45.2 1.0 OP1 0:U2539 4.4 41.5 1.0 C5' 0:C2536 4.6 41.0 1.0 N3 0:U2535 4.6 42.0 1.0 C15 0:CLY9000 4.7 61.1 1.0 N3 0:C2536 4.7 36.3 1.0 N1 0:G2482 4.7 38.6 1.0 N1 0:G2102 4.7 52.0 1.0 C2' 0:U2535 4.7 42.5 1.0 C8 0:G2102 4.8 49.8 1.0 C4 0:G2482 4.9 41.6 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Clindamycin Bound to the G2099A Mutant 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 Crystal Structure of Clindamycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8402 b:73.8 occ:1.00 O4 0:U172 2.9 36.0 1.0 O 0:HOH9013 2.9 46.1 1.0 O4 0:U163 3.1 32.2 1.0 O 0:HOH9147 3.2 43.1 1.0 OP2 0:C162 3.3 30.2 1.0 O 0:HOH9110 3.3 41.2 1.0 O 0:HOH7806 3.4 30.8 1.0 O M:HOH8891 3.4 69.6 1.0 CD M:ARG82 3.5 54.1 1.0 C4 0:U172 3.9 34.2 1.0 N3 0:U172 4.0 33.4 1.0 C4 0:U163 4.2 30.6 1.0 NE M:ARG82 4.2 55.5 1.0 O 0:HOH9327 4.3 42.4 1.0 N4 0:C171 4.5 36.5 1.0 P 0:C162 4.5 30.7 1.0 OP2 0:A169 4.5 32.7 1.0 C5 0:U163 4.6 31.0 1.0 CG M:ARG82 4.7 53.8 1.0 O6 0:G164 4.7 33.4 1.0 OP1 0:A169 4.7 31.3 1.0 CB M:ARG82 4.8 54.5 1.0 OP1 0:C162 4.9 30.2 1.0 MG 0:MG8054 4.9 43.8 1.0 N3 0:C173 5.0 30.3 1.0

D.Tu, G.Blaha, P.B.Moore, T.A.Steitz. Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide A Structural Explanation For Resistance. Cell(Cambridge,Mass.) V. 121 257 2005.
ISSN: ISSN 0092-8674
PubMed: 15851032
DOI: 10.1016/J.CELL.2005.02.005