Potassium in PDB 1k9m: Co-Crystal Structure of Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k9m was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, 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)	19.99 / 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 (%)	21.9 / 26.2

The structure of Co-Crystal Structure of Tylosin 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)	22 atoms
Sodium	(Na)	85 atoms

The binding sites of Potassium atom in the Co-Crystal Structure of Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1k9m). 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k9m:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8601 b:62.6 occ:1.00 O6 A:G2102 2.8 43.6 1.0 O6 A:G2482 2.9 27.4 1.0 O2 A:C2536 3.0 29.9 1.0 N7 A:G2482 3.1 29.4 1.0 O4' A:C2536 3.2 32.4 1.0 N7 A:G2102 3.3 44.1 1.0 C6 A:G2102 3.5 43.6 1.0 C6 A:G2482 3.5 26.8 1.0 C2 A:C2536 3.6 30.5 1.0 C5 A:G2482 3.6 28.7 1.0 C1' A:C2536 3.7 31.9 1.0 C5 A:G2102 3.7 43.8 1.0 N1 A:C2536 3.9 31.1 1.0 N6 A:A2486 4.1 47.2 1.0 C4' A:C2536 4.1 32.4 1.0 O2 A:U2535 4.1 39.2 1.0 C8 A:G2482 4.3 29.0 1.0 C2 A:U2535 4.4 39.2 1.0 C8 A:G2102 4.5 43.8 1.0 N3 A:C2536 4.5 29.7 1.0 C5' A:C2536 4.6 32.9 1.0 N3 A:U2535 4.7 38.3 1.0 C2' A:U2535 4.8 38.8 1.0 N1 A:G2102 4.8 44.5 1.0 N1 A:G2482 4.9 25.9 1.0 OP1 A:U2539 4.9 37.4 1.0 C4 A:G2482 5.0 29.1 1.0

Potassium binding site 2 out of 3 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8602 b:56.7 occ:1.00 O A:HOH9014 2.5 42.2 1.0 O A:HOH9116 2.6 31.4 1.0 O4 A:U163 3.0 36.7 1.0 O A:HOH7833 3.1 45.4 1.0 O A:HOH4923 3.1 72.5 1.0 O4 A:U172 3.2 42.3 1.0 OP2 A:C162 3.3 24.1 1.0 O A:HOH9150 3.5 46.4 1.0 CD N:ARG82 3.6 80.8 1.0 O A:HOH7832 3.9 37.9 1.0 C4 A:U172 4.0 43.5 1.0 C4 A:U163 4.1 35.6 1.0 N3 A:U172 4.1 43.2 1.0 O A:HOH9324 4.1 44.5 1.0 OP2 A:A169 4.3 31.5 1.0 N4 A:C171 4.3 41.1 1.0 P A:C162 4.4 23.7 1.0 NE N:ARG82 4.5 80.5 1.0 C5 A:U163 4.5 35.2 1.0 OP1 A:C162 4.6 23.7 1.0 MG A:MG8054 4.6 50.2 1.0 CG N:ARG82 4.7 81.6 1.0 O6 A:G164 4.7 33.1 1.0 OP1 A:A169 4.7 33.1 1.0 CB N:ARG82 4.8 82.8 1.0 P A:A169 4.9 30.7 1.0

Potassium binding site 3 out of 3 in the Co-Crystal Structure of Tylosin 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 Tylosin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8603 b:76.3 occ:1.00 O A:HOH5695 2.6 56.5 1.0 O A:HOH6286 3.4 45.0 1.0 O A:HOH6105 3.4 71.2 1.0 OP1 A:C2476 4.1 28.8 1.0 OP1 A:C2477 4.2 31.8 1.0 OP2 A:C2476 4.6 29.4 1.0 O3' A:C2476 4.6 32.8 1.0 C5' A:C2476 4.7 32.2 1.0 P A:C2477 4.7 32.3 1.0 P A:C2476 4.8 29.5 1.0 OP2 A:C2477 4.8 30.0 1.0 N3 A:A2103 4.9 42.1 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