Potassium in PDB 1kd1: Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1 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 (%)	22 / 26.9

The structure of Co-Crystal Structure of Spiramycin 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 Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1kd1). 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 Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Co-Crystal Structure of Spiramycin 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 Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8601 b:73.4 occ:1.00 O6 A:G2482 2.4 36.9 1.0 N7 A:G2482 2.7 38.6 1.0 O2 A:C2536 2.8 40.3 1.0 C6 A:G2482 3.0 36.7 1.0 C5 A:G2482 3.1 38.3 1.0 O6 A:G2102 3.1 54.6 1.0 O4' A:C2536 3.2 37.7 1.0 C2 A:C2536 3.3 40.0 1.0 N7 A:G2102 3.6 54.7 1.0 C1' A:C2536 3.6 38.2 1.0 N1 A:C2536 3.7 39.4 1.0 C6 A:G2102 3.8 55.2 1.0 N6 A:A2486 3.9 51.7 1.0 C8 A:G2482 3.9 38.4 1.0 C5 A:G2102 4.0 55.5 1.0 N3 A:C2536 4.1 39.0 1.0 O2 A:U2535 4.2 42.3 1.0 C4' A:C2536 4.3 36.9 1.0 C2 A:U2535 4.3 42.6 1.0 N1 A:G2482 4.3 35.2 1.0 N3 A:U2535 4.4 41.9 1.0 C4 A:G2482 4.4 37.9 1.0 C6 A:C2536 4.8 39.1 1.0 C2' A:U2535 4.8 42.0 1.0 C8 A:G2102 4.8 54.9 1.0 N9 A:G2482 4.8 38.1 1.0 C5' A:C2536 4.8 36.5 1.0 N1 A:U2535 4.9 42.5 1.0

Potassium binding site 2 out of 3 in the Co-Crystal Structure of Spiramycin 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 Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8602 b:68.8 occ:1.00 O A:HOH9016 2.7 45.0 1.0 O A:HOH9110 2.8 47.4 1.0 O4 A:U172 3.1 47.2 1.0 O A:HOH7820 3.1 63.1 1.0 O A:HOH4927 3.2 75.9 1.0 CD N:ARG82 3.3 92.3 1.0 O4 A:U163 3.3 42.2 1.0 O A:HOH9146 3.5 32.9 1.0 OP2 A:C162 3.5 26.6 1.0 O A:HOH7819 3.9 23.8 1.0 C4 A:U172 4.0 46.9 1.0 O A:HOH9321 4.1 43.3 1.0 N3 A:U172 4.1 45.9 1.0 NE N:ARG82 4.2 92.2 1.0 C4 A:U163 4.2 41.1 1.0 N4 A:C171 4.3 44.3 1.0 OP2 A:A169 4.4 36.6 1.0 CG N:ARG82 4.5 91.7 1.0 P A:C162 4.6 26.6 1.0 C5 A:U163 4.7 40.8 1.0 OP1 A:A169 4.7 37.6 1.0 CB N:ARG82 4.7 92.4 1.0 OP1 A:C162 4.7 27.0 1.0 MG A:MG8054 4.7 48.2 1.0 O6 A:G164 4.7 41.8 1.0 P A:A169 5.0 35.2 1.0

Potassium binding site 3 out of 3 in the Co-Crystal Structure of Spiramycin 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 Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:K8603 b:88.9 occ:1.00 O A:HOH5691 2.6 71.9 1.0 O A:HOH6273 2.9 67.9 1.0 O A:HOH6094 3.1 74.5 1.0 OP1 A:C2476 4.1 36.8 1.0 OP1 A:C2477 4.6 36.0 1.0 OP2 A:C2476 4.6 35.2 1.0 O A:HOH4935 4.6 46.3 1.0 P A:C2476 4.8 34.8 1.0 N3 A:A2103 4.9 72.5 1.0 C5' A:C2476 5.0 38.7 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