Potassium in PDB 1vqk: The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqk was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.873, 298.569, 575.390, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25

The structure of The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium	(Sr)	114 atoms
Magnesium	(Mg)	93 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	75 atoms

The binding sites of Potassium atom in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqk). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqk:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the 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 The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K9001 b:95.1 occ:1.00 O6 0:G2482 2.7 41.6 1.0 O6 0:G2102 2.7 65.5 1.0 N7 0:G2482 2.8 40.6 1.0 O4' 0:C2536 2.9 43.9 1.0 O2 0:C2536 3.2 42.8 1.0 C6 0:G2482 3.3 40.2 1.0 C5 0:G2482 3.3 41.0 1.0 C2 0:C2536 3.6 41.1 1.0 C6 0:G2102 3.6 64.4 1.0 C1' 0:C2536 3.7 43.2 1.0 N7 0:G2102 3.8 65.6 1.0 N6 0:A2486 3.8 51.1 1.0 N1 0:C2536 3.8 41.7 1.0 C4' 0:C2536 3.9 45.6 1.0 C8 0:G2482 4.0 41.4 1.0 C5 0:G2102 4.0 65.5 1.0 O 0:HOH5357 4.2 98.7 1.0 O2 0:U2535 4.2 51.8 1.0 C5' 0:C2536 4.3 44.1 1.0 N3 0:C2536 4.4 42.0 1.0 C2 0:U2535 4.4 48.0 1.0 C2' 0:U2535 4.5 46.5 1.0 C4 0:G2482 4.7 40.5 1.0 N1 0:G2482 4.7 40.8 1.0 N3 0:U2535 4.7 46.4 1.0 N1 0:G2102 4.8 64.4 1.0 C6 0:C2536 4.8 39.7 1.0 OP1 0:U2539 4.8 76.3 1.0 O5' 0:C2536 4.9 44.9 1.0 O2' 0:U2535 4.9 45.3 1.0 C8 0:G2102 5.0 65.8 1.0 N1 0:U2535 5.0 47.4 1.0 N9 0:G2482 5.0 41.6 1.0

Potassium binding site 2 out of 2 in the The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the 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 The Structure of Ccda-Phe-Cap-Bio Bound to the A Site of the Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K9002 b:86.8 occ:1.00 O4 0:U172 2.8 33.4 1.0 O 0:HOH9642 2.9 30.4 1.0 CD M:ARG82 2.9 65.2 1.0 O M:HOH9324 3.0 25.6 1.0 O 0:HOH9738 3.1 43.8 1.0 O4 0:U163 3.1 33.6 1.0 OP2 0:C162 3.3 28.1 1.0 O 0:HOH5514 3.4 69.5 1.0 O 0:HOH8383 3.5 84.0 1.0 NE M:ARG82 3.5 65.2 1.0 C4 0:U172 3.8 33.9 1.0 O 0:HOH8382 3.9 51.1 1.0 N3 0:U172 4.0 33.5 1.0 O 0:HOH9949 4.1 40.8 1.0 C4 0:U163 4.2 30.5 1.0 CG M:ARG82 4.2 68.7 1.0 CZ M:ARG82 4.5 68.0 1.0 N4 0:C171 4.5 35.6 1.0 P 0:C162 4.6 29.1 1.0 CB M:ARG82 4.6 70.9 1.0 OP2 0:A169 4.6 29.0 1.0 C5 0:U163 4.8 30.6 1.0 O6 0:G164 4.8 30.2 1.0 OP1 0:A169 4.8 29.8 1.0 OP1 0:C162 5.0 29.5 1.0

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006