Potassium in PDB 3cme: The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme was solved by M.Simonovic, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.82 / 2.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	210.786, 297.778, 572.588, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.5

The structure of The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium	(Sr)	108 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 3cme). 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 3cme:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8401 b:82.0 occ:1.00 O6 0:G2482 3.2 37.4 1.0 O6 0:G2102 3.2 52.0 1.0 O4' 0:C2536 3.3 37.6 1.0 N7 0:G2482 3.5 37.3 1.0 N7 0:G2102 3.5 53.1 1.0 O2 0:C2536 3.6 33.9 1.0 O2 0:U2535 3.8 45.6 1.0 C6 0:G2482 4.0 36.7 1.0 C4' 0:C2536 4.0 38.2 1.0 C6 0:G2102 4.0 53.6 1.0 OP1 0:U2539 4.0 48.8 1.0 C5 0:G2482 4.1 37.5 1.0 N6 0:A2486 4.1 41.6 1.0 C5 0:G2102 4.1 53.3 1.0 C1' 0:C2536 4.2 37.5 1.0 C2 0:C2536 4.3 33.2 1.0 C2 0:U2535 4.4 44.9 1.0 C5' 0:C2536 4.4 38.9 1.0 C2' 0:U2535 4.6 43.3 1.0 N1 0:C2536 4.6 34.9 1.0 C8 0:G2482 4.7 37.4 1.0 C8 0:G2102 4.7 52.5 1.0 O2' 0:U2535 4.8 43.3 1.0 N3 0:U2535 4.8 45.4 1.0

Potassium binding site 2 out of 2 in the The Structure of Ca and Cca-Phe-Cap-Bio Bound to the Large 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 Ca and Cca-Phe-Cap-Bio Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8402 b:0.5 occ:1.00 O4 0:U163 3.3 38.8 1.0 O 0:HOH3033 3.4 42.2 1.0 O 0:HOH2937 3.4 66.1 1.0 O 0:HOH3066 3.4 37.5 1.0 O4 0:U172 3.4 32.7 1.0 OP2 0:C162 3.5 30.6 1.0 CD M:ARG82 3.6 61.7 1.0 O 0:HOH5807 3.6 34.1 1.0 O 0:HOH9619 3.9 94.1 1.0 OP2 0:A169 4.0 34.9 1.0 OP1 0:A169 4.0 32.3 1.0 O 0:HOH9620 4.2 45.2 1.0 C4 0:U163 4.3 37.1 1.0 C4 0:U172 4.3 31.6 1.0 O6 0:G164 4.4 27.6 1.0 N3 0:U172 4.4 30.6 1.0 NE M:ARG82 4.5 60.2 1.0 P 0:A169 4.5 33.6 1.0 N4 0:C171 4.5 40.5 1.0 O 0:HOH3243 4.6 53.9 1.0 CB M:ARG82 4.7 64.4 1.0 C5 0:U163 4.7 36.8 1.0 P 0:C162 4.8 31.9 1.0 CG M:ARG82 4.8 63.9 1.0 MG 0:MG8041 5.0 33.2 1.0

M.Simonovic, T.A.Steitz. Peptidyl-Cca Deacylation on the Ribosome Promoted By Induced Fit and the O3'-Hydroxyl Group of A76 of the Unacylated A-Site Trna. Rna V. 14 2372 2008.
ISSN: ISSN 1355-8382
PubMed: 18818369
DOI: 10.1261/RNA.1118908