Potassium in PDB 1q7y: Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y was solved by J.L.Hansen, T.M.Schmeing, 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 / 3.20
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 (%)	22.5 / 28

The structure of Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Potassium atom in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit (pdb code 1q7y). 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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit, PDB code: 1q7y:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:K8201 b:76.7 occ:1.00 O6 A:G2482 2.7 38.7 1.0 O6 A:G2102 2.7 36.0 1.0 O2 A:C2536 2.9 38.6 1.0 O4' A:C2536 2.9 41.5 1.0 N7 A:G2482 3.1 38.7 1.0 C6 A:G2482 3.3 39.1 1.0 N7 A:G2102 3.4 38.1 1.0 C2 A:C2536 3.4 39.5 1.0 C5 A:G2482 3.5 39.5 1.0 C6 A:G2102 3.5 37.7 1.0 C1' A:C2536 3.5 40.5 1.0 N1 A:C2536 3.7 40.3 1.0 C5 A:G2102 3.8 38.1 1.0 N6 A:A2486 3.9 37.1 1.0 C4' A:C2536 4.0 40.2 1.0 C8 A:G2482 4.3 37.5 1.0 O2 A:U2535 4.3 44.1 1.0 N3 A:C2536 4.3 39.3 1.0 C5' A:C2536 4.5 39.2 1.0 C2 A:U2535 4.6 43.3 1.0 C8 A:G2102 4.6 39.0 1.0 N1 A:G2482 4.6 38.6 1.0 C2' A:U2535 4.7 41.7 1.0 C6 A:C2536 4.7 40.1 1.0 OP1 A:U2539 4.7 42.7 1.0 N1 A:G2102 4.8 37.8 1.0 C4 A:G2482 4.8 38.7 1.0 N3 A:U2535 4.9 43.7 1.0 C2' A:C2536 5.0 39.7 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit


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 Ccdap-Puromycin Bound at the Peptidyl Transferase Center of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:K8202 b:56.3 occ:1.00 O A:HOH8536 2.6 35.5 1.0 O A:HOH4425 2.7 26.5 1.0 O4 A:U172 2.9 43.3 1.0 O A:HOH8633 2.9 71.3 1.0 O A:HOH8665 2.9 25.7 1.0 OP2 A:C162 3.2 28.6 1.0 O A:HOH7295 3.2 15.3 1.0 O4 A:U163 3.4 42.6 1.0 CD N:ARG82 3.5 40.8 1.0 O A:HOH8841 3.6 31.7 1.0 C4 A:U172 3.9 42.8 1.0 N3 A:U172 4.2 41.1 1.0 NE N:ARG82 4.2 41.9 1.0 C4 A:U163 4.3 42.0 1.0 O A:HOH7294 4.5 17.7 1.0 P A:C162 4.5 28.6 1.0 N4 A:C171 4.6 37.1 1.0 CB N:ARG82 4.6 40.6 1.0 OP1 A:A169 4.7 37.7 1.0 C5 A:U163 4.7 42.3 1.0 CG N:ARG82 4.7 40.0 1.0 N4 A:C173 4.8 37.6 1.0 OP2 A:A169 4.8 39.9 1.0 N3 A:C173 4.8 35.4 1.0 OP2 A:A161 4.8 29.2 1.0 O5' A:A161 5.0 28.9 1.0

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz. Structural Insights Into Peptide Bond Formation Proc.Natl.Acad.Sci.Usa V. 99 11670 2002.
ISSN: ISSN 0027-8424
PubMed: 12185246
DOI: 10.1073/PNAS.172404099