Sodium in PDB 1dk1: Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex

The structure of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex, PDB code: 1dk1 was solved by A.Nikulin, A.Serganov, E.Ennifar, S.Tischenko, N.Nevskaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.80
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	128.800, 128.800, 65.100, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 29.1

The structure of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex also contains other interesting chemical elements:

Magnesium	(Mg)	9 atoms
Potassium	(K)	1 atom

The binding sites of Sodium atom in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex (pdb code 1dk1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex, PDB code: 1dk1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na210 b:60.0 occ:0.94 O B:HOH319 2.7 41.3 1.0 O4' B:C8 4.1 70.6 1.0 N2 B:G14 4.1 35.6 1.0 C1' B:C8 4.1 65.6 1.0 O2 B:C7 4.6 61.7 1.0 O2' B:C8 4.7 63.9 1.0 O2' B:C15 5.0 59.6 1.0 C4' B:C8 5.0 55.9 1.0

Sodium binding site 2 out of 2 in the Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Detailed View of A Key Element of the Ribosome Assembly: Crystal Structure of the S15-Rrna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na211 b:74.8 occ:0.95 O2 B:C4 2.8 68.9 1.0 N2 B:G54 3.0 43.6 1.0 O2 B:C55 3.5 61.6 1.0 C2 B:C4 4.0 61.4 1.0 O4' B:G5 4.1 70.6 1.0 O2' B:C4 4.2 62.1 1.0 C2 B:C55 4.2 50.0 1.0 C2 B:G54 4.4 48.4 1.0 C1' B:C55 4.4 58.8 1.0 C1' B:G5 4.5 58.9 1.0 C2' B:C4 4.5 64.2 1.0 N2 B:G3 4.6 50.8 1.0 C1' B:C4 4.6 58.9 1.0 N1 B:C55 4.6 49.2 1.0 N1 B:C4 4.8 59.0 1.0 N3 B:C4 4.9 51.4 1.0

A.Nikulin, A.Serganov, E.Ennifar, S.Tishchenko, N.Nevskaya, W.Shepard, C.Portier, M.Garber, B.Ehresmann, C.Ehresmann, S.Nikonov, P.Dumas. Crystal Structure of the S15-Rrna Complex. Nat.Struct.Biol. V. 7 273 2000.
ISSN: ISSN 1072-8368
PubMed: 10742169
DOI: 10.1038/74028