Sodium in PDB 2vnu: Crystal Structure of Sc RRP44

The structure of Crystal Structure of Sc RRP44, PDB code: 2vnu was solved by E.Lorentzen, J.Basquin, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.06 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	72.350, 87.250, 136.270, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 27.8

The structure of Crystal Structure of Sc RRP44 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Sc RRP44 (pdb code 2vnu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Sc RRP44, PDB code: 2vnu:

Sodium binding site 1 out of 1 in the Crystal Structure of Sc RRP44


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Sc RRP44 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1501 b:7.2 occ:1.00 OD2 D:ASP543 2.6 15.4 1.0 O D:HOH2162 2.9 8.2 1.0 OG D:SER541 3.0 11.8 1.0 O D:PHE652 3.1 13.4 1.0 CB D:ASP543 3.3 15.7 1.0 CG D:ASP543 3.4 16.2 1.0 N D:ASP543 3.5 14.6 1.0 C D:SER541 3.7 12.0 1.0 O D:SER541 3.7 12.0 1.0 CB D:SER541 3.7 12.0 1.0 CB D:ALA651 3.8 15.3 1.0 N D:PHE652 3.9 14.6 1.0 N D:ILE542 3.9 11.9 1.0 C D:ILE542 4.0 13.3 1.0 CA D:ASP543 4.0 15.8 1.0 CA D:ALA651 4.1 15.6 1.0 C D:PHE652 4.1 13.2 1.0 CA D:ILE542 4.1 12.8 1.0 C D:ALA651 4.1 15.3 1.0 CG1 D:ILE550 4.2 16.6 1.0 CD1 D:ILE550 4.2 15.6 1.0 CA D:SER541 4.3 12.0 1.0 O D:HOH2160 4.3 18.7 1.0 OD1 D:ASP543 4.6 16.4 1.0 CA D:PHE652 4.6 13.9 1.0 CG2 D:ILE550 4.6 16.0 1.0 O D:ILE542 4.8 13.4 1.0 C D:ASP543 4.9 16.7 1.0 O D:ALA651 4.9 16.1 1.0

E.Lorentzen, J.Basquin, R.Tomecki, A.Dziembowski, E.Conti. Structure of the Active Subunit of the Yeast Exosome Core, RRP44: Diverse Modes of Substrate Recruitment in the Rnase II Nuclease Family Mol.Cell V. 29 717 2008.
ISSN: ISSN 1097-2765
PubMed: 18374646
DOI: 10.1016/J.MOLCEL.2008.02.018