Sodium in PDB 6n6d: Vibrio Cholerae Oligoribonuclease Bound to Pag

The structure of Vibrio Cholerae Oligoribonuclease Bound to Pag, PDB code: 6n6d was solved by J.D.Lormand, H.Sondermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.87 / 1.53
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.734, 89.734, 59.485, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 15.8

The binding sites of Sodium atom in the Vibrio Cholerae Oligoribonuclease Bound to Pag (pdb code 6n6d). 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 Vibrio Cholerae Oligoribonuclease Bound to Pag, PDB code: 6n6d:

Sodium binding site 1 out of 1 in the Vibrio Cholerae Oligoribonuclease Bound to Pag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Vibrio Cholerae Oligoribonuclease Bound to Pag within 5.0Å range: probe atom residue distance (Å) B Occ D:Na701 b:16.0 occ:1.00 O D:HOH812 2.3 24.7 1.0 OD1 A:ASP12 2.3 18.5 1.0 O A:HOH217 2.4 17.9 1.0 O A:HOH249 2.4 15.9 1.0 OP1 D:G604 2.5 18.5 1.0 O3' D:A603 2.6 15.4 1.0 P D:G604 3.2 16.4 1.0 CG A:ASP12 3.5 19.6 1.0 O D:HOH801 3.7 19.3 1.0 C3' D:A603 3.9 15.4 1.0 O2' D:A603 4.0 21.2 1.0 OD2 A:ASP12 4.0 21.1 1.0 O A:HOH344 4.1 18.1 1.0 C5' D:G604 4.1 15.3 1.0 OD2 A:ASP112 4.1 15.9 1.0 O5' D:G604 4.2 15.1 1.0 O A:HOH320 4.2 19.6 1.0 C4' D:A603 4.2 17.6 1.0 O A:LEU13 4.2 15.8 1.0 OD1 A:ASP112 4.2 16.4 1.0 OP2 D:G604 4.3 17.2 1.0 O A:ASN107 4.4 16.9 1.0 C2' D:A603 4.6 18.7 1.0 CG A:ASP112 4.6 15.0 1.0 O D:HOH805 4.7 21.6 1.0 CB A:ASP12 4.7 14.2 1.0 C5' D:A603 4.8 16.1 1.0 N A:LEU13 4.9 16.1 1.0 CA A:ASP12 5.0 14.6 1.0

S.K.Kim, J.D.Lormand, C.A.Weiss, K.A.Eger, H.Turdiev, A.Turdiev, W.C.Winkler, H.Sondermann, V.T.Lee. A Dedicated Diribonucleotidase Resolves A Key Bottleneck For the Terminal Step of Rna Degradation. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31225796
DOI: 10.7554/ELIFE.46313