Sodium in PDB 6n6k: Human REXO2 Bound to Pag

The structure of Human REXO2 Bound to Pag, PDB code: 6n6k 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)	26.38 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.806, 87.423, 124.276, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17.2

The binding sites of Sodium atom in the Human REXO2 Bound to Pag (pdb code 6n6k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human REXO2 Bound to Pag, PDB code: 6n6k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human REXO2 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 Human REXO2 Bound to Pag within 5.0Å range: probe atom residue distance (Å) B Occ D:Na701 b:13.9 occ:1.00 O A:HOH432 2.2 11.5 0.3 OD1 A:ASP15 2.3 16.4 1.0 O A:HOH589 2.3 21.6 1.0 O A:HOH507 2.4 13.5 1.0 OP1 D:G604 2.5 14.9 1.0 O A:HOH432 2.5 15.8 0.7 O3' D:A603 2.6 12.5 0.5 O3' D:A603 2.6 11.8 0.5 P D:G604 3.2 13.2 1.0 CG A:ASP15 3.5 15.6 1.0 C3' D:A603 3.8 12.3 0.5 C3' D:A603 3.8 12.4 0.5 O2' D:A603 3.8 14.2 0.5 O2' D:A603 3.9 14.5 0.5 O A:HOH417 3.9 15.8 1.0 O A:HOH530 4.0 48.5 1.0 OD2 A:ASP15 4.0 16.8 1.0 O A:HOH474 4.1 18.8 1.0 C5' D:G604 4.1 13.7 1.0 C4' D:A603 4.1 12.0 0.5 C4' D:A603 4.1 11.9 0.5 O5' D:G604 4.1 12.6 1.0 OD2 A:ASP115 4.2 13.0 1.0 OD1 A:ASP115 4.2 13.6 1.0 O A:ASN110 4.3 12.4 1.0 O A:LEU16 4.3 12.7 1.0 O A:HOH459 4.3 23.9 1.0 OP2 D:G604 4.3 15.3 1.0 C2' D:A603 4.5 12.0 0.5 C2' D:A603 4.5 12.5 0.5 CG A:ASP115 4.7 12.1 1.0 CB A:ASP15 4.7 13.4 1.0 O D:HOH803 4.8 18.3 1.0 C5' D:A603 4.8 12.4 0.5 C5' D:A603 4.8 10.7 0.5 N A:LEU16 4.8 11.2 1.0 CA A:ASP15 5.0 12.6 1.0

Sodium binding site 2 out of 2 in the Human REXO2 Bound to Pag


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human REXO2 Bound to Pag within 5.0Å range: probe atom residue distance (Å) B Occ C:Na701 b:13.0 occ:1.00 O B:HOH326 2.3 13.4 0.7 OD1 B:ASP15 2.3 13.1 1.0 O B:HOH471 2.4 18.9 0.6 O B:HOH398 2.4 13.3 1.0 O B:HOH471 2.4 11.6 0.4 OP1 C:G604 2.5 15.6 1.0 O3' C:A603 2.5 10.7 0.5 O B:HOH326 2.6 11.6 0.3 O3' C:A603 2.6 12.5 0.5 P C:G604 3.1 12.8 1.0 CG B:ASP15 3.5 12.4 1.0 O2' C:A603 3.7 13.0 0.5 C3' C:A603 3.7 12.7 0.5 C3' C:A603 3.8 11.5 0.5 O2' C:A603 3.9 15.2 0.5 O C:HOH801 4.0 14.7 1.0 OD2 B:ASP15 4.0 14.8 1.0 C4' C:A603 4.0 12.3 0.5 O B:HOH444 4.0 10.5 0.3 C5' C:G604 4.1 13.3 1.0 O B:HOH444 4.1 13.2 0.7 O5' C:G604 4.1 12.8 1.0 C4' C:A603 4.1 12.0 0.5 OD2 B:ASP115 4.1 13.2 1.0 O B:HOH424 4.2 14.2 0.6 O B:LEU16 4.2 13.1 1.0 OD1 B:ASP115 4.3 12.7 1.0 O B:ASN110 4.3 11.7 1.0 O B:HOH424 4.3 14.8 0.4 OP2 C:G604 4.3 15.1 1.0 C2' C:A603 4.4 12.0 0.5 C2' C:A603 4.5 11.3 0.5 CB B:ASP15 4.6 11.2 1.0 CG B:ASP115 4.7 13.2 1.0 C5' C:A603 4.7 12.7 0.5 C5' C:A603 4.7 12.9 0.5 O C:HOH802 4.8 20.4 1.0 N B:LEU16 4.8 11.3 1.0 CA B:ASP15 5.0 9.8 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