Sodium in PDB 6n6i: Human REXO2 Bound to Pgg

The structure of Human REXO2 Bound to Pgg, PDB code: 6n6i 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)	42.97 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.814, 87.289, 123.797, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17.8

The binding sites of Sodium atom in the Human REXO2 Bound to Pgg (pdb code 6n6i). 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 Pgg, PDB code: 6n6i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human REXO2 Bound to Pgg


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 Pgg within 5.0Å range: probe atom residue distance (Å) B Occ D:Na701 b:11.7 occ:1.00 O A:HOH493 2.3 12.7 1.0 O A:HOH501 2.3 11.4 0.7 OD1 A:ASP15 2.3 13.6 1.0 O A:HOH433 2.4 13.4 0.4 OP1 D:G604 2.4 11.5 1.0 O A:HOH501 2.4 13.5 0.3 O A:HOH433 2.5 10.8 0.6 O3' D:G603 2.6 10.7 1.0 P D:G604 3.1 11.0 1.0 CG A:ASP15 3.5 14.2 1.0 O2' D:G603 3.8 12.0 1.0 C3' D:G603 3.8 10.2 1.0 O A:HOH413 3.9 12.7 1.0 O A:HOH576 3.9 18.0 0.6 OD2 A:ASP15 4.0 13.3 1.0 C5' D:G604 4.1 10.4 1.0 O A:HOH476 4.1 15.8 1.0 O5' D:G604 4.1 10.7 1.0 OD1 A:ASP115 4.2 10.6 1.0 C4' D:G603 4.2 10.2 1.0 OD2 A:ASP115 4.2 10.8 1.0 O A:LEU16 4.2 10.0 1.0 O A:ASN110 4.3 10.6 1.0 OP2 D:G604 4.4 12.7 1.0 O A:HOH576 4.4 19.9 0.4 C2' D:G603 4.5 10.2 1.0 O A:HOH499 4.5 18.9 1.0 CG A:ASP115 4.6 10.0 1.0 CB A:ASP15 4.7 10.9 1.0 O3 A:GOL301 4.8 17.1 1.0 N A:LEU16 4.8 8.3 1.0 C5' D:G603 4.9 11.5 1.0 C3 A:GOL301 4.9 27.6 1.0

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


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 Pgg within 5.0Å range: probe atom residue distance (Å) B Occ C:Na702 b:10.7 occ:1.00 O C:HOH801 2.3 10.7 0.5 OD1 B:ASP15 2.3 11.6 1.0 O C:HOH806 2.3 12.3 0.6 O B:HOH480 2.4 11.0 1.0 OP1 C:G604 2.4 12.1 1.0 O C:HOH806 2.5 14.6 0.4 O C:HOH801 2.6 9.2 0.5 O3' C:G603 2.6 10.1 1.0 P C:G604 3.2 11.1 1.0 CG B:ASP15 3.5 11.7 1.0 O2' C:G603 3.8 12.7 1.0 C3' C:G603 3.8 10.1 1.0 O B:HOH409 4.0 12.2 1.0 OD2 B:ASP15 4.0 11.3 1.0 C5' C:G604 4.0 11.6 1.0 O B:HOH450 4.1 8.4 0.4 O5' C:G604 4.1 10.6 1.0 OD2 B:ASP115 4.1 10.8 1.0 C4' C:G603 4.1 10.2 1.0 O B:LEU16 4.2 10.3 1.0 O B:HOH450 4.2 10.4 0.6 OD1 B:ASP115 4.2 11.6 1.0 O B:HOH501 4.2 14.4 0.4 O1 C:EDO701 4.3 21.8 0.5 O B:HOH501 4.3 13.4 0.6 O B:ASN110 4.3 9.8 1.0 OP2 C:G604 4.4 13.0 1.0 C2' C:G603 4.4 10.6 1.0 CG B:ASP115 4.6 11.5 1.0 CB B:ASP15 4.7 8.4 1.0 O2 C:EDO701 4.7 16.6 0.4 O2 C:EDO701 4.8 15.1 0.5 N B:LEU16 4.8 9.6 1.0 C5' C:G603 4.9 10.2 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