Sodium in PDB 6n6j: Human REXO2 Bound to Paa

The structure of Human REXO2 Bound to Paa, PDB code: 6n6j 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)	31.67 / 1.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.863, 87.566, 124.225, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 17

The binding sites of Sodium atom in the Human REXO2 Bound to Paa (pdb code 6n6j). 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 Paa, PDB code: 6n6j:
Jump to Sodium binding site number: 1; 2;

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


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 Paa within 5.0Å range: probe atom residue distance (Å) B Occ D:Na701 b:12.0 occ:1.00 O D:HOH802 2.2 12.5 0.4 O A:HOH507 2.3 11.8 1.0 OD1 A:ASP15 2.3 14.2 1.0 O A:HOH476 2.4 13.7 0.6 OP1 D:A604 2.5 12.7 1.0 O A:HOH476 2.5 12.7 0.4 O D:HOH802 2.5 11.0 0.6 O3' D:A603 2.6 11.0 0.5 O3' D:A603 2.6 10.9 0.5 P D:A604 3.2 11.4 1.0 CG A:ASP15 3.5 11.8 1.0 C3' D:A603 3.8 11.1 0.5 O2' D:A603 3.8 13.3 0.5 C3' D:A603 3.8 11.0 0.5 O A:HOH411 3.9 13.1 1.0 O2' D:A603 3.9 12.0 0.5 O A:HOH598 4.0 15.7 0.5 C5' D:A604 4.0 12.6 1.0 OD2 A:ASP15 4.1 14.3 1.0 O A:HOH454 4.1 16.7 1.0 O5' D:A604 4.1 11.3 1.0 C4' D:A603 4.2 10.7 0.5 C4' D:A603 4.2 10.3 0.5 OD1 A:ASP115 4.2 11.6 1.0 OD2 A:ASP115 4.2 10.9 1.0 O A:LEU16 4.3 10.6 1.0 O A:ASN110 4.3 10.3 1.0 OP2 D:A604 4.4 13.5 1.0 O A:HOH598 4.4 21.5 0.5 C2' D:A603 4.5 10.9 0.5 O A:HOH487 4.5 19.3 1.0 C2' D:A603 4.5 11.2 0.5 CG A:ASP115 4.7 10.3 1.0 CB A:ASP15 4.7 11.8 1.0 O3 A:GOL301 4.7 16.1 1.0 N A:LEU16 4.9 9.8 1.0 C5' D:A603 4.9 11.5 0.5 C5' D:A603 4.9 10.1 0.5 C3 A:GOL301 5.0 31.1 1.0

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


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 Paa within 5.0Å range: probe atom residue distance (Å) B Occ C:Na702 b:11.1 occ:1.00 O C:HOH802 2.3 11.2 0.6 OD1 B:ASP15 2.3 11.6 1.0 O C:HOH805 2.3 12.3 0.5 O B:HOH472 2.4 11.6 1.0 O C:HOH805 2.4 12.4 0.5 OP1 C:A604 2.5 12.5 1.0 O3' C:A603 2.6 10.0 0.5 O C:HOH802 2.6 10.1 0.4 O3' C:A603 2.6 10.3 0.5 P C:A604 3.2 11.0 1.0 CG B:ASP15 3.5 10.8 1.0 O2' C:A603 3.7 12.9 0.5 C3' C:A603 3.8 11.3 0.5 C3' C:A603 3.9 9.9 0.5 O C:HOH803 3.9 12.2 1.0 O2' C:A603 3.9 12.9 0.5 OD2 B:ASP15 4.0 11.4 1.0 C5' C:A604 4.0 11.4 1.0 C4' C:A603 4.1 10.2 0.5 O B:HOH447 4.1 10.1 0.5 O5' C:A604 4.1 11.6 1.0 OD2 B:ASP115 4.1 11.2 1.0 O B:HOH481 4.1 14.0 0.5 C4' C:A603 4.2 9.9 0.5 O B:HOH447 4.2 11.0 0.5 O B:LEU16 4.2 10.8 1.0 OD1 B:ASP115 4.3 11.1 1.0 O B:ASN110 4.3 9.8 1.0 O B:HOH481 4.3 14.1 0.5 C2' C:A603 4.4 11.1 0.5 OP2 C:A604 4.4 12.5 1.0 O1 C:EDO701 4.4 22.7 0.4 C2' C:A603 4.5 11.0 0.5 O2 C:EDO701 4.6 13.1 0.5 CB B:ASP15 4.7 10.0 1.0 CG B:ASP115 4.7 10.2 1.0 O2 C:EDO701 4.8 14.1 0.4 C5' C:A603 4.8 10.8 0.5 C5' C:A603 4.8 11.3 0.5 N B:LEU16 4.8 9.3 1.0 C2 C:EDO701 4.9 17.7 0.4

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