Sodium in PDB 7lw9: Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na

The structure of Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na, PDB code: 7lw9 was solved by C.L.Tsai, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.11 / 2.71
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.073, 83.664, 96.15, 90, 90, 90
R / Rfree (%)	19.4 / 25.3

The structure of Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Samarium	(Sm)	2 atoms

The binding sites of Sodium atom in the Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na (pdb code 7lw9). 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 Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na, PDB code: 7lw9:

Sodium binding site 1 out of 1 in the Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Exonuclease 5 Crystal Structure in Complex with Ssdna, Sm, and Na within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:80.7 occ:1.00 O A:HOH608 2.4 54.0 1.0 OE1 A:GLU165 2.4 87.4 1.0 OD1 A:ASP182 2.6 44.2 1.0 O B:HOH202 2.7 72.5 1.0 O A:HOH613 2.7 75.2 1.0 O A:HOH611 2.9 53.6 1.0 CD A:GLU165 3.4 96.5 1.0 OE2 A:GLU165 3.6 106.0 1.0 CG A:ASP182 3.8 46.4 1.0 O A:HOH618 4.0 45.1 1.0 O A:ACT502 4.3 51.0 1.0 C4' B:DA9 4.4 52.5 1.0 CA A:ASP182 4.5 31.7 1.0 CG1 A:VAL180 4.5 36.0 1.0 OD2 A:ASP182 4.6 47.6 1.0 SM A:SM504 4.7 44.9 1.0 C5' B:DA9 4.8 52.1 1.0 CB A:ASP182 4.8 37.7 1.0 CG A:GLU165 4.8 60.3 1.0 CB A:VAL180 4.9 29.5 1.0 O A:VAL180 4.9 33.7 1.0 N A:ASP182 4.9 38.6 1.0 O3' B:DA9 5.0 53.2 1.0

S.Hambarde, C.L.Tsai, R.K.Pandita, A.Bacolla, A.Maitra, V.Charaka, C.R.Hunt, R.Kumar, O.Limbo, R.Le Meur, W.J.Chazin, S.E.Tsutakawa, P.Russell, K.Schlacher, T.K.Pandita, J.A.Tainer. EXO5-Dna Structure and Blm Interactions Direct Dna Resection Critical For Atr-Dependent Replication Restart. Mol.Cell 2021.
ISSN: ISSN 1097-2765
PubMed: 34197737
DOI: 10.1016/J.MOLCEL.2021.05.027