Sodium in PDB 5v09: Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii), PDB code: 5v09 was solved by Y.Shi, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.59 / 2.75
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.904, 73.904, 180.081, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25.4

The structure of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii) also contains other interesting chemical elements:

Manganese

(Mn)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii) (pdb code 5v09). 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 Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii), PDB code: 5v09:

Sodium binding site 1 out of 1 in the Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Exonuclease 1 EXO1 (D225A) in Complex with 5' Recessed-End Dna (Rvii) within 5.0Å range: probe atom residue distance (Å) B Occ Z:Na403 b:82.8 occ:1.00 O Z:HOH545 2.3 72.9 1.0 O A:HOH205 2.4 93.8 1.0 O Z:ILE233 2.4 79.7 1.0 O Z:SER222 2.5 67.5 1.0 OG Z:SER229 2.5 62.0 1.0 OP2 A:DA5 2.5 0.4 1.0 C Z:ILE233 3.5 77.4 1.0 O Z:HOH569 3.5 78.7 1.0 CB Z:SER229 3.5 61.5 1.0 C Z:SER222 3.7 63.1 1.0 CA Z:GLY234 3.7 65.9 1.0 P A:DA5 3.9 0.5 1.0 N Z:GLY234 4.0 70.5 1.0 OP1 A:DA5 4.4 0.8 1.0 CA Z:GLY223 4.5 56.8 1.0 N Z:GLY223 4.5 56.8 1.0 C3' A:DT4 4.6 0.3 1.0 CA Z:SER222 4.6 62.0 1.0 O3' A:DT4 4.7 0.4 1.0 CA Z:ILE233 4.7 72.8 1.0 CA Z:SER229 4.8 66.2 1.0 C2' A:DT4 4.9 0.7 1.0 N Z:ILE233 4.9 79.7 1.0 C Z:GLY234 4.9 69.5 1.0 O5' A:DA5 5.0 0.2 1.0

Y.Shi, H.W.Hellinga, L.S.Beese. Interplay of Catalysis, Fidelity, Threading, and Processivity in the Exo- and Endonucleolytic Reactions of Human Exonuclease I. Proc. Natl. Acad. Sci. V. 114 6010 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28533382
DOI: 10.1073/PNAS.1704845114