Sodium in PDB 5vi0: Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Abasic Site Analog

The structure of Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Abasic Site Analog, PDB code: 5vi0 was solved by R.Shi, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.42 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	80.636, 94.935, 134.030, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 22.5

The binding sites of Sodium atom in the Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Abasic Site Analog (pdb code 5vi0). 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 Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Abasic Site Analog, PDB code: 5vi0:

Sodium binding site 1 out of 1 in the Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Abasic Site Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Abasic Site Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:41.2 occ:1.00 O B:HOH625 2.4 19.2 1.0 O B:HOH540 2.5 15.9 1.0 O B:HOH656 2.5 17.8 1.0 O B:SER317 2.6 14.5 1.0 O B:HOH724 2.6 29.4 1.0 C B:SER317 3.8 12.4 1.0 CD2 B:PHE316 4.2 12.6 1.0 CA B:LEU318 4.2 16.3 1.0 O B:HOH686 4.4 31.0 1.0 N B:GLY319 4.5 18.1 1.0 N B:LEU318 4.5 16.9 1.0 CE2 B:PHE316 4.6 17.0 1.0 OE1 B:GLN324 4.7 22.4 1.0 C B:LEU318 4.8 14.3 1.0 CA B:SER317 4.9 21.6 1.0 N B:SER317 5.0 15.7 1.0

R.Shi, E.A.Mullins, X.X.Shen, K.T.Lay, P.K.Yuen, S.S.David, A.Rokas, B.F.Eichman. Selective Base Excision Repair of Dna Damage By the Non-Base-Flipping Dna Glycosylase Alkc. Embo J. V. 37 63 2018.
ISSN: ESSN 1460-2075
PubMed: 29054852
DOI: 10.15252/EMBJ.201797833