Sodium in PDB 5vhv: Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Oxocarbenium-Intermediate Analog

The structure of Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Oxocarbenium-Intermediate Analog, PDB code: 5vhv 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)	49.29 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	198.373, 198.373, 60.189, 90.00, 90.00, 120.00
R / Rfree (%)	14.1 / 16.4

The binding sites of Sodium atom in the Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Oxocarbenium-Intermediate Analog (pdb code 5vhv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Oxocarbenium-Intermediate Analog, PDB code: 5vhv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Oxocarbenium-Intermediate 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 Oxocarbenium-Intermediate Analog within 5.0Å range: probe atom residue distance (Å) B Occ C:Na101 b:22.8 occ:1.00 O C:HOH223 2.3 24.9 1.0 O4 D:DT6 2.3 25.3 1.0 O2 C:DT9 2.4 16.6 1.0 O D:HOH248 2.5 32.2 1.0 O D:HOH221 2.5 30.6 1.0 O4' C:DC10 2.7 15.0 1.0 H73 D:DT6 2.9 32.4 1.0 H4' C:DC10 3.1 19.9 1.0 H1' C:DT9 3.2 17.4 1.0 C4 D:DT6 3.2 28.6 1.0 C4' C:DC10 3.4 16.6 1.0 H5' C:DC10 3.5 20.8 1.0 H2 D:DA4 3.5 18.9 1.0 H1' C:DC10 3.5 17.5 1.0 C2 C:DT9 3.6 12.0 1.0 C1' C:DC10 3.6 14.6 1.0 C7 D:DT6 3.6 26.9 1.0 H71 D:DT6 3.8 32.4 1.0 C5 D:DT6 3.8 30.8 1.0 C5' C:DC10 4.0 17.4 1.0 N1 C:DC10 4.1 14.3 1.0 O C:HOH243 4.1 60.6 1.0 C1' C:DT9 4.1 14.5 1.0 H21 C:DG8 4.1 21.1 1.0 O2 C:DC10 4.1 15.7 1.0 N3 D:DT6 4.2 27.3 1.0 C2 C:DC10 4.3 12.5 1.0 H3 D:DT6 4.3 32.8 1.0 N1 C:DT9 4.3 14.9 1.0 C2 D:DA4 4.4 15.8 1.0 H72 D:DT6 4.5 32.4 1.0 N2 C:DG8 4.5 17.6 1.0 H22 C:DG8 4.5 21.1 1.0 H3 C:DT9 4.5 15.8 1.0 N3 C:DT9 4.6 13.2 1.0 H5'' C:DC10 4.6 20.8 1.0 H2'' C:DT9 4.7 18.7 1.0 C3' C:DC10 4.7 12.9 1.0 C6 C:DC10 4.8 14.4 1.0 C2' C:DC10 4.9 15.2 1.0 O C:HOH240 4.9 45.7 1.0 O18 D:9B4101 4.9 25.4 1.0 O5' C:DC10 4.9 14.8 1.0 O4' C:DT9 4.9 16.1 1.0 O D:HOH216 5.0 24.9 1.0 C2' C:DT9 5.0 15.5 1.0

Sodium binding site 2 out of 2 in the Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Oxocarbenium-Intermediate Analog


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pseudomonas Fluorescens Alkylpurine Dna Glycosylase Alkc Bound to Dna Containing An Oxocarbenium-Intermediate Analog within 5.0Å range: probe atom residue distance (Å) B Occ E:Na101 b:20.4 occ:1.00 O E:HOH322 2.3 27.9 1.0 O2 E:DT9 2.3 14.9 1.0 O4 F:DT6 2.4 24.5 1.0 O F:HOH248 2.4 34.3 1.0 O4' E:DC10 2.6 14.9 1.0 O F:HOH238 2.7 34.7 1.0 H73 F:DT6 3.0 32.1 1.0 H4' E:DC10 3.1 19.6 1.0 H1' E:DT9 3.2 15.4 1.0 C4 F:DT6 3.2 21.8 1.0 C4' E:DC10 3.4 16.4 1.0 H1' E:DC10 3.4 18.7 1.0 H5' E:DC10 3.5 18.6 1.0 C1' E:DC10 3.5 15.6 1.0 H2 F:DA4 3.5 17.7 1.0 C2 E:DT9 3.5 13.3 1.0 C7 F:DT6 3.7 26.7 1.0 C5 F:DT6 3.8 27.9 1.0 H71 F:DT6 3.9 32.1 1.0 C5' E:DC10 4.0 15.5 1.0 N1 E:DC10 4.0 15.6 1.0 O2 E:DC10 4.0 14.5 1.0 C1' E:DT9 4.1 12.8 1.0 H21 E:DG8 4.1 20.5 1.0 C2 E:DC10 4.2 14.5 1.0 N3 F:DT6 4.2 27.2 1.0 H3 F:DT6 4.3 32.6 1.0 N1 E:DT9 4.3 13.7 1.0 C2 F:DA4 4.4 14.7 1.0 H3 E:DT9 4.5 15.1 1.0 H22 E:DG8 4.6 20.5 1.0 N3 E:DT9 4.6 12.6 1.0 N2 E:DG8 4.6 17.0 1.0 H72 F:DT6 4.6 32.1 1.0 H5'' E:DC10 4.6 18.6 1.0 C3' E:DC10 4.6 13.6 1.0 C6 E:DC10 4.8 12.7 1.0 H2'' E:DT9 4.8 14.3 1.0 C2' E:DC10 4.8 13.6 1.0 O4' E:DT9 4.9 14.7 1.0 O5' E:DC10 4.9 13.9 1.0 O E:HOH340 4.9 44.0 1.0 H6 E:DC10 5.0 15.2 1.0 O18 F:9B4102 5.0 26.9 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