Sodium in PDB 8dw0: Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Enzyme-Generated Abasic Site (Ap) Product and Crystallized with Sodium Acetate

The structure of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Enzyme-Generated Abasic Site (Ap) Product and Crystallized with Sodium Acetate, PDB code: 8dw0 was solved by M.Demir, L.P.Russelburg, M.P.Horvath, S.S.David, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.02 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.94, 86.56, 142.77, 90, 90, 90
R / Rfree (%)	20 / 22.7

The structure of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Enzyme-Generated Abasic Site (Ap) Product and Crystallized with Sodium Acetate also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Sodium atom in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Enzyme-Generated Abasic Site (Ap) Product and Crystallized with Sodium Acetate (pdb code 8dw0). 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 Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Enzyme-Generated Abasic Site (Ap) Product and Crystallized with Sodium Acetate, PDB code: 8dw0:

Sodium binding site 1 out of 1 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Enzyme-Generated Abasic Site (Ap) Product and Crystallized with Sodium Acetate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with An Enzyme-Generated Abasic Site (Ap) Product and Crystallized with Sodium Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:36.9 occ:1.00 O C:HOH117 2.3 42.2 1.0 O A:HOH589 2.4 48.0 1.0 O A:VAL123 2.5 30.0 1.0 O A:LEU120 2.5 29.5 1.0 O A:SER118 2.8 38.9 1.0 OP1 C:DC21 2.8 28.3 1.0 H A:VAL123 3.2 33.4 1.0 HB A:VAL123 3.4 30.2 1.0 C A:VAL123 3.5 29.1 1.0 C A:LEU120 3.6 31.2 1.0 OP2 C:DC21 3.6 30.0 1.0 HA A:LYS121 3.7 37.4 1.0 N A:VAL123 3.7 27.9 1.0 P C:DC21 3.8 29.7 1.0 H A:GLY122 3.8 30.3 1.0 C A:SER118 3.9 41.5 1.0 C A:ARG119 4.0 32.5 1.0 CA A:VAL123 4.0 24.5 1.0 O C:HOH112 4.0 38.4 1.0 N A:LEU120 4.1 31.1 1.0 CB A:VAL123 4.2 26.5 1.0 HA A:ARG119 4.2 39.9 1.0 N A:GLY122 4.2 26.0 1.0 O A:ARG119 4.2 34.7 1.0 CA A:LYS121 4.3 33.3 1.0 HA2 A:GLY124 4.3 29.6 1.0 N A:LYS121 4.3 30.4 1.0 H A:LEU120 4.4 33.4 1.0 CA A:ARG119 4.5 35.2 1.0 CA A:LEU120 4.5 33.2 1.0 C A:LYS121 4.5 29.4 1.0 HA A:SER118 4.5 50.0 0.3 HA A:SER118 4.5 50.1 0.4 HA A:SER118 4.5 50.0 0.3 N A:ARG119 4.6 40.5 1.0 N A:GLY124 4.6 27.2 1.0 O3' C:DT20 4.7 24.4 1.0 C A:GLY122 4.7 26.2 1.0 HG12 A:VAL123 4.8 35.7 1.0 CA A:SER118 4.8 44.4 0.3 CA A:SER118 4.8 44.5 0.4 CA A:SER118 4.8 44.5 0.3 HG23 A:VAL123 4.9 37.4 1.0 CA A:GLY124 5.0 24.8 1.0 HA A:VAL123 5.0 29.2 1.0

M.Demir, L.P.Russelburg, J.Lin, C.H.Trasvina-Arenas, B.Huang, P.K.Yuen, M.P.Horvath, S.S.David. Structural Snapshots of Base Excision Mechanism By Dna Glycosylase Muty Reveal Retention of Stereochemistry For Abasic Site Product Formation To Be Published.