Calcium in PDB 8dwd: Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine

The structure of Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine, PDB code: 8dwd was solved by L.P.Russelburg, M.Demir, S.S.David, M.P.Horvath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.96 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.74, 85.92, 140.69, 90, 90, 90
R / Rfree (%)	22.2 / 24.5

The structure of Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Calcium atom in the Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine (pdb code 8dwd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine, PDB code: 8dwd:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:38.0 occ:1.00 O A:HOH524 2.0 40.3 1.0 OG A:SER118 2.3 53.8 1.0 O A:VAL123 2.3 36.6 1.0 O C:HOH107 2.3 42.8 1.0 O A:SER118 2.4 41.3 1.0 O A:HOH618 2.5 47.2 1.0 O A:HOH521 2.7 34.6 1.0 HA2 A:GLY124 3.3 41.9 1.0 C A:SER118 3.3 49.5 1.0 C A:VAL123 3.4 37.5 1.0 CB A:SER118 3.5 55.1 1.0 HA A:SER118 3.5 49.1 1.0 CA A:SER118 3.6 46.7 1.0 HB2 A:SER118 3.9 58.4 1.0 O A:HOH534 4.0 44.5 1.0 HB A:VAL123 4.0 35.6 1.0 HB3 A:SER118 4.1 58.4 1.0 OP2 C:DC21 4.1 33.4 1.0 CA A:GLY124 4.1 34.6 1.0 N A:GLY124 4.2 31.9 1.0 HG12 A:VAL123 4.4 44.8 1.0 N A:ARG119 4.5 43.6 1.0 O A:LEU120 4.5 34.7 1.0 CA A:VAL123 4.5 34.0 1.0 H A:VAL123 4.6 39.8 1.0 OP1 C:DC21 4.6 33.0 1.0 HA A:ARG119 4.7 52.5 1.0 CB A:VAL123 4.7 31.9 1.0 HA3 A:GLY124 4.8 41.9 1.0 N A:VAL123 4.8 32.1 1.0 O C:HOH118 4.8 40.0 1.0 P C:DC21 4.9 33.1 1.0 C A:GLY124 4.9 36.5 1.0 HG21 A:VAL128 5.0 45.1 1.0 O C:HOH135 5.0 46.8 1.0

Calcium binding site 2 out of 2 in the Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Adenine Glycosylase Muty Variant E43S in Complex with Dna Containing D(8-Oxo-G) Paired with An Ap Site Generated By the Enzyme Acting on Purine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:62.5 occ:0.50 HG1 A:THR259 1.9 69.4 1.0 O A:THR259 2.2 62.4 1.0 OG1 A:THR259 2.6 64.3 1.0 O A:HOH638 2.7 51.9 1.0 HB2 A:ASP257 3.1 62.0 1.0 C A:THR259 3.3 56.8 1.0 OD2 A:ASP257 3.4 75.3 1.0 CB A:THR259 3.7 56.8 1.0 CB A:ASP257 3.8 59.9 1.0 H A:THR259 3.8 59.2 1.0 HB3 A:ASP257 3.8 62.0 1.0 HA3 A:GLY260 3.8 55.3 1.0 CA A:THR259 4.0 58.1 1.0 HB A:THR259 4.0 61.9 1.0 CG A:ASP257 4.1 68.2 1.0 O A:HOH537 4.3 42.0 1.0 N A:THR259 4.3 53.9 1.0 N A:GLY260 4.4 51.1 1.0 CA A:GLY260 4.6 51.2 1.0 HA A:THR259 4.9 64.6 1.0 CG2 A:THR259 5.0 60.7 1.0

L.P.Russelburg, M.Demir, K.Cedeno, S.S.David, M.P.Horvath. Structural Basis For Base Engagement and Stereochemistry Revealed By Alteration of Catalytic Residue GLU43 in Dna Repair Glycosylase Muty To Be Published.