Calcium in PDB 8dvp: Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine

The structure of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine, PDB code: 8dvp 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)	73.49 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.68, 86.17, 140.77, 90, 90, 90
R / Rfree (%)	21.7 / 23.3

The structure of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Calcium atom in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine (pdb code 8dvp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine, PDB code: 8dvp:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:36.4 occ:1.00 O A:HOH558 2.2 40.4 1.0 O C:HOH205 2.2 41.7 1.0 O A:VAL123 2.3 30.1 1.0 OG A:SER118 2.4 44.0 1.0 O A:SER118 2.4 39.9 1.0 O A:HOH594 2.5 41.4 1.0 O A:HOH545 2.6 31.7 1.0 HA2 A:GLY124 3.3 28.1 1.0 C A:SER118 3.4 42.0 1.0 C A:VAL123 3.5 32.8 1.0 HA A:SER118 3.5 38.6 1.0 CB A:SER118 3.6 42.8 1.0 CA A:SER118 3.7 39.6 1.0 HB3 A:SER118 4.0 41.4 1.0 HB A:VAL123 4.1 28.1 1.0 O A:HOH627 4.1 50.7 1.0 CA A:GLY124 4.1 29.1 1.0 OP2 C:DC21 4.2 32.4 1.0 HB2 A:SER118 4.2 41.4 1.0 O A:HOH552 4.3 45.0 1.0 N A:GLY124 4.3 26.0 1.0 N A:ARG119 4.5 35.4 1.0 H A:VAL123 4.5 28.0 1.0 HG12 A:VAL123 4.6 34.1 1.0 CA A:VAL123 4.6 28.4 1.0 HA A:ARG119 4.6 40.0 1.0 O A:LEU120 4.6 33.2 1.0 OP1 C:DC21 4.7 32.9 1.0 CB A:VAL123 4.7 29.7 1.0 HD3 A:PRO125 4.8 36.6 1.0 C A:GLY124 4.8 30.6 1.0 HA3 A:GLY124 4.8 28.1 1.0 N A:VAL123 4.8 28.1 1.0 P C:DC21 4.9 30.2 1.0 CA A:ARG119 5.0 41.4 1.0

Calcium binding site 2 out of 3 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:58.9 occ:0.64 OG1 A:THR259 2.3 62.2 1.0 O A:HOH506 2.4 42.8 0.6 OD1 A:ASP257 2.4 69.7 1.0 O A:THR259 2.5 64.3 1.0 CG A:ASP257 3.2 66.1 1.0 C A:THR259 3.4 55.4 1.0 OD2 A:ASP257 3.6 70.4 1.0 CB A:THR259 3.6 57.9 1.0 H A:THR259 3.7 46.8 1.0 HB A:THR259 3.9 51.9 1.0 CA A:THR259 3.9 56.7 1.0 HA3 A:GLY260 4.0 45.7 1.0 N A:THR259 4.2 52.0 1.0 O A:HOH562 4.3 42.4 1.0 HB2 A:ASP257 4.4 48.9 1.0 N A:GLY260 4.4 52.1 1.0 CB A:ASP257 4.4 55.3 1.0 HG23 A:THR259 4.7 60.3 1.0 CA A:GLY260 4.7 51.1 1.0 CG2 A:THR259 4.7 66.6 1.0 HA A:THR259 4.9 51.6 1.0

Calcium binding site 3 out of 3 in the Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Glycosylase Muty Variant N146S in Complex with Dna Containing D(8-Oxo- G) Paired with Substrate Purine within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca101 b:32.1 occ:1.00 OP2 C:PRN18 2.3 36.9 1.0 O A:HOH531 2.4 28.8 1.0 O A:HOH556 2.4 31.7 1.0 OG A:SER146 2.5 30.6 1.0 O4' C:PRN18 2.5 31.0 1.0 OD2 A:ASP144 2.5 32.2 1.0 N3 C:PRN18 2.6 32.1 1.0 O C:HOH209 2.9 28.4 1.0 HB2 A:SER146 2.9 27.1 1.0 CB A:SER146 3.2 28.6 1.0 H1' C:PRN18 3.4 27.3 1.0 H2 C:PRN18 3.4 34.4 1.0 C1' C:PRN18 3.4 29.0 1.0 C2 C:PRN18 3.5 36.6 1.0 H4' C:PRN18 3.6 21.2 1.0 C4' C:PRN18 3.6 23.1 1.0 C4 C:PRN18 3.6 26.5 1.0 H A:SER146 3.6 29.1 1.0 CG A:ASP144 3.7 35.6 1.0 P C:PRN18 3.7 34.9 1.0 HG23 A:ILE191 3.8 26.5 1.0 HB3 A:SER146 3.8 27.1 1.0 N9 C:PRN18 3.9 29.7 1.0 H3' C:DA17 4.0 32.0 1.0 O5' C:PRN18 4.0 27.6 1.0 N A:SER146 4.3 30.3 1.0 HB2 A:ASP144 4.3 28.2 1.0 CA A:SER146 4.4 30.9 1.0 OD1 A:ASP144 4.4 35.5 1.0 OP1 C:DA17 4.4 37.4 1.0 C5' C:PRN18 4.4 26.2 1.0 O C:HOH213 4.5 39.5 1.0 H5'' C:DA17 4.6 37.2 1.0 O5' C:DA17 4.6 39.0 1.0 C3' C:PRN18 4.6 25.0 1.0 O3' C:PRN18 4.6 25.8 1.0 CB A:ASP144 4.6 29.4 1.0 CG2 A:ILE191 4.7 27.9 1.0 O3' C:DA17 4.7 29.0 1.0 OP1 C:PRN18 4.7 36.5 1.0 C2' C:PRN18 4.7 28.1 1.0 C3' C:DA17 4.7 33.4 1.0 HB2 A:ALA195 4.8 30.5 1.0 N1 C:PRN18 4.8 36.2 1.0 HG21 A:ILE191 4.9 26.5 1.0 HA A:SER146 4.9 29.0 1.0 O A:ILE191 5.0 28.6 1.0 C5 C:PRN18 5.0 28.3 1.0 HG12 A:ILE191 5.0 26.4 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.