Calcium in PDB 5edw: Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp

All present enzymatic activity of Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp:
2.7.7.7;

The structure of Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp, PDB code: 5edw was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.62
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.516, 101.994, 52.864, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 28.4

The binding sites of Calcium atom in the Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp (pdb code 5edw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp, PDB code: 5edw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:54.9 occ:1.00 O A:PHE8 2.2 46.9 1.0 OD1 A:ASP7 2.3 46.2 1.0 O2A A:TTP404 2.3 60.2 1.0 O2G A:TTP404 2.3 60.0 1.0 OD2 A:ASP105 2.3 49.0 1.0 O2B A:TTP404 2.4 52.1 1.0 CA A:CA402 3.2 75.0 1.0 CG A:ASP7 3.4 46.0 1.0 C A:PHE8 3.5 42.3 1.0 PB A:TTP404 3.5 56.3 1.0 CG A:ASP105 3.5 44.8 1.0 NZ A:LYS159 3.6 57.6 1.0 PA A:TTP404 3.6 75.5 1.0 PG A:TTP404 3.7 62.0 1.0 OD2 A:ASP7 3.9 48.4 1.0 O3A A:TTP404 3.9 66.6 1.0 CE A:LYS159 4.1 58.6 1.0 N A:PHE8 4.1 39.1 1.0 O3B A:TTP404 4.1 64.4 1.0 O3G A:TTP404 4.2 59.2 1.0 C5' A:TTP404 4.2 57.2 1.0 OD1 A:ASP105 4.2 45.8 1.0 CA A:PHE8 4.4 39.8 1.0 O5' A:TTP404 4.4 67.0 1.0 C A:ASP7 4.4 41.7 1.0 N A:ASP9 4.4 40.8 1.0 N A:TYR10 4.5 45.3 1.0 CA A:ASP9 4.5 47.5 1.0 CB A:ASP105 4.5 42.1 1.0 CB A:ASP7 4.6 40.4 1.0 O A:ASP105 4.7 37.0 1.0 O1A A:TTP404 4.7 71.2 1.0 O A:ASP7 4.8 47.6 1.0 O1B A:TTP404 4.8 49.9 1.0 O1G A:TTP404 4.8 64.4 1.0 C A:ASP9 4.8 45.4 1.0 CA A:ASP7 4.9 40.7 1.0 CB A:PHE8 5.0 35.4 1.0

Calcium binding site 2 out of 3 in the Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:75.0 occ:1.00 OE1 A:GLU106 2.3 64.9 1.0 O2A A:TTP404 2.4 60.2 1.0 OD2 A:ASP7 2.7 48.4 1.0 OD1 A:ASP7 2.9 46.2 1.0 CG A:ASP7 3.1 46.0 1.0 CA A:CA401 3.2 54.9 1.0 CD A:GLU106 3.3 53.6 1.0 CG A:GLU106 3.6 50.2 1.0 PA A:TTP404 3.6 75.5 1.0 O1A A:TTP404 3.7 71.2 1.0 OD2 A:ASP105 3.7 49.0 1.0 O5' P:DC13 3.9 80.4 1.0 OD1 A:ASP105 3.9 45.8 1.0 O2G A:TTP404 4.2 60.0 1.0 CG A:ASP105 4.2 44.8 1.0 OP1 P:DC13 4.2 83.6 1.0 OE2 A:GLU106 4.4 57.1 1.0 CE A:LYS159 4.5 58.6 1.0 C3' P:DC13 4.5 65.9 1.0 O5' A:TTP404 4.6 67.0 1.0 P P:DC13 4.6 90.4 1.0 CB A:ASP7 4.6 40.4 1.0 C5' A:TTP404 4.7 57.2 1.0 O3A A:TTP404 4.8 66.6 1.0 NZ A:LYS152 4.8 56.5 1.0 NZ A:LYS159 4.9 57.6 1.0 O3' P:DC13 4.9 56.6 1.0 O2B A:TTP404 4.9 52.1 1.0 CB A:GLU106 4.9 38.5 1.0 C5' P:DC13 4.9 71.2 1.0 O A:ASP105 5.0 37.0 1.0 OP2 P:DC13 5.0 79.7 1.0

Calcium binding site 3 out of 3 in the Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:68.4 occ:1.00 O A:ALA181 2.5 57.5 1.0 O A:HOH516 2.5 57.8 1.0 O A:HOH530 2.5 49.1 1.0 O A:ILE186 2.6 47.9 1.0 C A:ALA181 3.6 52.5 1.0 C A:ILE186 3.8 46.5 1.0 OP2 P:DT12 4.2 57.6 1.0 CA A:GLY187 4.3 51.6 1.0 OP1 P:DT12 4.4 50.1 1.0 CA A:ALA181 4.5 53.4 1.0 N A:GLY187 4.5 52.9 1.0 N A:ASP182 4.6 48.5 1.0 CB A:ALA181 4.6 51.1 1.0 CA A:ASP182 4.7 48.0 1.0 C A:GLY187 4.8 52.6 1.0 O A:VAL183 4.8 42.4 1.0 P P:DT12 4.9 53.0 1.0 CA A:ILE186 4.9 48.1 1.0 OD1 A:ASN188 5.0 77.1 1.0

M.-C.Koag, S.Lee. Structure of DPO4 Dna Polymerase Replicating Across the Genotoxic N7-Methylguanine Lesion To Be Published.