Calcium in PDB 7klf: Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dctp

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

The structure of Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dctp, PDB code: 7klf 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)	19.54 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.52, 102.373, 52.959, 90, 90, 90
R / Rfree (%)	23.1 / 27.9

The binding sites of Calcium atom in the Ternary Structure of DPO4 Bound to G in the Template Base Paired with Incoming Dctp (pdb code 7klf). 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 Dctp, PDB code: 7klf:
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 Dctp


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 Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:48.8 occ:1.00 OE2 A:GLU106 2.4 45.1 1.0 O A:HOH502 2.4 38.9 1.0 O2A A:DCP404 2.6 30.9 1.0 OD1 A:ASP105 2.9 31.0 1.0 OD1 A:ASP7 3.0 35.2 1.0 CG A:GLU106 3.0 36.1 1.0 CD A:GLU106 3.1 35.9 1.0 OD2 A:ASP7 3.2 35.4 1.0 OD2 A:ASP105 3.2 32.8 1.0 CG A:ASP7 3.4 31.9 1.0 CG A:ASP105 3.4 34.6 1.0 CA A:CA402 3.5 37.0 1.0 PA A:DCP404 3.7 40.0 1.0 C3' P:DC13 3.7 42.8 1.0 O3' P:DC13 3.8 38.6 1.0 O1A A:DCP404 4.0 48.7 1.0 C5' P:DC13 4.1 42.0 1.0 O5' P:DC13 4.2 59.0 1.0 C5' A:DCP404 4.3 31.6 1.0 OE1 A:GLU106 4.3 40.3 1.0 O5' A:DCP404 4.4 36.6 1.0 O A:ASP105 4.4 30.3 1.0 C4' P:DC13 4.4 46.3 1.0 CB A:GLU106 4.5 28.7 1.0 OG A:SER103 4.6 30.6 1.0 C A:ASP105 4.7 25.6 1.0 OP1 P:DC13 4.7 59.4 1.0 CB A:ASP7 4.7 30.4 1.0 CB A:ASP105 4.8 31.0 1.0 O2G A:DCP404 4.8 39.6 1.0 NZ A:LYS159 5.0 47.5 1.0 C2' P:DC13 5.0 43.4 1.0 O2B A:DCP404 5.0 31.8 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 Dctp


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 Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:37.0 occ:1.00 OD1 A:ASP7 2.3 35.2 1.0 O A:PHE8 2.3 32.1 1.0 O2A A:DCP404 2.3 30.9 1.0 O2B A:DCP404 2.3 31.8 1.0 O2G A:DCP404 2.4 39.6 1.0 OD2 A:ASP105 2.5 32.8 1.0 CG A:ASP7 3.4 31.9 1.0 C A:PHE8 3.4 27.2 1.0 O A:HOH522 3.5 38.8 1.0 CA A:CA401 3.5 48.8 1.0 PB A:DCP404 3.5 31.8 1.0 PG A:DCP404 3.6 40.4 1.0 PA A:DCP404 3.6 40.0 1.0 CG A:ASP105 3.6 34.6 1.0 O3A A:DCP404 3.9 35.9 1.0 OD2 A:ASP7 3.9 35.4 1.0 N A:PHE8 3.9 29.9 1.0 O3G A:DCP404 4.0 39.8 1.0 O3B A:DCP404 4.1 41.7 1.0 CA A:PHE8 4.3 26.5 1.0 C A:ASP7 4.3 32.0 1.0 OD1 A:ASP105 4.3 31.0 1.0 C5' A:DCP404 4.3 31.6 1.0 N A:ASP9 4.4 28.8 1.0 O5' A:DCP404 4.5 36.6 1.0 CE A:LYS159 4.5 45.4 1.0 N A:TYR10 4.5 28.5 1.0 CA A:ASP9 4.5 30.2 1.0 CB A:ASP7 4.5 30.4 1.0 CB A:ASP105 4.7 31.0 1.0 C A:ASP9 4.7 30.8 1.0 NZ A:LYS159 4.7 47.5 1.0 O A:ASP7 4.7 35.3 1.0 CA A:ASP7 4.8 27.3 1.0 O A:HOH502 4.8 38.9 1.0 O1A A:DCP404 4.8 48.7 1.0 O1G A:DCP404 4.9 46.8 1.0 O1B A:DCP404 4.9 35.9 1.0 CB A:PHE8 4.9 26.3 1.0 O A:ASP105 4.9 30.3 1.0 N A:PHE11 5.0 23.8 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 Dctp


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 Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:62.5 occ:1.00 O A:ALA181 2.5 55.9 1.0 O A:HOH539 2.5 70.6 1.0 O A:ILE186 2.7 48.8 1.0 O A:HOH508 2.8 52.3 1.0 C A:ALA181 3.7 57.5 1.0 C A:ILE186 3.9 52.7 1.0 OP2 P:DT12 4.2 58.7 1.0 OP1 P:DT12 4.3 51.9 1.0 CA A:GLY187 4.4 57.4 1.0 CA A:ALA181 4.5 53.2 1.0 N A:GLY187 4.6 52.6 1.0 N A:ASP182 4.6 53.2 1.0 CB A:ALA181 4.6 54.6 1.0 CA A:ASP182 4.7 53.3 1.0 P P:DT12 4.8 52.7 1.0 O A:VAL183 4.9 46.7 1.0 CA A:ILE186 4.9 49.3 1.0 C A:GLY187 4.9 58.4 1.0

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Atp To Be Published.