Calcium in PDB 7kle: Ternary Structure of DPO4 Bound to N7MG in the Template Base Paired with Incoming Dctp

All present enzymatic activity of Ternary Structure of DPO4 Bound to N7MG in the Template Base Paired with Incoming Dctp:
2.7.7.7;

The structure of Ternary Structure of DPO4 Bound to N7MG in the Template Base Paired with Incoming Dctp, PDB code: 7kle 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)	19.56 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.65, 102.472, 53.034, 90, 90, 90
R / Rfree (%)	22.9 / 28.8

The structure of Ternary Structure of DPO4 Bound to N7MG in the Template Base Paired with Incoming Dctp also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Calcium atom in the Ternary Structure of DPO4 Bound to N7MG in the Template Base Paired with Incoming Dctp (pdb code 7kle). 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 N7MG in the Template Base Paired with Incoming Dctp, PDB code: 7kle:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ternary Structure of DPO4 Bound to N7MG 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 N7MG in the Template Base Paired with Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:56.7 occ:1.00 OE2 A:GLU106 2.5 44.7 1.0 O P:HOH101 2.6 39.4 1.0 O1A A:DCP404 2.7 45.9 1.0 OD2 A:ASP7 2.8 34.6 1.0 OD1 A:ASP7 2.9 41.7 1.0 CD A:GLU106 3.0 42.0 1.0 CG A:GLU106 3.1 36.8 1.0 CG A:ASP7 3.1 36.2 1.0 OD2 A:ASP105 3.5 39.3 1.0 OD1 A:ASP105 3.5 43.9 1.0 CA A:CA402 3.6 33.8 1.0 CG A:ASP105 3.9 40.5 1.0 PA A:DCP404 3.9 55.6 1.0 C3' P:DC13 3.9 46.4 1.0 OE1 A:GLU106 4.0 41.1 1.0 O5' P:DC13 4.0 58.6 1.0 O3' P:DC13 4.1 47.8 1.0 OP1 P:DC13 4.2 58.7 1.0 O2A A:DCP404 4.2 56.8 1.0 C5' P:DC13 4.2 48.8 1.0 C5' A:DCP404 4.5 48.0 1.0 C4' P:DC13 4.5 47.0 1.0 CB A:ASP7 4.6 35.5 1.0 CB A:GLU106 4.6 31.5 1.0 O5' A:DCP404 4.7 50.4 1.0 P P:DC13 4.7 70.9 1.0 O A:ASP105 4.9 39.0 1.0 O1G A:DCP404 4.9 60.2 1.0 OG A:SER103 4.9 35.5 1.0

Calcium binding site 2 out of 3 in the Ternary Structure of DPO4 Bound to N7MG 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 N7MG in the Template Base Paired with Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:33.8 occ:1.00 O A:PHE8 2.3 37.3 1.0 O1G A:DCP404 2.4 60.2 1.0 OD1 A:ASP7 2.4 41.7 1.0 O1A A:DCP404 2.4 45.9 1.0 O1B A:DCP404 2.4 44.0 1.0 OD2 A:ASP105 2.5 39.3 1.0 CG A:ASP7 3.3 36.2 1.0 C A:PHE8 3.4 37.6 1.0 O A:HOH501 3.4 30.0 1.0 NZ A:LYS159 3.5 50.0 1.0 PB A:DCP404 3.6 49.2 1.0 CA A:CA401 3.6 56.7 1.0 PA A:DCP404 3.7 55.6 1.0 CG A:ASP105 3.7 40.5 1.0 OD2 A:ASP7 3.7 34.6 1.0 PG A:DCP404 3.7 86.8 1.0 N A:PHE8 3.9 36.1 1.0 O3A A:DCP404 3.9 61.4 1.0 O3B A:DCP404 4.0 56.1 1.0 CA A:PHE8 4.2 41.1 1.0 C A:ASP7 4.3 38.2 1.0 C5' A:DCP404 4.3 48.0 1.0 N A:ASP9 4.4 34.0 1.0 CB A:ASP7 4.4 35.5 1.0 O5' A:DCP404 4.4 50.4 1.0 OD1 A:ASP105 4.4 43.9 1.0 N A:TYR10 4.5 39.9 1.0 CA A:ASP9 4.5 37.9 1.0 CE A:LYS159 4.5 51.0 1.0 CB A:ASP105 4.6 37.4 1.0 O2G A:DCP404 4.7 66.4 1.0 CA A:ASP7 4.7 38.8 1.0 O3G A:DCP404 4.7 63.3 1.0 O A:ASP7 4.8 41.5 1.0 C A:ASP9 4.8 38.0 1.0 CB A:PHE8 4.9 34.5 1.0 O2A A:DCP404 4.9 56.8 1.0 O2B A:DCP404 4.9 45.6 1.0 O A:ASP105 4.9 39.0 1.0

Calcium binding site 3 out of 3 in the Ternary Structure of DPO4 Bound to N7MG 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 N7MG in the Template Base Paired with Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:64.0 occ:1.00 O A:HOH511 2.5 40.5 1.0 O A:HOH510 2.6 49.0 1.0 O A:ALA181 2.6 58.9 1.0 O A:ILE186 3.3 51.3 1.0 C A:ALA181 3.8 55.0 1.0 CA A:ASP182 4.4 52.1 1.0 OP2 P:DT12 4.4 68.9 1.0 N A:ASP182 4.5 50.5 1.0 OP1 P:DT12 4.5 51.1 1.0 C A:ILE186 4.5 58.3 1.0 OD1 A:ASP182 4.7 65.6 1.0 CA A:ALA181 4.8 55.9 1.0 P P:DT12 5.0 64.1 1.0 C A:ASP182 5.0 48.5 1.0 O A:VAL183 5.0 51.6 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.