Calcium in PDB 3qz8: Tt-4 Ternary Complex of DPO4

All present enzymatic activity of Tt-4 Ternary Complex of DPO4:
2.7.7.7;

The structure of Tt-4 Ternary Complex of DPO4, PDB code: 3qz8 was solved by J.D.Pata, Y.Wu, R.C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.68 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.906, 102.694, 52.617, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.2

The binding sites of Calcium atom in the Tt-4 Ternary Complex of DPO4 (pdb code 3qz8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Tt-4 Ternary Complex of DPO4, PDB code: 3qz8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tt-4 Ternary Complex of DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tt-4 Ternary Complex of DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca361 b:28.7 occ:1.00 O1B A:DCP364 2.2 27.1 1.0 O A:PHE8 2.2 27.1 1.0 OD2 A:ASP105 2.3 34.0 1.0 OD1 A:ASP7 2.3 33.9 1.0 O2A A:DCP364 2.3 28.5 1.0 O1G A:DCP364 2.3 34.7 1.0 H5'1 A:DCP364 3.4 45.6 1.0 CA A:CA362 3.4 53.0 1.0 CG A:ASP7 3.4 38.3 1.0 CG A:ASP105 3.4 36.2 1.0 C A:PHE8 3.4 29.1 1.0 PB A:DCP364 3.5 30.1 1.0 PA A:DCP364 3.5 33.9 1.0 PG A:DCP364 3.6 35.1 1.0 HZ3 A:LYS159 3.6 37.8 1.0 HZ1 A:LYS159 3.6 37.8 1.0 O3A A:DCP364 3.8 31.9 1.0 H A:PHE8 3.9 30.4 1.0 O3B A:DCP364 3.9 42.2 1.0 N A:PHE8 3.9 25.3 1.0 HA A:ASP9 3.9 34.9 1.0 OD2 A:ASP7 4.0 46.2 1.0 HE2 A:LYS159 4.0 47.5 1.0 OD1 A:ASP105 4.0 29.7 1.0 NZ A:LYS159 4.0 31.5 1.0 H A:PHE11 4.0 25.9 1.0 C5' A:DCP364 4.1 38.0 1.0 O3G A:DCP364 4.1 36.1 1.0 HB2 A:PHE11 4.1 25.6 1.0 H5'2 A:DCP364 4.2 45.6 1.0 O5' A:DCP364 4.2 31.5 1.0 C A:ASP7 4.3 31.4 1.0 CA A:PHE8 4.3 30.2 1.0 H A:TYR10 4.3 31.5 1.0 HB2 A:PHE8 4.4 29.8 1.0 N A:ASP9 4.4 29.9 1.0 HB2 A:ASP105 4.5 35.1 1.0 CA A:ASP9 4.5 29.0 1.0 N A:TYR10 4.5 26.3 1.0 CE A:LYS159 4.6 39.6 1.0 CB A:ASP7 4.6 30.8 1.0 CB A:ASP105 4.6 29.2 1.0 C A:ASP9 4.7 27.3 1.0 O A:ASP7 4.7 28.3 1.0 O A:HOH455 4.7 53.9 1.0 HA A:ASP7 4.7 35.1 1.0 O2G A:DCP364 4.8 33.8 1.0 CA A:ASP7 4.8 29.2 1.0 O A:ASP105 4.8 27.6 1.0 HZ2 A:LYS159 4.8 37.8 1.0 N A:PHE11 4.8 21.6 1.0 O A:HOH432 4.8 32.5 1.0 O2B A:DCP364 4.9 26.7 1.0 O1A A:DCP364 4.9 35.7 1.0 HB3 A:ASP7 4.9 37.0 1.0 HO3' A:DCP364 4.9 33.3 1.0 CB A:PHE8 4.9 24.9 1.0 CB A:PHE11 5.0 21.4 1.0 HB3 A:PHE11 5.0 25.6 1.0

Calcium binding site 2 out of 3 in the Tt-4 Ternary Complex of DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tt-4 Ternary Complex of DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca362 b:53.0 occ:1.00 O2A A:DCP364 2.4 28.5 1.0 O A:HOH432 2.5 32.5 1.0 OD1 A:ASP105 2.6 29.7 1.0 HG3 A:GLU106 2.8 44.9 1.0 HG2 A:GLU106 2.9 44.9 1.0 OD1 A:ASP7 3.0 33.9 1.0 CG A:GLU106 3.1 37.4 1.0 CD A:GLU106 3.2 42.5 1.0 OD2 A:ASP105 3.2 34.0 1.0 CG A:ASP105 3.2 36.2 1.0 OE2 A:GLU106 3.3 51.4 1.0 O A:HOH455 3.3 53.9 1.0 CA A:CA361 3.4 28.7 1.0 C3' P:DG13 3.5 32.0 1.0 OD2 A:ASP7 3.5 46.2 1.0 CG A:ASP7 3.5 38.3 1.0 H5'2 A:DCP364 3.5 45.6 1.0 PA A:DCP364 3.7 33.9 1.0 O3' P:DG13 3.8 44.2 1.0 O5' A:DCP364 3.8 31.5 1.0 HG A:SER103 3.9 40.3 1.0 HZ1 A:LYS159 3.9 37.8 1.0 OE1 A:GLU106 3.9 52.7 1.0 C5' A:DCP364 4.1 38.0 1.0 H5'1 A:DCP364 4.1 45.6 1.0 O1A A:DCP364 4.1 35.7 1.0 O5' P:DG13 4.2 46.5 1.0 C5' P:DG13 4.4 34.7 1.0 C4' P:DG13 4.4 42.5 1.0 O A:ASP105 4.4 27.6 1.0 OG A:SER103 4.5 33.6 1.0 CB A:GLU106 4.5 32.7 1.0 C2' P:DG13 4.5 38.6 1.0 C A:ASP105 4.7 29.1 1.0 HA A:ASP7 4.7 35.1 1.0 CB A:ASP105 4.7 29.2 1.0 NZ A:LYS159 4.7 31.5 1.0 O1B A:DCP364 4.7 27.1 1.0 HZ3 A:LYS159 4.7 37.8 1.0 O1G A:DCP364 4.8 34.7 1.0 CB A:ASP7 4.8 30.8 1.0 OP1 P:DG13 4.8 58.1 1.0 HZ A:PHE5 4.8 39.0 1.0 H A:ASP105 4.9 31.0 1.0 HB2 A:GLU106 4.9 39.2 1.0 HB2 A:ASP7 5.0 37.0 1.0 H A:PHE8 5.0 30.4 1.0 HB3 A:GLU106 5.0 39.2 1.0 HZ1 A:LYS152 5.0 64.6 1.0

Calcium binding site 3 out of 3 in the Tt-4 Ternary Complex of DPO4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tt-4 Ternary Complex of DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca363 b:45.6 occ:1.00 O A:ALA181 2.3 47.6 1.0 O A:ILE186 2.5 37.7 1.0 O P:HOH133 2.5 46.5 1.0 O A:HOH462 2.6 50.8 1.0 O A:HOH399 2.6 36.8 1.0 O A:HOH456 2.8 53.7 1.0 C A:ALA181 3.5 51.2 1.0 HA2 A:GLY187 3.7 51.1 1.0 C A:ILE186 3.7 44.2 1.0 HA A:ASP182 3.8 51.6 1.0 HB1 A:ALA181 3.9 60.1 1.0 HB A:ILE186 4.1 45.1 1.0 HA A:ALA181 4.1 55.8 1.0 CA A:ALA181 4.3 46.5 1.0 N A:ASP182 4.4 44.7 1.0 CA A:GLY187 4.5 42.6 1.0 CA A:ASP182 4.5 43.0 1.0 OP1 P:DG12 4.5 39.5 1.0 OP2 P:DG12 4.5 37.9 1.0 CB A:ALA181 4.5 50.1 1.0 N A:GLY187 4.6 38.4 1.0 H A:ILE186 4.7 43.9 1.0 HG22 A:ILE186 4.7 47.0 1.0 O A:VAL183 4.7 38.0 1.0 CA A:ILE186 4.8 36.9 1.0 CB A:ILE186 4.8 37.6 1.0 C A:GLY187 4.9 49.4 1.0 OD1 A:ASP182 4.9 62.2 1.0 HB2 A:ALA191 5.0 42.9 1.0 HB3 A:ALA181 5.0 60.1 1.0

Y.Wu, R.C.Wilson, J.D.Pata. The Y-Family Dna Polymerase DPO4 Uses A Template Slippage Mechanism to Create Single-Base Deletions. J.Bacteriol. V. 193 2630 2011.
ISSN: ISSN 0021-9193
PubMed: 21421759
DOI: 10.1128/JB.00012-11