Calcium in PDB 3qz7: T-3 Ternary Complex of DPO4

All present enzymatic activity of T-3 Ternary Complex of DPO4:
2.7.7.7;

The structure of T-3 Ternary Complex of DPO4, PDB code: 3qz7 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)	25.54 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.708, 102.461, 52.743, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.7

The binding sites of Calcium atom in the T-3 Ternary Complex of DPO4 (pdb code 3qz7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the T-3 Ternary Complex of DPO4, PDB code: 3qz7:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the T-3 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 T-3 Ternary Complex of DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca362 b:38.6 occ:1.00 O2A A:DCP361 2.2 40.6 1.0 OD1 A:ASP7 2.2 47.3 1.0 O A:PHE8 2.3 39.8 1.0 O1B A:DCP361 2.3 34.8 1.0 OD2 A:ASP105 2.3 43.7 1.0 O1G A:DCP361 2.3 43.0 1.0 H5'1 A:DCP361 3.3 47.3 1.0 CG A:ASP7 3.3 53.1 1.0 PA A:DCP361 3.3 44.9 1.0 PB A:DCP361 3.4 41.6 1.0 C A:PHE8 3.5 40.8 1.0 CA A:CA363 3.5 71.4 1.0 CG A:ASP105 3.5 45.4 1.0 PG A:DCP361 3.5 47.3 1.0 HZ2 A:LYS159 3.6 60.1 1.0 O3A A:DCP361 3.7 41.1 1.0 OD2 A:ASP7 3.8 49.0 1.0 O3B A:DCP361 3.8 51.4 1.0 HA A:ASP9 3.9 45.0 1.0 HZ3 A:LYS159 3.9 60.1 1.0 O3G A:DCP361 4.0 45.7 1.0 C5' A:DCP361 4.0 39.4 1.0 N A:PHE8 4.0 41.3 1.0 H5'2 A:DCP361 4.0 47.3 1.0 H A:PHE8 4.0 49.6 1.0 H A:PHE11 4.1 37.6 1.0 O5' A:DCP361 4.1 41.3 1.0 NZ A:LYS159 4.2 50.1 1.0 OD1 A:ASP105 4.2 39.6 1.0 HB2 A:PHE11 4.2 38.1 1.0 C A:ASP7 4.3 46.2 1.0 CA A:PHE8 4.3 41.3 1.0 HB2 A:PHE8 4.4 45.7 1.0 HE2 A:LYS159 4.4 73.0 1.0 HB2 A:ASP105 4.4 56.1 1.0 N A:ASP9 4.4 44.8 1.0 H A:TYR10 4.5 38.4 1.0 CA A:ASP9 4.5 37.5 1.0 CB A:ASP7 4.6 41.4 1.0 CB A:ASP105 4.6 46.8 1.0 N A:TYR10 4.6 32.0 1.0 O A:ASP7 4.6 48.7 1.0 O A:HOH396 4.7 45.2 1.0 HO3' A:DCP361 4.7 44.5 1.0 C A:ASP9 4.7 40.8 1.0 O1A A:DCP361 4.8 37.9 1.0 O2G A:DCP361 4.8 44.1 1.0 O2B A:DCP361 4.8 37.6 1.0 N A:PHE11 4.8 31.4 1.0 HA A:ASP7 4.8 48.2 1.0 CE A:LYS159 4.9 60.8 1.0 HB3 A:ASP7 4.9 49.6 1.0 HZ1 A:LYS159 4.9 60.1 1.0 CA A:ASP7 4.9 40.2 1.0 O A:ASP105 4.9 40.9 1.0 CB A:PHE8 4.9 38.1 1.0 HA A:TYR10 4.9 43.3 1.0

Calcium binding site 2 out of 3 in the T-3 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 T-3 Ternary Complex of DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca363 b:71.4 occ:1.00 O A:HOH396 2.2 45.2 1.0 OE1 A:GLU106 2.4 66.0 1.0 O2A A:DCP361 2.4 40.6 1.0 OD1 A:ASP105 2.6 39.6 1.0 HG3 A:GLU106 2.6 69.2 1.0 HG2 A:GLU106 2.7 69.2 1.0 H3' P:DG13 2.8 71.3 1.0 CG A:GLU106 2.9 57.7 1.0 OD2 A:ASP7 3.0 49.0 1.0 CD A:GLU106 3.0 55.0 1.0 OD2 A:ASP105 3.1 43.7 1.0 CG A:ASP105 3.2 45.4 1.0 OD1 A:ASP7 3.2 47.3 1.0 CG A:ASP7 3.3 53.1 1.0 CA A:CA362 3.5 38.6 1.0 H5'2 A:DCP361 3.5 47.3 1.0 C3' P:DG13 3.7 59.4 1.0 PA A:DCP361 3.7 44.9 1.0 O5' A:DCP361 3.8 41.3 1.0 O3' P:DG13 3.9 57.4 1.0 H5'' P:DG13 3.9 71.3 1.0 HG A:SER103 4.0 57.7 1.0 C5' A:DCP361 4.1 39.4 1.0 O1A A:DCP361 4.1 37.9 1.0 H5'1 A:DCP361 4.2 47.3 1.0 HZ3 A:LYS159 4.2 60.1 1.0 OE2 A:GLU106 4.2 59.0 1.0 O A:ASP105 4.4 40.9 1.0 CB A:GLU106 4.4 42.0 1.0 C5' P:DG13 4.6 59.4 1.0 OP1 P:DG13 4.6 69.2 1.0 HO3' P:DG13 4.6 68.8 1.0 C4' P:DG13 4.6 65.4 1.0 CB A:ASP7 4.6 41.4 1.0 C A:ASP105 4.6 44.6 1.0 OG A:SER103 4.6 48.1 1.0 O5' P:DG13 4.6 70.5 1.0 CB A:ASP105 4.7 46.8 1.0 HA A:ASP7 4.7 48.2 1.0 HZ2 A:LYS159 4.7 60.1 1.0 HZ A:PHE5 4.7 57.4 1.0 HB2 A:ASP7 4.7 49.6 1.0 C2' P:DG13 4.8 56.2 1.0 H2' P:DG13 4.8 67.5 1.0 O1G A:DCP361 4.8 43.0 1.0 HB2 A:GLU106 4.8 50.3 1.0 H4' P:DG13 4.8 78.4 1.0 NZ A:LYS159 4.9 50.1 1.0 HB3 A:GLU106 4.9 50.3 1.0 O1B A:DCP361 4.9 34.8 1.0 H2'' P:DG13 4.9 67.5 1.0 H A:ASP105 5.0 43.4 1.0

Calcium binding site 3 out of 3 in the T-3 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 T-3 Ternary Complex of DPO4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca364 b:94.5 occ:1.00 O A:ALA181 2.5 79.8 1.0 O A:HOH404 3.0 62.5 1.0 HA A:ASP182 3.5 85.9 1.0 C A:ALA181 3.7 75.5 1.0 O A:ILE186 3.8 53.1 1.0 CA A:ASP182 4.3 71.6 1.0 HB1 A:ALA181 4.4 94.5 1.0 OP2 P:DG12 4.4 74.7 1.0 N A:ASP182 4.4 71.6 1.0 HA A:ALA181 4.7 90.4 1.0 CA A:ALA181 4.7 75.4 1.0 OP1 P:DG12 4.7 62.1 1.0 OD1 A:ASP182 4.8 87.9 1.0 HA2 A:GLY187 4.8 86.8 1.0 C A:ASP182 4.8 73.4 1.0 C A:ILE186 5.0 60.7 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