Calcium in PDB 4tqr: Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp

All present enzymatic activity of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp:
2.7.7.7;

The structure of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp, PDB code: 4tqr was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.32 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.537, 89.406, 112.390, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 20.2

The structure of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp (pdb code 4tqr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp, PDB code: 4tqr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca102 b:36.7 occ:1.00 O P:HOH249 2.2 40.3 1.0 O T:HOH276 2.3 37.7 1.0 O P:HOH245 2.3 36.8 1.0 O P:HOH242 2.4 32.0 1.0 O T:HOH279 2.4 56.5 1.0 O T:HOH275 2.5 35.6 1.0 O P:HOH243 2.6 39.1 1.0 O P:HOH210 4.4 40.3 1.0 O T:HOH242 4.4 36.2 1.0 O P:HOH216 4.4 41.6 1.0 C4' T:DC14 4.5 38.9 1.0 C5' T:DC14 4.5 40.4 1.0 C5' P:DG8 4.5 33.8 1.0 O P:HOH247 4.6 51.9 1.0 O4' T:DC14 4.7 36.3 1.0 C4' P:DG8 4.7 30.4 1.0 O2 T:DT13 4.8 32.5 1.0 O P:HOH209 4.8 33.9 1.0 N3 P:DA7 4.9 30.1 1.0 O4' P:DG8 4.9 29.3 1.0

Calcium binding site 2 out of 2 in the Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of Y-Family Dna Polymerase DPO4 with (5'S)-8,5'-Cyclo- 2'-Deoxyguanosine and Dttp within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca102 b:19.8 occ:1.00 OP2 T:2LF5 2.2 23.0 1.0 OP2 T:DC2 2.3 19.1 1.0 O T:HOH254 2.4 19.1 1.0 O T:HOH218 2.5 23.8 1.0 O A:HOH591 2.5 22.9 1.0 O T:HOH220 2.5 26.0 1.0 O T:HOH255 2.5 24.5 1.0 P T:2LF5 3.7 27.6 1.0 P T:DC2 3.7 18.0 1.0 O A:HOH655 4.1 33.9 1.0 O T:HOH243 4.1 45.6 1.0 O5' T:DC2 4.2 16.3 1.0 OP1 T:2LF5 4.3 42.1 1.0 O T:HOH293 4.4 37.1 1.0 OP1 T:DC4 4.4 22.9 1.0 O5' T:2LF5 4.4 36.9 1.0 N7 T:2LF5 4.4 24.2 1.0 O5' T:DT1 4.5 22.2 0.6 C5' T:DC2 4.5 17.4 1.0 O3' T:DT1 4.5 17.8 1.0 C3' T:DT1 4.5 18.2 1.0 OP1 T:DC2 4.7 20.6 1.0 O3' T:DC4 4.7 24.9 1.0 O T:HOH203 4.7 28.4 1.0 C3' T:DC4 4.8 25.1 1.0 C5' T:2LF5 4.9 30.1 1.0 C8 T:2LF5 5.0 19.7 1.0 OG A:SER34 5.0 27.5 1.0

W.Xu, A.M.Ouellette, Z.Wawrzak, S.J.Shriver, S.M.Anderson, L.Zhao. Kinetic and Structural Mechanisms of (5'S)-8,5'-Cyclo-2'-Deoxyguanosine-Induced Dna Replication Stalling. Biochemistry V. 54 639 2015.
ISSN: ISSN 0006-2960
PubMed: 25569151
DOI: 10.1021/BI5014936