Calcium in PDB 2j6u: Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp.

All present enzymatic activity of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp.:
2.7.7.7;

The structure of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp., PDB code: 2j6u was solved by R.L.Eoff, A.Irimia, F.P.Guengerich, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.69 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.318, 102.285, 52.485, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.5

The binding sites of Calcium atom in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp. (pdb code 2j6u). 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 Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp., PDB code: 2j6u:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp.


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 Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:47.8 occ:1.00 OD2 A:ASP10 2.6 47.5 1.0 O P:HOH2022 2.6 42.9 1.0 OE2 A:GLU109 2.6 45.6 1.0 C3' P:DT14 2.7 89.5 0.5 OD1 A:ASP10 2.7 45.6 1.0 O2A P:DGT1016 2.7 40.0 1.0 CG A:ASP10 2.9 44.4 1.0 O3' P:DT14 3.0 90.0 0.7 OD1 A:ASP108 3.0 44.6 1.0 C3' P:DT14 3.1 89.5 0.3 OD2 A:ASP108 3.5 39.8 1.0 O5' P:DT14 3.5 77.5 0.1 O5' P:DT14 3.6 77.5 0.2 CA A:CA1002 3.6 43.4 1.0 C4' P:DT14 3.6 87.6 0.0 CG A:ASP108 3.6 41.8 1.0 O3' P:DT14 3.7 90.0 0.0 OP1 P:DT14 3.7 93.5 0.0 CD A:GLU109 3.7 44.4 1.0 PA P:DGT1016 3.8 35.7 1.0 C5' P:DT14 3.8 83.4 0.8 C2' P:DT14 3.9 90.2 0.2 O A:HOH2050 3.9 62.1 1.0 C5' P:DT14 3.9 83.4 0.5 C4' P:DT14 3.9 87.6 0.0 CB A:GLU109 4.0 40.5 1.0 O1A P:DGT1016 4.1 34.0 1.0 C2' P:DT14 4.2 90.2 0.4 CB A:ASP10 4.3 45.6 1.0 CG A:GLU109 4.3 42.1 1.0 O5' P:DGT1016 4.3 36.1 1.0 NZ A:LYS162 4.5 51.1 1.0 OG A:SER106 4.6 35.8 1.0 O A:ASP108 4.7 35.9 1.0 OE1 A:GLU109 4.7 48.4 1.0 C5' P:DGT1016 4.8 36.0 1.0 P P:DT14 4.8 73.7 0.1 P P:DT14 4.8 73.7 0.2 NZ A:LYS155 4.8 51.6 1.0 C A:ASP108 4.8 37.9 1.0 O2G P:DGT1016 4.9 48.5 1.0 O4' P:DT14 4.9 89.4 0.0 P P:DT14 4.9 94.0 0.7 C1' P:DT14 4.9 90.4 0.5 OP1 P:DT14 4.9 73.3 0.0 CA A:ASP10 5.0 42.3 1.0 OP1 P:DT14 5.0 73.3 0.0

Calcium binding site 2 out of 3 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp.


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 Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:43.4 occ:1.00 O2A P:DGT1016 2.3 40.0 1.0 O A:PHE11 2.5 39.3 1.0 O2G P:DGT1016 2.5 48.5 1.0 OD2 A:ASP10 2.6 47.5 1.0 O1B P:DGT1016 2.6 41.2 1.0 OD2 A:ASP108 2.6 39.8 1.0 O P:HOH2026 2.9 48.7 1.0 CG A:ASP10 3.3 44.4 1.0 PG P:DGT1016 3.4 44.4 1.0 O3B P:DGT1016 3.5 42.6 1.0 PB P:DGT1016 3.5 43.1 1.0 C A:PHE11 3.5 36.8 1.0 PA P:DGT1016 3.6 35.7 1.0 CA A:CA1001 3.6 47.8 1.0 OD1 A:ASP10 3.6 45.6 1.0 O A:HOH2050 3.6 62.1 1.0 O3G P:DGT1016 3.8 46.7 1.0 CG A:ASP108 3.8 41.8 1.0 O3A P:DGT1016 4.0 40.4 1.0 N A:PHE11 4.0 39.4 1.0 NZ A:LYS162 4.1 51.1 1.0 C A:ASP10 4.2 41.1 1.0 CA A:PHE11 4.3 37.6 1.0 N A:TYR13 4.3 35.1 1.0 N A:ASP12 4.3 36.2 1.0 CB A:ASP10 4.3 45.6 1.0 OD1 A:ASP108 4.4 44.6 1.0 CA A:ASP12 4.4 35.9 1.0 O A:ASP10 4.5 42.2 1.0 C5' P:DGT1016 4.5 36.0 1.0 O5' P:DGT1016 4.6 36.1 1.0 C A:ASP12 4.6 33.6 1.0 CE A:LYS162 4.6 52.2 1.0 O P:HOH2022 4.7 42.9 1.0 CA A:ASP10 4.7 42.3 1.0 O1A P:DGT1016 4.7 34.0 1.0 N A:PHE14 4.8 35.6 1.0 O1G P:DGT1016 4.8 48.8 1.0 O2B P:DGT1016 4.9 43.4 1.0 CB A:ASP108 5.0 38.6 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Dgtp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:72.9 occ:1.00 O A:HOH2062 2.7 67.7 1.0 O P:HOH2018 2.7 34.8 1.0 O A:ALA184 2.8 52.9 1.0 O A:ILE189 2.9 42.8 1.0 O P:HOH2023 2.9 47.5 1.0 O3' P:DT14 3.5 92.5 0.9 C A:ILE189 3.9 43.3 1.0 C A:ALA184 4.0 52.6 1.0 OP2 P:DC13 4.0 50.8 1.0 CA A:GLY190 4.3 46.9 1.0 OP1 P:DC13 4.3 51.0 1.0 N A:GLY190 4.6 44.6 1.0 P P:DC13 4.7 47.1 1.0 C3' P:DT14 4.8 92.9 0.6 CA A:ALA184 4.8 53.1 1.0 C A:GLY190 4.8 48.4 1.0 CB A:ALA184 4.9 51.1 1.0 O A:VAL186 5.0 44.7 1.0 N A:ASP185 5.0 49.8 1.0

R.L.Eoff, A.Irimia, M.Egli, F.P.Guengerich. Sulfolobus Solfataricus Dna Polymerase DPO4 Is Partially Inhibited By "Wobble" Pairing Between O6- Methylguanine and Cytosine, But Accurate Bypass Is Preferred. J.Biol.Chem. V. 282 1456 2007.
ISSN: ISSN 0021-9258
PubMed: 17105728
DOI: 10.1074/JBC.M609661200