Calcium in PDB 2j6s: Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6- Methylguanine Modified Dna, and Datp.

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

The structure of Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6- Methylguanine Modified Dna, and Datp., PDB code: 2j6s was solved by A.Irimia, R.L.Eoff, F.P.Guengerich, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.09 / 2.50
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.682, 103.271, 52.674, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 28

The binding sites of Calcium atom in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6- Methylguanine Modified Dna, and Datp. (pdb code 2j6s). 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 Datp., PDB code: 2j6s:
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 Datp.


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 Datp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:27.2 occ:1.00 OD2 A:ASP105 2.5 17.0 1.0 O A:PHE8 2.5 18.4 1.0 OD1 A:ASP7 2.6 25.7 1.0 O3B A:DTP1000 2.7 31.2 1.0 O A:HOH2009 2.8 26.0 1.0 O1B A:DTP1000 2.9 28.7 1.0 O5' A:DTP1000 3.3 31.3 1.0 O1G A:DTP1000 3.3 37.8 1.0 PB A:DTP1000 3.3 25.6 1.0 CA A:CA1002 3.3 32.1 1.0 CG A:ASP7 3.4 27.0 1.0 O1A A:DTP1000 3.4 27.2 1.0 CG A:ASP105 3.5 18.9 1.0 C A:PHE8 3.6 18.5 1.0 PG A:DTP1000 3.6 33.5 1.0 OD2 A:ASP7 3.7 28.6 1.0 PA A:DTP1000 3.7 30.5 1.0 NZ A:LYS159 3.9 17.4 0.5 O3A A:DTP1000 3.9 32.2 1.0 OD1 A:ASP105 3.9 20.7 1.0 C5' A:DTP1000 4.2 26.9 1.0 N A:PHE8 4.2 20.3 1.0 N A:TYR10 4.3 18.5 1.0 O A:HOH2087 4.4 42.7 1.0 C A:ASP7 4.4 23.5 1.0 O2G A:DTP1000 4.4 38.0 1.0 CA A:PHE8 4.4 18.9 1.0 N A:ASP9 4.4 18.1 1.0 CA A:ASP9 4.5 18.0 1.0 C A:ASP9 4.6 16.4 1.0 CB A:ASP7 4.6 25.1 1.0 N A:PHE11 4.7 19.3 1.0 O2B A:DTP1000 4.7 29.6 1.0 O A:ASP7 4.7 24.4 1.0 CB A:ASP105 4.8 17.7 1.0 CE A:LYS159 4.8 20.8 0.5 O3G A:DTP1000 4.8 37.3 1.0 O A:ASP105 4.9 14.8 1.0 CA A:ASP7 4.9 24.0 1.0 CB A:PHE11 5.0 23.1 1.0 CA A:TYR10 5.0 20.1 1.0

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


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 Datp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:32.1 occ:1.00 O P:HOH2022 2.2 32.1 1.0 O A:HOH2087 2.5 42.7 1.0 OD1 A:ASP105 2.7 20.7 1.0 OD1 A:ASP7 2.7 25.7 1.0 OE2 A:GLU106 2.8 29.9 1.0 OD2 A:ASP7 2.8 28.6 1.0 CG A:ASP7 3.0 27.0 1.0 O1A A:DTP1000 3.0 27.2 1.0 O5' A:DTP1000 3.3 31.3 1.0 CG A:GLU106 3.3 27.7 1.0 CA A:CA1001 3.3 27.2 1.0 CG A:ASP105 3.4 18.9 1.0 OD2 A:ASP105 3.5 17.0 1.0 CD A:GLU106 3.5 28.3 1.0 C3' P:DC14 3.7 55.8 1.0 PA A:DTP1000 3.8 30.5 1.0 O5' P:DC14 3.9 51.3 1.0 O3' P:DC14 4.0 58.0 1.0 O A:HOH2008 4.3 39.2 1.0 O A:ASP105 4.3 14.8 1.0 CB A:GLU106 4.3 24.8 1.0 CB A:ASP7 4.4 25.1 1.0 C5' A:DTP1000 4.4 26.9 1.0 C5' P:DC14 4.5 52.9 1.0 NZ A:LYS159 4.5 17.4 0.5 OG A:SER103 4.6 25.9 1.0 O2A A:DTP1000 4.6 36.0 1.0 C4' P:DC14 4.6 55.0 1.0 C A:ASP105 4.6 17.9 1.0 O A:HOH2009 4.7 26.0 1.0 OE1 A:GLU106 4.7 29.2 1.0 C2' P:DC14 4.7 55.6 1.0 CB A:ASP105 4.9 17.7 1.0 N A:GLU106 4.9 20.5 1.0 CA A:GLU106 4.9 22.6 1.0 O3B A:DTP1000 5.0 31.2 1.0

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


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 Datp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:50.7 occ:1.00 O P:HOH2019 2.3 39.1 1.0 O A:HOH2046 2.4 32.9 1.0 O A:ALA181 2.4 38.5 1.0 O A:HOH2047 2.5 40.3 1.0 O A:HOH2048 2.5 19.9 1.0 O A:ILE186 2.8 27.9 1.0 C A:ALA181 3.6 37.1 1.0 C A:ILE186 4.0 28.0 1.0 CA A:ALA181 4.4 38.0 1.0 OP2 P:DC13 4.4 29.4 1.0 OP1 P:DC13 4.4 24.8 1.0 CA A:GLY187 4.5 30.1 1.0 N A:ASP182 4.5 37.3 1.0 O P:HOH2008 4.5 37.2 1.0 CA A:ASP182 4.6 36.0 1.0 N A:GLY187 4.7 28.7 1.0 CB A:ALA181 4.7 37.6 1.0 O A:VAL183 4.9 30.8 1.0 P P:DC13 5.0 26.2 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