Calcium in PDB 2j6t: 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: 2j6t 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)	22.50 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.012, 102.949, 53.013, 90.00, 90.00, 90.00
R / Rfree (%)	23.7 / 26.9

The binding sites of Calcium atom in the Ternary Complex of Sulfolobus Solfataricus DPO4 Dna Polymerase, O6-Methylguanine Modified Dna, and Datp. (pdb code 2j6t). 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: 2j6t:
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:25.2 occ:1.00 O A:PHE8 2.3 26.0 1.0 OD2 A:ASP105 2.4 26.1 1.0 O1B A:DTP1000 2.6 30.2 1.0 O A:HOH2004 2.6 30.8 1.0 OD1 A:ASP7 2.6 32.2 1.0 O1G A:DTP1000 2.9 37.1 1.0 O5' A:DTP1000 3.0 32.0 1.0 C A:PHE8 3.4 25.4 1.0 CG A:ASP7 3.4 31.5 1.0 PB A:DTP1000 3.5 28.0 1.0 CG A:ASP105 3.7 26.9 1.0 O1A A:DTP1000 3.7 34.4 1.0 OD2 A:ASP7 3.7 34.1 1.0 CA A:CA1002 3.7 34.1 1.0 PA A:DTP1000 3.8 32.9 1.0 C5' A:DTP1000 3.8 30.8 1.0 PG A:DTP1000 3.8 36.8 1.0 O3B A:DTP1000 3.9 33.7 1.0 O3A A:DTP1000 4.0 32.6 1.0 N A:PHE8 4.0 25.8 1.0 O2G A:DTP1000 4.2 38.1 1.0 CA A:PHE8 4.2 25.2 1.0 N A:ASP9 4.2 25.5 1.0 C A:ASP7 4.3 26.7 1.0 N A:TYR10 4.3 23.3 1.0 CA A:ASP9 4.3 24.1 1.0 OD1 A:ASP105 4.4 26.8 1.0 C A:ASP9 4.4 23.9 1.0 CB A:ASP7 4.5 28.6 1.0 O A:ASP7 4.5 27.7 1.0 NZ A:LYS159 4.6 44.1 1.0 N A:PHE11 4.6 23.6 1.0 CB A:ASP105 4.6 25.8 1.0 CA A:ASP7 4.8 26.1 1.0 O2B A:DTP1000 4.8 31.2 1.0 CB A:PHE11 4.8 21.9 1.0 O A:ASP105 4.9 25.1 1.0 CB A:PHE8 4.9 23.2 1.0 CA A:TYR10 5.0 24.8 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:34.1 occ:1.00 OE2 A:GLU106 2.5 45.3 1.0 O A:HOH2025 2.7 26.3 1.0 OD1 A:ASP7 2.9 32.2 1.0 OD1 A:ASP105 3.0 26.8 1.0 O5' A:DTP1000 3.0 32.0 1.0 OD2 A:ASP7 3.0 34.1 1.0 CG A:GLU106 3.2 36.8 1.0 OD2 A:ASP105 3.2 26.1 1.0 CG A:ASP7 3.2 31.5 1.0 CD A:GLU106 3.2 40.9 1.0 O1A A:DTP1000 3.3 34.4 1.0 CG A:ASP105 3.5 26.9 1.0 PA A:DTP1000 3.7 32.9 1.0 CA A:CA1001 3.7 25.2 1.0 C5' A:DTP1000 4.0 30.8 1.0 O2A A:DTP1000 4.3 32.9 1.0 OG A:SER103 4.4 33.3 1.0 O A:HOH2003 4.4 45.7 1.0 CB A:GLU106 4.4 31.7 1.0 OE1 A:GLU106 4.5 40.4 1.0 O A:ASP105 4.5 25.1 1.0 CB A:ASP7 4.6 28.6 1.0 O A:HOH2063 4.7 28.2 1.0 C A:ASP105 4.8 25.9 1.0 NZ A:LYS159 4.8 44.1 1.0 CB A:ASP105 4.9 25.8 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:41.4 occ:1.00 O A:ALA181 2.4 38.8 1.0 O P:HOH2015 2.5 48.9 1.0 O P:HOH2004 2.5 47.4 1.0 O A:HOH2041 2.6 44.5 1.0 O A:HOH2040 2.7 28.4 1.0 O A:ILE186 2.8 22.9 1.0 C A:ALA181 3.6 39.1 1.0 C A:ILE186 4.0 24.5 1.0 OP2 P:DC13 4.4 26.6 1.0 CA A:ALA181 4.5 39.7 1.0 CA A:ASP182 4.5 39.5 1.0 N A:ASP182 4.5 39.5 1.0 OP1 P:DC13 4.6 27.2 1.0 CA A:GLY187 4.6 26.7 1.0 O A:VAL183 4.7 32.9 1.0 CB A:ALA181 4.7 40.8 1.0 N A:GLY187 4.8 25.0 1.0 C A:ASP182 4.9 38.1 1.0 C A:GLY187 5.0 26.2 1.0 CB A:ILE186 5.0 21.7 1.0 OD1 A:ASP182 5.0 47.9 1.0 CA A:ILE186 5.0 23.3 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