Calcium in PDB 2v4q: Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna

All present enzymatic activity of Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna:
2.7.7.7;

The structure of Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna, PDB code: 2v4q was solved by R.L.Eoff, J.B.Stafford, J.Szekely, C.J.Rizzo, M.Egli, F.P.Guengerich, L.J.Marnett, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.72 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.610, 103.140, 52.010, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25.4

The binding sites of Calcium atom in the Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna (pdb code 2v4q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna, PDB code: 2v4q:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1000 b:43.1 occ:1.00 O2A A:DGT594 2.3 54.7 1.0 O2B A:DGT594 2.5 50.1 1.0 O A:PHE8 2.5 38.4 1.0 OD2 A:ASP105 2.6 38.2 1.0 OD1 A:ASP7 2.7 51.2 1.0 O3G A:DGT594 2.7 50.0 1.0 OD2 A:ASP7 2.8 47.6 1.0 CG A:ASP7 3.0 49.0 1.0 CA A:CA1001 3.4 57.1 1.0 PA A:DGT594 3.5 51.4 1.0 C A:PHE8 3.6 39.5 1.0 PB A:DGT594 3.7 48.6 1.0 CG A:ASP105 3.8 37.7 1.0 PG A:DGT594 3.8 48.8 1.0 N A:PHE8 3.9 43.1 1.0 O3A A:DGT594 4.0 48.6 1.0 O2G A:DGT594 4.0 52.7 1.0 C A:ASP7 4.1 44.7 1.0 C5' A:DGT594 4.2 43.9 1.0 O3B A:DGT594 4.2 51.6 1.0 CB A:ASP7 4.3 49.0 1.0 CA A:PHE8 4.3 40.8 1.0 OD1 A:ASP105 4.4 36.3 1.0 O5' A:DGT594 4.4 47.6 1.0 NZ A:LYS159 4.4 60.3 0.9 O A:ASP7 4.4 45.8 1.0 O P:HOH2014 4.5 56.5 1.0 N A:ASP9 4.5 39.8 1.0 CA A:ASP7 4.5 45.4 1.0 CA A:ASP9 4.6 41.2 1.0 O A:ASP105 4.7 40.9 1.0 N A:TYR10 4.7 40.2 1.0 CE A:LYS159 4.7 60.7 0.6 O1A A:DGT594 4.8 53.1 1.0 CB A:ASP105 4.8 38.8 1.0 O1B A:DGT594 4.9 49.7 1.0 C A:ASP9 4.9 41.3 1.0 CB A:PHE8 5.0 40.7 1.0

Calcium binding site 2 out of 3 in the Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:57.1 occ:1.00 O P:HOH2014 2.3 56.5 1.0 O2A A:DGT594 2.6 54.7 1.0 OD1 A:ASP105 2.7 36.3 1.0 OD2 A:ASP7 2.7 47.6 1.0 OE2 A:GLU106 2.9 63.4 1.0 OD2 A:ASP105 3.0 38.2 1.0 CD A:GLU106 3.1 57.3 1.0 CG A:ASP105 3.2 37.7 1.0 OE1 A:GLU106 3.4 60.4 1.0 CA A:CA1000 3.4 43.1 1.0 PA A:DGT594 3.7 51.4 1.0 CG A:ASP7 3.8 49.0 1.0 CB A:GLU106 3.9 47.9 1.0 CG A:GLU106 4.0 52.9 1.0 O5' A:DGT594 4.1 47.6 1.0 O1A A:DGT594 4.1 53.1 1.0 OG A:SER103 4.2 47.1 1.0 OP2 P:DC14 4.2 76.6 1.0 C5' A:DGT594 4.3 43.9 1.0 O A:ASP105 4.3 40.9 1.0 C A:ASP105 4.5 41.6 1.0 CB A:ASP105 4.6 38.8 1.0 OD1 A:ASP7 4.6 51.2 1.0 O5' P:DC14 4.6 77.0 0.9 CB A:ASP7 4.6 49.0 1.0 N A:GLU106 4.8 42.9 1.0 O3G A:DGT594 4.9 50.0 1.0 CA A:GLU106 4.9 45.7 1.0 C5' P:DC14 5.0 76.9 1.0

Calcium binding site 3 out of 3 in the Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Post-Insertion Complex of the Y-Family Dna Polymerase DPO4 with M1DG Containing Template Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:77.5 occ:1.00 O A:ALA181 2.6 67.2 1.0 O P:HOH2013 2.7 63.2 1.0 O A:HOH2031 2.8 56.4 1.0 O A:HOH2015 3.1 68.9 1.0 O A:ILE186 3.1 52.2 1.0 C A:ALA181 3.8 67.4 1.0 OP2 P:DC13 3.9 50.6 1.0 OP1 P:DC13 4.2 49.5 1.0 C A:ILE186 4.2 53.0 1.0 P P:DC13 4.6 47.6 1.0 CA A:ASP182 4.6 64.4 1.0 N A:ASP182 4.7 65.5 1.0 CA A:ALA181 4.7 68.8 1.0 CA A:GLY187 4.8 55.1 1.0 O A:VAL183 4.9 57.6 1.0 CB A:ALA181 4.9 69.3 1.0 N A:GLY187 5.0 53.5 1.0

R.L.Eoff, J.B.Stafford, J.Szekely, C.J.Rizzo, M.Egli, F.P.Guengerich, L.J.Marnett. Structural and Functional Analysis of Sulfolobus Solfataricus Y-Family Dna Polymerase DPO4- Catalyzed Bypass of the Malondialdehyde- Deoxyguanosine Adduct. Biochemistry V. 48 7079 2009.
ISSN: ISSN 0006-2960
PubMed: 19492857
DOI: 10.1021/BI9003588