Calcium in PDB 2uvv: Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs

All present enzymatic activity of Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs:
2.7.7.7;

The structure of Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs, PDB code: 2uvv was solved by A.Irimia, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.32 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.776, 103.725, 53.032, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 25.7

The binding sites of Calcium atom in the Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs (pdb code 2uvv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs, PDB code: 2uvv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:40.7 occ:1.00 O A:HOH547 2.1 32.8 1.0 OE2 A:GLU106 2.6 26.6 1.0 O1A A:DGT401 2.6 21.8 1.0 OD1 A:ASP105 3.0 30.7 1.0 OD2 A:ASP7 3.0 29.9 1.0 OD1 A:ASP7 3.1 32.4 1.0 CG A:ASP7 3.3 26.9 1.0 OD2 A:ASP105 3.4 24.9 1.0 CG A:ASP105 3.6 26.7 1.0 C3' P:DC14 3.6 48.9 1.0 CD A:GLU106 3.7 33.5 1.0 CA A:CA403 3.8 23.6 1.0 PA A:DGT401 3.8 26.4 1.0 C5' P:DC14 3.9 52.2 1.0 O5' P:DC14 4.0 53.8 1.0 O2A A:DGT401 4.0 29.5 1.0 CB A:GLU106 4.1 28.6 1.0 O5' A:DGT401 4.3 21.9 1.0 O3' P:DC14 4.3 46.7 1.0 C4' P:DC14 4.3 50.3 1.0 CG A:GLU106 4.3 33.6 1.0 C5' A:DGT401 4.4 23.4 1.0 OP1 P:DC14 4.5 53.5 1.0 O A:HOH519 4.5 46.5 1.0 NZ A:LYS159 4.5 28.2 1.0 OG A:SER103 4.7 38.9 1.0 CB A:ASP7 4.7 22.8 1.0 OE1 A:GLU106 4.7 35.2 1.0 C2' P:DC14 4.7 49.2 1.0 O A:ASP105 4.8 22.0 1.0 P P:DC14 4.9 54.3 1.0 O2G A:DGT401 4.9 28.4 1.0 C A:ASP105 5.0 25.1 1.0 NZ A:LYS152 5.0 40.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:23.6 occ:1.00 O2G A:DGT401 2.3 28.4 1.0 O1B A:DGT401 2.3 27.2 1.0 O1A A:DGT401 2.4 21.8 1.0 O A:PHE8 2.4 19.3 1.0 OD2 A:ASP105 2.4 24.9 1.0 OD2 A:ASP7 2.5 29.9 1.0 CG A:ASP7 3.4 26.9 1.0 PB A:DGT401 3.5 26.2 1.0 C A:PHE8 3.5 19.9 1.0 O A:HOH581 3.6 38.1 1.0 PG A:DGT401 3.6 31.9 1.0 CG A:ASP105 3.6 26.7 1.0 PA A:DGT401 3.6 26.4 1.0 CA A:CA402 3.8 40.7 1.0 O3A A:DGT401 3.9 26.3 1.0 OD1 A:ASP7 3.9 32.4 1.0 O3B A:DGT401 4.0 29.7 1.0 N A:PHE8 4.0 21.2 1.0 C5' A:DGT401 4.1 23.4 1.0 NZ A:LYS159 4.1 28.2 1.0 O1G A:DGT401 4.1 29.5 1.0 C A:ASP7 4.2 21.8 1.0 OD1 A:ASP105 4.3 30.7 1.0 CA A:PHE8 4.3 21.4 1.0 O5' A:DGT401 4.3 21.9 1.0 N A:TYR10 4.5 19.8 1.0 N A:ASP9 4.5 22.1 1.0 CA A:ASP9 4.5 21.5 1.0 CB A:ASP7 4.5 22.8 1.0 O A:ASP7 4.6 21.3 1.0 CB A:ASP105 4.6 26.2 1.0 CE A:LYS159 4.6 31.7 1.0 C A:ASP9 4.7 19.8 1.0 CA A:ASP7 4.8 21.6 1.0 O2B A:DGT401 4.8 24.9 1.0 N A:PHE11 4.8 19.0 1.0 O3G A:DGT401 4.8 30.1 1.0 O A:ASP105 4.8 22.0 1.0 CB A:PHE8 4.8 21.2 1.0 O A:HOH547 4.8 32.8 1.0 O2A A:DGT401 4.9 29.5 1.0

Calcium binding site 3 out of 3 in the Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structures of Mutant DPO4 Dna Polymerases with 8-Oxog Containing Dna Template-Primer Constructs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:43.3 occ:1.00 O A:ALA181 2.5 38.0 1.0 O A:HOH594 2.5 46.5 1.0 O P:HOH109 2.5 35.3 1.0 O P:HOH107 2.6 35.9 1.0 O A:ILE186 2.6 27.8 1.0 O A:HOH621 2.7 38.3 1.0 O A:HOH633 2.8 47.7 1.0 C A:ALA181 3.6 38.9 1.0 C A:ILE186 3.9 29.8 1.0 OP1 P:DC13 4.3 38.4 1.0 CA A:ALA181 4.3 39.4 1.0 OP2 P:DC13 4.4 39.3 1.0 CA A:GLY187 4.4 33.0 1.0 CB A:ALA181 4.5 39.2 1.0 N A:ASP182 4.5 39.2 1.0 O A:VAL183 4.6 27.2 1.0 N A:GLY187 4.6 30.9 1.0 CA A:ASP182 4.7 37.5 1.0 P P:DC13 4.9 34.0 1.0 C A:GLY187 4.9 34.0 1.0 CA A:ILE186 4.9 28.7 1.0 CB A:ILE186 4.9 30.7 1.0

R.L.Eoff, A.Irimia, K.C.Angel, M.Egli, F.P.Guengerich. Hydrogen Bonding of 7,8-Dihydro-8-Oxodeoxyguanosine with A Charged Residue in the Little Finger Domain Determines Miscoding Events in Sulfolobus Solfataricus Dna Polymerase DPO4. J.Biol.Chem. V. 282 19831 2007.
ISSN: ISSN 0021-9258
PubMed: 17468100
DOI: 10.1074/JBC.M702290200