Calcium in PDB 2uvr: 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: 2uvr 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)	46.07 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.719, 104.197, 52.723, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 26.5

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 2uvr). 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: 2uvr:
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:Ca3000 b:56.4 occ:1.00 O A:HOH2015 2.7 37.3 1.0 OE2 A:GLU106 2.8 54.2 1.0 OD2 A:ASP7 2.9 41.4 1.0 CD A:GLU106 3.0 51.9 1.0 CG A:GLU106 3.0 48.3 1.0 O1A A:DGT1000 3.0 37.1 1.0 OD1 A:ASP105 3.1 39.5 1.0 OD1 A:ASP7 3.3 41.8 1.0 O A:HOH2045 3.3 44.7 1.0 CG A:ASP7 3.3 39.2 1.0 OD2 A:ASP105 3.4 40.0 1.0 CG A:ASP105 3.6 39.2 1.0 O5' P:DC14 3.7 47.5 1.0 C5' P:DC14 3.7 46.6 1.0 OE1 A:GLU106 3.9 53.2 1.0 C3' P:DC14 3.9 48.3 1.0 CA A:CA3001 4.2 34.4 1.0 PA A:DGT1000 4.2 37.3 1.0 OP1 P:DC14 4.2 46.9 1.0 O2A A:DGT1000 4.4 42.3 1.0 C4' P:DC14 4.4 47.6 1.0 O A:ASP105 4.4 42.1 1.0 O5' A:DGT1000 4.5 39.2 1.0 C5' A:DGT1000 4.5 37.5 1.0 CB A:GLU106 4.5 43.9 1.0 P P:DC14 4.6 48.5 1.0 OG A:SER103 4.6 45.4 1.0 O3' P:DC14 4.6 49.0 1.0 NZ A:LYS152 4.6 33.7 1.0 CB A:ASP7 4.7 39.0 1.0 C A:ASP105 4.9 41.4 1.0 C2' P:DC14 5.0 47.4 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:Ca3001 b:34.4 occ:1.00 O A:PHE8 2.1 32.3 1.0 OD2 A:ASP105 2.5 40.0 1.0 O3B A:DGT1000 2.7 45.3 1.0 OD2 A:ASP7 2.7 41.4 1.0 O1A A:DGT1000 2.7 37.1 1.0 O2G A:DGT1000 3.1 49.7 1.0 C A:PHE8 3.3 32.3 1.0 O2B A:DGT1000 3.4 40.1 1.0 PG A:DGT1000 3.5 49.6 1.0 CG A:ASP7 3.5 39.2 1.0 O A:HOH2046 3.5 73.7 1.0 PB A:DGT1000 3.6 39.3 1.0 CG A:ASP105 3.8 39.2 1.0 O A:ASP7 3.8 37.3 1.0 O A:HOH2045 3.9 44.7 1.0 C A:ASP7 3.9 37.0 1.0 OD1 A:ASP7 4.0 41.8 1.0 PA A:DGT1000 4.0 37.3 1.0 N A:PHE8 4.1 34.6 1.0 CA A:CA3000 4.2 56.4 1.0 CA A:ASP9 4.2 32.9 1.0 CA A:PHE8 4.2 31.9 1.0 N A:TYR10 4.2 34.3 1.0 N A:ASP9 4.2 32.7 1.0 O3G A:DGT1000 4.2 49.1 1.0 O3A A:DGT1000 4.3 39.9 1.0 C A:ASP9 4.4 33.3 1.0 CB A:ASP7 4.5 39.0 1.0 OD1 A:ASP105 4.5 39.5 1.0 C5' A:DGT1000 4.6 37.5 1.0 CA A:ASP7 4.6 38.2 1.0 CB A:ASP105 4.7 37.6 1.0 CB A:PHE8 4.7 28.4 1.0 N A:PHE11 4.8 33.6 1.0 O1G A:DGT1000 4.8 48.5 1.0 O5' A:DGT1000 4.9 39.2 1.0 O A:ASP105 4.9 42.1 1.0 O1B A:DGT1000 4.9 39.6 1.0 CA A:TYR10 5.0 35.2 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:Ca3002 b:43.4 occ:1.00 O A:HOH2028 2.1 57.0 1.0 O P:HOH2011 2.2 48.5 1.0 O A:HOH2027 2.5 29.4 1.0 O A:ILE186 2.6 45.6 1.0 O A:ALA181 2.8 50.0 1.0 O P:HOH2012 2.9 48.7 1.0 C A:ILE186 3.6 45.3 1.0 C A:ALA181 3.7 49.6 1.0 OP1 P:DC13 4.2 39.9 1.0 OP2 P:DC13 4.3 38.7 1.0 N A:GLY187 4.4 46.8 1.0 CA A:GLY187 4.4 47.0 1.0 N A:ASP182 4.4 47.9 1.0 CA A:ASP182 4.4 47.1 1.0 CB A:ILE186 4.4 43.2 1.0 CA A:ILE186 4.4 43.9 1.0 CA A:ALA181 4.5 50.1 1.0 N A:ILE186 4.7 42.9 1.0 CB A:ALA181 4.8 50.4 1.0 P P:DC13 4.8 39.7 1.0 CG2 A:ILE186 4.8 44.0 1.0 C A:ASP182 4.8 46.6 1.0 O A:VAL183 4.8 43.4 1.0 C A:GLY187 4.8 47.8 1.0 O A:GLY187 4.9 49.2 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