Calcium in PDB 2uvw: 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: 2uvw 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)	30.81 / 2.09
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.778, 103.728, 52.915, 90.00, 90.00, 90.00
R / Rfree (%)	24.9 / 27.4

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 2uvw). 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: 2uvw:
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:66.8 occ:1.00 O1A A:DGT1000 2.5 19.6 1.0 O A:HOH2071 2.6 28.9 1.0 OD1 A:ASP105 2.8 30.0 1.0 OD2 A:ASP105 3.1 28.6 1.0 CG A:GLU106 3.3 40.6 1.0 C3' P:DA14 3.3 39.8 1.0 CG A:ASP105 3.3 29.2 1.0 CD A:GLU106 3.3 40.5 1.0 OD2 A:ASP7 3.3 30.3 1.0 O A:HOH2089 3.4 55.2 1.0 OE2 A:GLU106 3.4 45.2 1.0 O3' P:DA14 3.5 41.8 1.0 CA A:CA3001 3.6 29.4 1.0 O5' P:DA14 3.8 45.8 1.0 PA A:DGT1000 3.8 28.5 1.0 OD1 A:ASP7 3.8 35.0 1.0 CG A:ASP7 3.8 34.0 1.0 C5' P:DA14 3.9 42.0 1.0 OE1 A:GLU106 3.9 46.4 1.0 O5' A:DGT1000 3.9 26.7 1.0 C5' A:DGT1000 4.0 27.3 1.0 C4' P:DA14 4.1 41.9 1.0 O2A A:DGT1000 4.1 28.7 1.0 OP1 P:DA14 4.3 47.8 1.0 OG A:SER103 4.3 29.2 1.0 C2' P:DA14 4.4 39.0 1.0 O A:ASP105 4.5 29.6 1.0 CB A:GLU106 4.6 35.4 1.0 P P:DA14 4.7 47.5 1.0 CB A:ASP105 4.7 28.2 1.0 C A:ASP105 4.7 29.5 1.0 O2G A:DGT1000 4.8 32.2 1.0 NZ A:LYS159 4.9 41.5 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:29.4 occ:1.00 OD2 A:ASP7 2.3 30.3 1.0 O1A A:DGT1000 2.4 19.6 1.0 OD2 A:ASP105 2.4 28.6 1.0 O A:PHE8 2.4 27.4 1.0 O2B A:DGT1000 2.4 27.3 1.0 O2G A:DGT1000 2.4 32.2 1.0 CG A:ASP7 3.4 34.0 1.0 C A:PHE8 3.5 28.1 1.0 CA A:CA3000 3.6 66.8 1.0 CG A:ASP105 3.6 29.2 1.0 PB A:DGT1000 3.6 27.2 1.0 PG A:DGT1000 3.7 30.2 1.0 PA A:DGT1000 3.8 28.5 1.0 O A:HOH2011 3.9 38.2 1.0 OD1 A:ASP7 3.9 35.0 1.0 N A:PHE8 3.9 28.6 1.0 NZ A:LYS159 4.0 41.5 1.0 C5' A:DGT1000 4.0 27.3 1.0 O3G A:DGT1000 4.1 32.8 1.0 O3A A:DGT1000 4.1 27.4 1.0 O3B A:DGT1000 4.1 28.9 1.0 C A:ASP7 4.2 29.7 1.0 CA A:PHE8 4.2 26.6 1.0 OD1 A:ASP105 4.3 30.0 1.0 O5' A:DGT1000 4.4 26.7 1.0 CE A:LYS159 4.5 45.3 1.0 N A:ASP9 4.5 29.6 1.0 O A:HOH2089 4.5 55.2 1.0 CB A:ASP7 4.5 30.6 1.0 N A:TYR10 4.6 23.5 1.0 O A:ASP7 4.6 30.1 1.0 CA A:ASP9 4.6 27.9 1.0 CB A:ASP105 4.6 28.2 1.0 O A:ASP105 4.7 29.6 1.0 CA A:ASP7 4.7 30.1 1.0 C A:ASP9 4.8 26.7 1.0 CB A:PHE8 4.8 24.6 1.0 N A:PHE11 4.9 25.9 1.0 O1B A:DGT1000 4.9 27.1 1.0 O1G A:DGT1000 5.0 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:Ca3002 b:41.5 occ:1.00 O A:ALA181 2.4 38.2 1.0 O A:HOH2099 2.4 37.5 1.0 O A:HOH2101 2.5 38.0 1.0 O P:HOH2026 2.6 38.0 1.0 O A:ILE186 2.6 29.2 1.0 O P:HOH2027 2.6 35.3 1.0 C A:ALA181 3.5 39.2 1.0 C A:ILE186 3.8 30.2 1.0 O P:HOH2007 4.0 61.3 1.0 CA A:ALA181 4.2 38.3 1.0 CA A:GLY187 4.3 31.4 1.0 CB A:ALA181 4.3 39.4 1.0 OP1 P:DC13 4.4 36.6 1.0 N A:ASP182 4.5 39.2 1.0 OP2 P:DC13 4.6 36.6 1.0 N A:GLY187 4.6 29.7 1.0 CA A:ASP182 4.7 37.6 1.0 C A:GLY187 4.7 33.0 1.0 O A:VAL183 4.8 30.9 1.0 CA A:ILE186 4.9 28.7 1.0 CB A:ILE186 4.9 29.6 1.0 O A:GLY187 5.0 33.9 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