Calcium in PDB 4nlg: Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh

All present enzymatic activity of Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh:
2.7.7.7;

The structure of Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh, PDB code: 4nlg was solved by P.Mukherjee, R.C.Wilson, J.D.Pata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.70 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.193, 103.067, 53.049, 90.00, 105.39, 90.00
R / Rfree (%)	17.4 / 23.1

The binding sites of Calcium atom in the Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh (pdb code 4nlg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh, PDB code: 4nlg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:51.4 occ:1.00 O A:HOH508 2.4 44.9 1.0 OD1 A:ASP105 2.5 36.8 1.0 OD1 A:ASP7 2.5 57.1 1.0 O2A A:DCP403 2.6 50.3 1.0 O3' P:DG13 2.6 61.0 1.0 OD2 A:ASP7 2.7 55.7 1.0 CG A:ASP7 2.9 53.5 1.0 OE1 A:GLU106 3.2 80.6 1.0 CD A:GLU106 3.3 75.7 1.0 CG A:ASP105 3.5 38.3 1.0 OE2 A:GLU106 3.5 84.1 1.0 CA A:CA402 3.6 42.0 1.0 PA A:DCP403 3.7 45.2 1.0 C3' P:DG13 3.7 69.7 1.0 OD2 A:ASP105 3.7 41.6 1.0 O1A A:DCP403 3.9 44.0 1.0 CG A:GLU106 4.0 60.3 1.0 CB A:GLU106 4.2 54.3 1.0 O5' A:DCP403 4.2 46.5 1.0 CB A:ASP7 4.4 41.0 1.0 NZ A:LYS160 4.4 50.2 1.0 C5' A:DCP403 4.5 38.6 1.0 O A:ASP105 4.6 44.8 1.0 O3G A:DCP403 4.6 69.5 1.0 C4' P:DG13 4.7 68.8 1.0 OG A:SER103 4.8 49.2 1.0 C2' P:DG13 4.8 76.1 1.0 C A:ASP105 4.8 38.8 1.0 CB A:ASP105 4.8 36.3 1.0 NZ A:LYS153 4.9 58.3 1.0

Calcium binding site 2 out of 2 in the Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Y-Family Dna Polymerase Chimera Dbh-DPO4(243-245)-Dbh within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:42.0 occ:1.00 O3G A:DCP403 2.2 69.5 1.0 O A:PHE8 2.2 35.7 1.0 OD2 A:ASP105 2.3 41.6 1.0 O2A A:DCP403 2.4 50.3 1.0 O2B A:DCP403 2.4 49.5 1.0 OD1 A:ASP7 2.5 57.1 1.0 CG A:ASP7 3.3 53.5 1.0 CG A:ASP105 3.4 38.3 1.0 PB A:DCP403 3.4 41.1 1.0 C A:PHE8 3.4 40.7 1.0 PG A:DCP403 3.4 45.5 1.0 CA A:CA401 3.6 51.4 1.0 PA A:DCP403 3.6 45.2 1.0 OD1 A:ASP105 3.7 36.8 1.0 OD2 A:ASP7 3.8 55.7 1.0 O3B A:DCP403 3.8 43.0 1.0 O3A A:DCP403 3.8 64.6 1.0 N A:PHE8 3.9 40.6 1.0 NZ A:LYS160 4.0 50.2 1.0 O1G A:DCP403 4.0 45.3 1.0 C A:ASP7 4.2 43.9 1.0 CA A:PHE8 4.3 42.0 1.0 CB A:ASP7 4.4 41.0 1.0 N A:ASP9 4.4 38.1 1.0 C5' A:DCP403 4.4 38.6 1.0 CA A:ASP9 4.5 39.5 1.0 O5' A:DCP403 4.5 46.5 1.0 N A:TYR10 4.6 40.1 1.0 O1B A:DCP403 4.6 44.7 1.0 O1A A:DCP403 4.6 44.0 1.0 CA A:ASP7 4.7 40.1 1.0 CB A:ASP105 4.7 36.3 1.0 O2G A:DCP403 4.7 52.4 1.0 O A:ASP7 4.7 45.1 1.0 C A:ASP9 4.7 37.5 1.0 O A:ASP105 4.8 44.8 1.0 N A:PHE11 4.8 38.1 1.0 CE A:LYS160 4.9 48.7 1.0 O A:HOH508 4.9 44.9 1.0 CB A:PHE8 4.9 38.5 1.0 CB A:PHE11 4.9 37.5 1.0

P.Mukherjee, R.C.Wilson, I.Lahiri, J.D.Pata. Three Residues of the Interdomain Linker Determine the Conformation and Single-Base Deletion Fidelity of Y-Family Translesion Polymerases. J.Biol.Chem. V. 289 6323 2014.
ISSN: ISSN 0021-9258
PubMed: 24415763
DOI: 10.1074/JBC.M113.537860