Calcium in PDB 4f4x: Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2

All present enzymatic activity of Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2:
2.7.7.7;

The structure of Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2, PDB code: 4f4x was solved by J.D.Pata, R.C.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.74 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.122, 102.306, 52.879, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 25

The binding sites of Calcium atom in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2 (pdb code 4f4x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2, PDB code: 4f4x:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2


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-DPO4 #2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:61.9 occ:1.00 OP2 P:DC10 2.8 34.6 1.0 OD2 A:ASP295 3.0 56.1 1.0 OD1 A:ASP295 3.1 45.0 1.0 CG A:ASP295 3.4 48.5 1.0 P P:DC10 4.0 50.3 1.0 NH2 A:ARG329 4.4 43.6 1.0 C3' P:DT9 4.5 42.6 1.0 OP1 P:DC10 4.6 58.2 1.0 O P:HOH218 4.6 36.8 1.0 O3' P:DT9 4.6 45.1 1.0 O A:ILE296 4.7 32.5 1.0 OP1 P:DT9 4.7 51.3 1.0 CB A:ASP295 4.8 39.2 1.0 O P:HOH221 5.0 49.2 1.0

Calcium binding site 2 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2


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-DPO4 #2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:26.9 occ:1.00 O A:PHE8 2.5 23.3 1.0 OD2 A:ASP7 2.5 29.3 1.0 O1B A:DCP404 2.6 20.6 1.0 O3G A:DCP404 2.6 23.1 1.0 O2A A:DCP404 2.6 21.1 1.0 OD2 A:ASP105 2.7 30.6 1.0 OD1 A:ASP105 2.8 44.3 1.0 CG A:ASP105 3.1 40.1 1.0 PB A:DCP404 3.5 22.4 1.0 CA A:CA403 3.6 37.7 1.0 CG A:ASP7 3.6 33.0 1.0 C A:PHE8 3.6 33.9 1.0 PG A:DCP404 3.7 28.6 1.0 PA A:DCP404 3.7 28.3 1.0 NZ A:LYS160 3.9 49.1 1.0 N A:PHE8 3.9 22.0 1.0 O3A A:DCP404 3.9 29.4 1.0 O3B A:DCP404 4.0 26.2 1.0 OD1 A:ASP7 4.1 39.3 1.0 C5' A:DCP404 4.2 21.8 1.0 O1G A:DCP404 4.2 26.0 1.0 CA A:PHE8 4.3 27.4 1.0 C A:ASP7 4.3 24.3 1.0 O5' A:DCP404 4.4 29.4 1.0 CB A:ASP105 4.5 36.9 1.0 N A:TYR10 4.6 21.2 1.0 N A:ASP9 4.6 24.7 1.0 CA A:ASP9 4.7 24.7 1.0 O1A A:DCP404 4.8 28.0 1.0 CB A:ASP7 4.8 24.9 1.0 C A:ASP9 4.8 22.3 1.0 N A:PHE11 4.8 26.3 1.0 CB A:PHE8 4.8 21.6 1.0 O2B A:DCP404 4.8 21.7 1.0 CE A:LYS160 4.8 57.5 1.0 O A:ASP7 4.8 29.8 1.0 O A:HOH537 4.8 32.7 1.0 CA A:ASP7 4.9 21.2 1.0 O2G A:DCP404 4.9 34.4 1.0 O A:ASP105 4.9 22.6 1.0 CB A:PHE11 4.9 19.9 1.0

Calcium binding site 3 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:37.7 occ:1.00 O A:HOH537 2.3 32.7 1.0 OP1 P:DC14 2.5 32.2 1.0 OE1 A:GLU106 2.6 34.4 1.0 O2A A:DCP404 2.6 21.1 1.0 OD1 A:ASP105 2.7 44.3 1.0 OD1 A:ASP7 2.8 39.3 1.0 CG A:ASP7 3.4 33.0 1.0 CG A:ASP105 3.5 40.1 1.0 OD2 A:ASP7 3.6 29.3 1.0 CA A:CA402 3.6 26.9 1.0 P P:DC14 3.8 40.1 1.0 CD A:GLU106 3.8 36.5 1.0 PA A:DCP404 3.9 28.3 1.0 O A:HOH529 4.0 40.0 1.0 O1A A:DCP404 4.0 28.0 1.0 C5' P:DC14 4.2 43.9 1.0 CB A:ASP105 4.2 36.9 1.0 O5' P:DC14 4.3 46.2 1.0 OD2 A:ASP105 4.3 30.6 1.0 O5' A:DCP404 4.3 29.4 1.0 CB A:GLU106 4.4 27.8 1.0 OP2 P:DC14 4.5 50.2 1.0 CG A:GLU106 4.5 27.7 1.0 CB A:ASP7 4.7 24.9 1.0 C5' A:DCP404 4.7 21.8 1.0 OE2 A:GLU106 4.7 31.0 1.0 NZ A:LYS153 4.8 47.0 1.0 O3G A:DCP404 4.8 23.1 1.0 O A:ASP105 4.9 22.6 1.0 O3' P:DG13 4.9 45.1 1.0 C A:ASP105 5.0 19.9 1.0

Calcium binding site 4 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #2 within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca101 b:45.1 occ:1.00 O P:HOH204 2.6 30.8 1.0 O T:HOH130 2.6 30.6 1.0 O P:HOH214 2.7 35.2 1.0 O P:HOH205 2.8 29.6 1.0 O2 P:DC14 4.3 32.1 1.0 O4' P:DG12 4.4 47.6 1.0 N2 P:DG11 4.4 30.2 1.0 O P:HOH223 4.5 45.3 1.0 O P:HOH220 4.5 47.3 1.0 C4' P:DG12 4.5 45.1 1.0 N3 P:DG11 4.5 30.5 1.0 C5' P:DG12 4.5 38.5 1.0 O4' T:DA11 4.6 46.6 1.0 N3 T:DG10 4.8 31.0 1.0 N3 P:DC14 4.9 33.1 1.0 C2 P:DC14 4.9 32.7 1.0 O P:HOH222 4.9 32.8 1.0 O A:HOH550 4.9 50.4 1.0 C4' T:DA11 4.9 52.0 1.0 C5' T:DA11 5.0 49.7 1.0 C2 P:DG11 5.0 32.1 1.0

R.C.Wilson, M.A.Jackson, J.D.Pata. Y-Family Polymerase Conformation Is A Major Determinant of Fidelity and Translesion Specificity. Structure V. 21 20 2013.
ISSN: ISSN 0969-2126
PubMed: 23245850
DOI: 10.1016/J.STR.2012.11.005