Calcium in PDB 4f4w: Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #1

All present enzymatic activity of Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #1:
2.7.7.7;

The structure of Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #1, PDB code: 4f4w 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)	28.01 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.820, 99.655, 101.625, 90.00, 90.16, 90.00
R / Rfree (%)	18.7 / 21.9

The binding sites of Calcium atom in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #1 (pdb code 4f4w). 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 #1, PDB code: 4f4w:
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 #1


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 #1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:19.4 occ:1.00 OD2 A:ASP7 2.2 27.1 1.0 O3G A:DCP401 2.4 19.3 1.0 O A:PHE8 2.4 17.4 1.0 OD2 A:ASP105 2.4 17.6 1.0 O1B A:DCP401 2.4 18.7 1.0 O2A A:DCP401 2.5 11.2 1.0 O A:HOH651 3.3 40.4 1.0 PB A:DCP401 3.4 17.4 1.0 CG A:ASP7 3.4 31.9 1.0 HZ2 A:LYS160 3.5 35.8 1.0 CA A:CA403 3.5 30.2 1.0 CG A:ASP105 3.5 24.5 1.0 C A:PHE8 3.5 18.2 1.0 PG A:DCP401 3.6 21.3 1.0 PA A:DCP401 3.6 17.3 1.0 O3A A:DCP401 3.7 18.6 1.0 H A:PHE8 3.8 21.1 1.0 N A:PHE8 3.9 17.7 1.0 O3B A:DCP401 3.9 20.6 1.0 OD1 A:ASP105 4.0 28.2 1.0 H A:PHE11 4.0 17.0 1.0 HZ3 A:LYS160 4.0 35.8 1.0 OD1 A:ASP7 4.0 32.4 1.0 HA A:ASP9 4.0 22.5 1.0 HB2 A:PHE11 4.1 13.8 1.0 NZ A:LYS160 4.1 29.9 1.0 H A:TYR10 4.1 18.4 1.0 C5' A:DCP401 4.2 16.7 1.0 O1G A:DCP401 4.2 17.6 1.0 C A:ASP7 4.2 14.1 1.0 CA A:PHE8 4.3 15.9 1.0 HE2 A:LYS160 4.3 49.8 1.0 HB2 A:PHE8 4.3 19.4 1.0 O5' A:DCP401 4.4 19.2 1.0 N A:TYR10 4.5 15.3 1.0 N A:ASP9 4.5 15.2 1.0 CB A:ASP7 4.6 18.6 1.0 O A:HOH510 4.6 27.8 1.0 CA A:ASP9 4.6 18.8 1.0 HB2 A:ASP105 4.6 28.9 1.0 O A:ASP7 4.7 16.9 1.0 CB A:ASP105 4.7 24.1 1.0 O2B A:DCP401 4.7 15.2 1.0 HA A:ASP7 4.7 20.6 1.0 C A:ASP9 4.7 15.0 1.0 HB3 A:ASP7 4.7 22.2 1.0 N A:PHE11 4.7 14.2 1.0 O1A A:DCP401 4.7 18.8 1.0 CA A:ASP7 4.8 17.2 1.0 CE A:LYS160 4.8 41.6 1.0 O2G A:DCP401 4.8 21.9 1.0 HZ1 A:LYS160 4.8 35.8 1.0 O A:ASP105 4.9 17.3 1.0 CB A:PHE11 4.9 11.6 1.0 CB A:PHE8 4.9 16.2 1.0 HB3 A:PHE11 4.9 13.8 1.0 HA A:TYR10 4.9 18.4 1.0

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


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 #1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:30.2 occ:1.00 O A:HOH510 2.1 27.8 1.0 O2A A:DCP401 2.4 11.2 1.0 OE1 A:GLU106 2.4 37.0 1.0 O3' P:DC13 2.8 34.3 1.0 OD1 A:ASP7 2.8 32.4 1.0 OD1 A:ASP105 2.8 28.2 1.0 OD2 A:ASP7 3.1 27.1 1.0 CG A:ASP7 3.2 31.9 1.0 HB3 A:GLU106 3.5 31.1 1.0 CA A:CA402 3.5 19.4 1.0 CG A:ASP105 3.6 24.5 1.0 OD2 A:ASP105 3.6 17.6 1.0 CD A:GLU106 3.6 32.9 1.0 PA A:DCP401 3.6 17.3 1.0 C3' P:DC13 3.8 39.4 1.0 HZ3 A:LYS160 4.0 35.8 1.0 O1A A:DCP401 4.0 18.8 1.0 O A:HOH685 4.0 39.3 1.0 O5' A:DCP401 4.1 19.2 1.0 HG2 A:GLU106 4.2 25.7 1.0 CG A:GLU106 4.3 21.5 1.0 C5' A:DCP401 4.3 16.7 1.0 CB A:GLU106 4.3 25.9 1.0 HZ2 A:LYS160 4.5 35.8 1.0 O A:HOH516 4.5 35.6 1.0 OE2 A:GLU106 4.5 27.8 1.0 OG A:SER103 4.6 25.9 1.0 CB A:ASP7 4.6 18.6 1.0 NZ A:LYS160 4.7 29.9 1.0 O3G A:DCP401 4.7 19.3 1.0 HA A:ASP7 4.7 20.6 1.0 O A:ASP105 4.7 17.3 1.0 HZ3 A:LYS153 4.7 48.5 1.0 HB2 A:GLU106 4.8 31.1 1.0 C4' P:DC13 4.8 35.7 1.0 HZ A:PHE5 4.8 25.7 1.0 C5' P:DC13 4.9 34.9 1.0 HB2 A:ASP7 4.9 22.2 1.0 O3A A:DCP401 4.9 18.6 1.0 HG A:SER103 4.9 31.0 1.0 C A:ASP105 4.9 19.2 1.0 C2' P:DC13 4.9 27.8 1.0

Calcium binding site 3 out of 4 in the Y-Family Dna Polymerase Chimera Dbh-DPO4-DPO4 #1


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 #1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:18.3 occ:1.00 OD1 B:ASP7 2.2 27.7 1.0 OD2 B:ASP105 2.3 16.0 1.0 O3G B:DCP401 2.3 19.3 1.0 O B:PHE8 2.4 18.7 1.0 O1B B:DCP401 2.4 16.8 1.0 O2A B:DCP401 2.5 11.1 1.0 O B:HOH612 3.1 42.4 1.0 CG B:ASP105 3.4 23.3 1.0 PB B:DCP401 3.4 16.6 1.0 CG B:ASP7 3.4 29.1 1.0 HZ1 B:LYS160 3.5 39.5 1.0 CA B:CA403 3.5 29.4 1.0 C B:PHE8 3.5 17.1 1.0 PG B:DCP401 3.6 21.0 1.0 PA B:DCP401 3.6 17.7 1.0 O3A B:DCP401 3.7 18.6 1.0 OD1 B:ASP105 3.7 25.9 1.0 H B:PHE8 3.8 20.7 1.0 N B:PHE8 3.9 17.3 1.0 O3B B:DCP401 3.9 19.8 1.0 OD2 B:ASP7 4.0 32.7 1.0 HA B:ASP9 4.0 19.9 1.0 H B:PHE11 4.0 19.2 1.0 HB2 B:PHE11 4.0 14.8 1.0 HZ2 B:LYS160 4.1 39.5 1.0 NZ B:LYS160 4.2 33.0 1.0 C5' B:DCP401 4.2 15.9 1.0 O1G B:DCP401 4.2 16.2 1.0 H B:TYR10 4.2 19.0 1.0 C B:ASP7 4.2 17.6 1.0 HE2 B:LYS160 4.3 46.4 1.0 CA B:PHE8 4.3 14.0 1.0 HB2 B:PHE8 4.4 22.5 1.0 O5' B:DCP401 4.4 17.6 1.0 N B:TYR10 4.5 15.9 1.0 N B:ASP9 4.5 16.6 1.0 CA B:ASP9 4.5 16.7 1.0 CB B:ASP7 4.6 21.6 1.0 O B:HOH512 4.6 31.5 1.0 HB2 B:ASP105 4.6 29.4 1.0 CB B:ASP105 4.6 24.5 1.0 O B:ASP7 4.7 19.5 1.0 C B:ASP9 4.7 16.2 1.0 O2B B:DCP401 4.7 14.7 1.0 HA B:ASP7 4.7 21.8 1.0 O1A B:DCP401 4.7 21.0 1.0 N B:PHE11 4.7 16.1 1.0 CE B:LYS160 4.8 38.7 1.0 HB3 B:ASP7 4.8 25.9 1.0 CA B:ASP7 4.8 18.2 1.0 O2G B:DCP401 4.8 25.3 1.0 O B:ASP105 4.9 16.2 1.0 HZ3 B:LYS160 4.9 39.5 1.0 CB B:PHE11 4.9 12.4 1.0 CB B:PHE8 4.9 18.8 1.0 HB3 B:PHE11 4.9 14.8 1.0 HA B:TYR10 4.9 18.8 1.0 HD3 B:LYS160 5.0 53.1 1.0

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


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 #1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:29.4 occ:1.00 O B:HOH512 2.1 31.5 1.0 O2A B:DCP401 2.4 11.1 1.0 OE1 B:GLU106 2.4 38.1 1.0 OD1 B:ASP105 2.6 25.9 1.0 O3' E:DC13 2.7 31.3 1.0 OD2 B:ASP7 2.9 32.7 1.0 OD1 B:ASP7 3.1 27.7 1.0 CG B:ASP7 3.3 29.1 1.0 HB3 B:GLU106 3.4 30.1 1.0 CG B:ASP105 3.5 23.3 1.0 CA B:CA402 3.5 18.3 1.0 CD B:GLU106 3.6 33.1 1.0 PA B:DCP401 3.6 17.7 1.0 OD2 B:ASP105 3.6 16.0 1.0 C3' E:DC13 3.8 36.6 1.0 HG B:SER103 3.9 29.6 1.0 O1A B:DCP401 4.0 21.0 1.0 HZ2 B:LYS160 4.0 39.5 1.0 O5' B:DCP401 4.1 17.6 1.0 CB B:GLU106 4.2 25.1 1.0 HG2 B:GLU106 4.2 28.3 1.0 CG B:GLU106 4.3 23.7 1.0 C5' B:DCP401 4.3 15.9 1.0 OE2 B:GLU106 4.5 26.6 1.0 HZ1 B:LYS160 4.5 39.5 1.0 OG B:SER103 4.6 24.7 1.0 O B:HOH530 4.6 37.7 1.0 CB B:ASP7 4.7 21.6 1.0 HZ3 B:LYS153 4.7 41.4 1.0 O B:ASP105 4.7 16.2 1.0 HB2 B:GLU106 4.7 30.1 1.0 HA B:ASP7 4.7 21.8 1.0 NZ B:LYS160 4.7 33.0 1.0 C4' E:DC13 4.8 34.3 1.0 O3G B:DCP401 4.8 19.3 1.0 HZ B:PHE5 4.8 30.7 1.0 C B:ASP105 4.8 19.2 1.0 HB2 B:ASP7 4.9 25.9 1.0 C2' E:DC13 4.9 27.5 1.0 C5' E:DC13 4.9 34.1 1.0 O3A B:DCP401 4.9 18.6 1.0 CB B:ASP105 4.9 24.5 1.0 HZ1 B:LYS153 4.9 41.4 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