Calcium in PDB 4f4z: Y-Family Dna Polymerase Chimera DPO4-DPO4-Dbh

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

The structure of Y-Family Dna Polymerase Chimera DPO4-DPO4-Dbh, PDB code: 4f4z 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)	27.07 / 2.31
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.966, 51.196, 98.842, 75.60, 82.97, 70.14
R / Rfree (%)	18.5 / 26

The binding sites of Calcium atom in the Y-Family Dna Polymerase Chimera DPO4-DPO4-Dbh (pdb code 4f4z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Y-Family Dna Polymerase Chimera DPO4-DPO4-Dbh, PDB code: 4f4z:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Y-Family Dna Polymerase Chimera DPO4-DPO4-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 DPO4-DPO4-Dbh within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:0.2 occ:1.00 OE2 B:GLU106 3.1 67.8 1.0 O B:HOH525 3.1 47.6 1.0 OD1 B:ASP7 3.3 58.0 1.0 OD2 B:ASP7 3.5 66.7 1.0 O5' C:DG13 3.6 77.5 1.0 C5' C:DG13 3.6 82.0 1.0 CG B:ASP7 3.8 51.6 1.0 OD2 B:ASP105 3.9 61.0 1.0 NZ B:LYS159 3.9 46.9 1.0 OP1 C:DG13 3.9 79.0 1.0 CD B:GLU106 4.0 60.5 1.0 CG B:GLU106 4.2 49.2 1.0 OD1 B:ASP105 4.2 73.0 1.0 CG B:ASP105 4.2 62.3 1.0 P C:DG13 4.4 76.7 1.0 C4' C:DG13 4.6 89.5 1.0 C3' C:DG13 4.7 92.4 1.0 CE B:LYS159 4.7 57.2 1.0

Calcium binding site 2 out of 3 in the Y-Family Dna Polymerase Chimera DPO4-DPO4-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 DPO4-DPO4-Dbh within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:88.0 occ:1.00 O B:HOH541 3.0 55.0 1.0 O B:ALA181 3.2 70.7 1.0 O B:VAL183 3.2 58.1 1.0 OP2 C:DC12 3.2 57.5 1.0 O B:ILE186 3.3 58.2 1.0 C B:VAL183 3.8 52.0 1.0 OP1 C:DC12 4.1 58.4 1.0 C B:ASP182 4.1 59.4 1.0 P C:DC12 4.1 51.0 1.0 C B:ALA181 4.2 65.3 1.0 CA B:PRO184 4.2 48.7 1.0 O B:ASP182 4.2 60.0 1.0 N B:PRO184 4.3 51.7 1.0 C B:ILE186 4.3 49.3 1.0 N B:VAL183 4.3 34.8 1.0 CA B:ASP182 4.3 52.2 1.0 N B:ILE186 4.5 45.3 1.0 N B:GLY185 4.6 49.1 1.0 CA B:VAL183 4.7 43.7 1.0 N B:ASP182 4.7 62.2 1.0 C B:PRO184 4.8 46.9 1.0 O5' C:DC12 4.9 47.6 1.0 CA B:ILE186 4.9 53.8 1.0

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


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 DPO4-DPO4-Dbh within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:91.9 occ:1.00 OD2 A:ASP7 3.0 60.4 1.0 OP1 P:DG13 3.1 73.3 1.0 OE2 A:GLU106 3.2 76.9 1.0 O A:HOH522 3.4 49.9 1.0 OD2 A:ASP105 3.5 63.3 1.0 CG A:ASP7 3.9 57.6 1.0 OD1 A:ASP7 4.0 56.7 1.0 O A:HOH518 4.0 58.7 1.0 NZ A:LYS159 4.1 83.0 1.0 P P:DG13 4.2 79.0 1.0 C5' P:DG13 4.2 98.4 1.0 CD A:GLU106 4.3 73.7 1.0 CG A:ASP105 4.4 52.9 1.0 C4' P:DG13 4.5 0.9 1.0 OP2 P:DG13 4.6 66.9 1.0 OD1 A:ASP105 4.6 55.2 1.0 CG A:GLU106 4.6 69.9 1.0 O5' P:DG13 4.6 91.6 1.0 O A:HOH503 4.7 43.4 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