Calcium in PDB 3pr4: DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt

All present enzymatic activity of DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt:
2.7.7.7;

The structure of DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt, PDB code: 3pr4 was solved by K.N.Kirouac, Z.Suo, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.11 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.347, 102.004, 52.226, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.5

The binding sites of Calcium atom in the DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt (pdb code 3pr4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt, PDB code: 3pr4:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca343 b:35.3 occ:1.00 O1B A:ATP342 2.3 55.6 1.0 O A:PHE8 2.4 36.4 1.0 OD2 A:ASP105 2.4 43.4 1.0 OD2 A:ASP7 2.4 47.0 1.0 O2A A:ATP342 2.4 47.0 1.0 O A:HOH383 2.8 46.0 1.0 CG A:ASP7 3.4 43.7 1.0 CG A:ASP105 3.5 44.3 1.0 C A:PHE8 3.5 36.9 1.0 PA A:ATP342 3.5 47.4 1.0 PB A:ATP342 3.7 57.2 1.0 OD1 A:ASP7 3.8 43.9 1.0 C5' A:ATP342 3.8 46.7 1.0 O5' A:ATP342 3.9 46.7 1.0 N A:PHE8 4.0 40.1 1.0 O3A A:ATP342 4.1 47.9 1.0 C A:ASP7 4.1 42.1 1.0 CA A:CA344 4.2 83.6 1.0 OD1 A:ASP105 4.2 47.0 1.0 O3B A:ATP342 4.3 38.5 1.0 CA A:PHE8 4.3 38.6 1.0 O A:ASP7 4.3 45.1 1.0 CB A:ASP105 4.5 41.4 1.0 N A:TYR10 4.5 44.1 1.0 N A:ASP9 4.5 39.8 1.0 O A:ASP105 4.6 38.5 1.0 CB A:ASP7 4.6 40.8 1.0 CA A:ASP9 4.7 42.3 1.0 CA A:ASP7 4.7 39.6 1.0 N A:PHE11 4.7 37.3 1.0 C A:ASP9 4.7 41.6 1.0 CB A:PHE8 4.8 38.7 1.0 O A:HOH359 4.8 52.0 1.0 O1A A:ATP342 4.9 48.9 1.0 NZ A:LYS159 4.9 41.8 1.0 CB A:PHE11 5.0 31.6 1.0

Calcium binding site 2 out of 3 in the DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca344 b:83.6 occ:1.00 OE1 A:GLU106 2.8 49.0 1.0 O A:HOH383 2.9 46.0 1.0 OD1 A:ASP7 2.9 43.9 1.0 O P:HOH18 3.3 62.1 1.0 OP1 P:DC13 3.4 98.7 1.0 O1B A:ATP342 3.4 55.6 1.0 OD2 A:ASP7 3.5 47.0 1.0 CG A:ASP7 3.5 43.7 1.0 O5' P:DC13 3.5 67.6 1.0 O A:HOH346 3.6 48.7 1.0 CD A:GLU106 3.7 47.4 1.0 NZ A:LYS159 3.7 41.8 1.0 C5' P:DC13 3.8 68.1 1.0 P P:DC13 4.0 97.9 1.0 O A:HOH359 4.1 52.0 1.0 CA A:CA343 4.2 35.3 1.0 CG A:GLU106 4.3 42.1 1.0 PB A:ATP342 4.4 57.2 1.0 O2B A:ATP342 4.4 57.7 1.0 NZ A:LYS152 4.4 47.8 1.0 OE2 A:GLU106 4.5 49.6 1.0 C3' P:DC13 4.5 68.8 1.0 CE A:LYS152 4.7 45.0 1.0 C4' P:DC13 4.7 68.3 1.0 OP2 P:DC13 4.8 97.3 1.0 CE A:LYS159 4.8 42.6 1.0 CB A:ASP7 4.9 40.8 1.0

Calcium binding site 3 out of 3 in the DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DPO4 Y12A Mutant Incorporating Dadp Opposite Template Dt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca345 b:69.7 occ:1.00 O A:ILE186 2.5 50.3 1.0 O A:ALA181 2.6 49.9 1.0 O A:HOH381 2.7 37.1 1.0 O A:HOH398 2.9 53.1 1.0 C A:ILE186 3.7 48.7 1.0 O A:HOH393 3.7 53.4 1.0 OP1 P:DT12 3.8 58.1 1.0 C A:ALA181 3.8 51.6 1.0 O A:VAL183 4.2 38.9 1.0 OP2 P:DT12 4.3 58.5 1.0 CA A:ASP182 4.5 52.0 1.0 CA A:ILE186 4.5 45.2 1.0 P P:DT12 4.5 56.3 1.0 N A:ILE186 4.6 42.7 1.0 N A:ASP182 4.6 53.1 1.0 N A:GLY187 4.6 49.2 1.0 CA A:GLY187 4.7 52.6 1.0 CB A:ILE186 4.7 44.1 1.0 C A:ASP182 4.7 47.3 1.0 CA A:ALA181 4.8 53.0 1.0 N A:VAL183 4.9 47.9 1.0 C A:VAL183 5.0 40.1 1.0

K.N.Kirouac, Z.Suo, H.Ling. Structural Mechanism of Ribonucleotide Discrimination By A Y-Family Dna Polymerase. J.Mol.Biol. V. 407 382 2011.
ISSN: ISSN 0022-2836
PubMed: 21295588
DOI: 10.1016/J.JMB.2011.01.037