Calcium in PDB 4rua: Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct

All present enzymatic activity of Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct:
2.7.7.7;

The structure of Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct, PDB code: 4rua was solved by A.Patra, S.Banerjee, M.P.Stone, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.07
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	95.451, 102.716, 53.432, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 25.8

The binding sites of Calcium atom in the Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct (pdb code 4rua). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct, PDB code: 4rua:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:81.5 occ:1.00 O A:ALA181 2.4 87.1 1.0 O P:HOH2006 2.4 52.0 1.0 O A:ILE186 2.4 67.2 1.0 O A:HOH521 2.6 59.2 1.0 O P:HOH2008 2.6 83.5 1.0 C A:ALA181 3.5 85.2 1.0 C A:ILE186 3.6 72.2 1.0 CA A:GLY187 4.1 82.4 1.0 CA A:ALA181 4.2 82.8 1.0 OP2 P:DC513 4.3 72.4 1.0 N A:GLY187 4.3 76.5 1.0 CB A:ALA181 4.4 88.2 1.0 OP1 P:DC513 4.4 83.6 1.0 C A:GLY187 4.5 79.6 1.0 N A:ASP182 4.6 83.4 1.0 O A:VAL183 4.7 71.4 1.0 CA A:ILE186 4.7 68.2 1.0 CA A:ASP182 4.8 87.8 1.0 CB A:ILE186 4.9 70.0 1.0 O A:GLY187 4.9 72.6 1.0 P P:DC513 4.9 75.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:76.2 occ:1.00 O A:PHE8 2.2 61.6 1.0 O1B A:DTP401 2.2 0.8 1.0 O3G A:DTP401 2.3 0.4 1.0 OD1 A:ASP7 2.3 87.8 1.0 OD1 A:ASP105 2.4 84.2 1.0 O1A A:DTP401 2.4 72.5 1.0 CG A:ASP105 3.0 76.3 1.0 CG A:ASP7 3.1 77.4 1.0 PB A:DTP401 3.1 90.5 1.0 OD2 A:ASP105 3.2 65.7 1.0 OD2 A:ASP7 3.2 72.8 1.0 PG A:DTP401 3.4 0.9 1.0 O3B A:DTP401 3.4 93.6 1.0 PA A:DTP401 3.4 83.9 1.0 C A:PHE8 3.4 63.6 1.0 O3A A:DTP401 3.4 84.3 1.0 C5' A:DTP401 4.0 90.5 1.0 O1G A:DTP401 4.0 0.3 1.0 O5' A:DTP401 4.1 90.0 1.0 N A:PHE8 4.2 68.9 1.0 CA A:ASP9 4.3 68.2 1.0 N A:ASP9 4.3 63.4 1.0 CB A:ASP105 4.3 69.4 1.0 CA A:PHE8 4.4 63.2 1.0 N A:TYR10 4.4 72.6 1.0 C A:ASP9 4.5 67.7 1.0 CB A:ASP7 4.5 68.1 1.0 O2B A:DTP401 4.6 76.8 1.0 O2G A:DTP401 4.6 96.3 1.0 C A:ASP7 4.6 72.7 1.0 NZ A:LYS159 4.6 0.7 1.0 O2A A:DTP401 4.8 89.1 1.0 CB A:PHE11 4.8 62.2 1.0 N A:PHE11 4.8 66.1 1.0 CA A:ASP7 5.0 67.0 1.0 O A:ASP105 5.0 63.4 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Y-Family Dna Polymerase DPO4 Bypassing A Mefapy- Dg Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:0.9 occ:1.00 O A:HOH523 2.4 93.9 1.0 OE2 A:GLU106 2.8 89.7 1.0 O2A A:DTP401 3.1 89.1 1.0 O5' A:DTP401 3.2 90.0 1.0 PA A:DTP401 3.3 83.9 1.0 O1A A:DTP401 3.4 72.5 1.0 O3' P:DC513 3.4 72.2 1.0 OD2 A:ASP105 3.5 65.7 1.0 CD A:GLU106 3.6 0.8 1.0 C5' A:DTP401 3.6 90.5 1.0 OE1 A:GLU106 3.9 0.1 1.0 OG A:SER103 4.0 77.3 1.0 C2' P:DC513 4.3 77.3 1.0 C8 A:DTP401 4.4 1.0 1.0 C3' P:DC513 4.5 77.4 1.0 CG A:ASP105 4.5 76.3 1.0 O4' A:DTP401 4.6 0.4 1.0 CG A:GLU106 4.7 96.2 1.0 CB A:SER103 4.7 75.6 1.0 C4' A:DTP401 4.8 91.1 1.0 OD2 A:ASP7 4.8 72.8 1.0 CB A:ASP105 4.9 69.4 1.0 O3A A:DTP401 5.0 84.3 1.0 O T:HOH501 5.0 48.4 1.0

A.Patra, S.Banerjee, T.L.Johnson Salyard, C.K.Malik, P.P.Christov, C.J.Rizzo, M.P.Stone, M.Egli. Structural Basis For Error-Free Bypass of the 5-N-Methylformamidopyrimidine-Dg Lesion By Human Dna Polymerase Eta and Sulfolobus Solfataricus P2 Polymerase IV. J.Am.Chem.Soc. V. 137 7011 2015.
ISSN: ISSN 0002-7863
PubMed: 25988947
DOI: 10.1021/JACS.5B02701