Calcium in PDB 4ruc: Crystal Structure of Y-Family Dna Polymerase DPO4 Extending From A Mefapy-Dg:Dc Pair

All present enzymatic activity of Crystal Structure of Y-Family Dna Polymerase DPO4 Extending From A Mefapy-Dg:Dc Pair:
2.7.7.7;

The structure of Crystal Structure of Y-Family Dna Polymerase DPO4 Extending From A Mefapy-Dg:Dc Pair, PDB code: 4ruc 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)	69.88 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.383, 103.972, 52.563, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 23.6

The binding sites of Calcium atom in the Crystal Structure of Y-Family Dna Polymerase DPO4 Extending From A Mefapy-Dg:Dc Pair (pdb code 4ruc). 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 Extending From A Mefapy-Dg:Dc Pair, PDB code: 4ruc:
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 Extending From A Mefapy-Dg:Dc Pair


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 Extending From A Mefapy-Dg:Dc Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:70.4 occ:1.00 OD2 A:ASP7 2.5 48.6 1.0 OD2 A:ASP105 2.6 68.8 1.0 OE2 A:GLU106 2.6 77.0 1.0 O1A A:DTP401 2.6 61.8 1.0 O5' P:DC514 3.1 0.9 1.0 CD A:GLU106 3.2 73.8 1.0 CG A:GLU106 3.4 65.9 1.0 PA A:DTP401 3.6 55.8 1.0 O2A A:DTP401 3.7 76.6 1.0 C3' P:DC514 3.7 88.5 1.0 CG A:ASP7 3.7 52.8 1.0 CG A:ASP105 3.8 61.6 1.0 C5' P:DC514 3.8 0.8 1.0 CA A:CA403 3.9 58.8 1.0 OP1 P:DC514 4.2 93.3 1.0 P P:DC514 4.2 0.1 1.0 O3' P:DC514 4.2 87.5 1.0 OE1 A:GLU106 4.3 91.9 1.0 C4' P:DC514 4.3 90.3 1.0 O5' A:DTP401 4.4 54.8 1.0 OD1 A:ASP7 4.4 65.7 1.0 C5' A:DTP401 4.5 56.5 1.0 OD1 A:ASP105 4.6 75.1 1.0 C2' P:DC514 4.6 91.6 1.0 CB A:ASP105 4.6 53.3 1.0 NZ A:LYS152 4.6 64.6 1.0 O3G A:DTP401 4.7 68.3 1.0 CB A:ASP7 4.8 50.0 1.0 OP2 P:DC514 4.9 0.7 1.0 CB A:GLU106 4.9 59.2 1.0 O3A A:DTP401 4.9 64.6 1.0 NZ A:LYS159 5.0 97.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Y-Family Dna Polymerase DPO4 Extending From A Mefapy-Dg:Dc Pair


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 Extending From A Mefapy-Dg:Dc Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:58.8 occ:1.00 O3G A:DTP401 2.1 68.3 1.0 O1A A:DTP401 2.2 61.8 1.0 O A:PHE8 2.3 49.1 1.0 O1B A:DTP401 2.3 57.2 1.0 OD1 A:ASP7 2.5 65.7 1.0 OD1 A:ASP105 2.5 75.1 1.0 OD2 A:ASP105 2.9 68.8 1.0 CG A:ASP105 3.0 61.6 1.0 CG A:ASP7 3.1 52.8 1.0 OD2 A:ASP7 3.1 48.6 1.0 PB A:DTP401 3.3 58.5 1.0 PG A:DTP401 3.4 79.7 1.0 PA A:DTP401 3.4 55.8 1.0 C A:PHE8 3.5 44.7 1.0 O3A A:DTP401 3.5 64.6 1.0 O3B A:DTP401 3.6 67.5 1.0 CA A:CA402 3.9 70.4 1.0 C5' A:DTP401 4.0 56.5 1.0 N A:PHE8 4.1 45.4 1.0 O5' A:DTP401 4.2 54.8 1.0 O1G A:DTP401 4.3 85.5 1.0 CB A:ASP105 4.4 53.3 1.0 O2G A:DTP401 4.4 77.6 1.0 N A:ASP9 4.4 47.1 1.0 CA A:PHE8 4.4 43.6 1.0 CA A:ASP9 4.4 47.1 1.0 N A:TYR10 4.5 45.9 1.0 CB A:ASP7 4.5 50.0 1.0 C A:ASP7 4.5 46.7 1.0 O2A A:DTP401 4.6 76.6 1.0 O2B A:DTP401 4.7 62.5 1.0 C A:ASP9 4.7 46.5 1.0 NZ A:LYS159 4.7 97.0 1.0 N A:PHE11 4.9 47.2 1.0 CA A:ASP7 4.9 46.6 1.0 CB A:PHE11 5.0 48.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Y-Family Dna Polymerase DPO4 Extending From A Mefapy-Dg:Dc Pair


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 Extending From A Mefapy-Dg:Dc Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:70.7 occ:1.00 O A:ALA181 2.4 66.9 1.0 O A:HOH2004 2.4 41.4 1.0 O A:HOH2005 2.4 54.0 1.0 O P:HOH601 2.5 56.5 1.0 O A:ILE186 2.7 59.1 1.0 OP1 P:DA513 3.3 60.3 1.0 C A:ALA181 3.6 71.0 1.0 O A:VAL183 3.6 54.0 1.0 C A:ILE186 3.7 56.5 1.0 CA A:ASP182 4.3 71.5 1.0 N A:ASP182 4.4 72.5 1.0 P P:DA513 4.5 56.5 1.0 C A:VAL183 4.5 55.0 1.0 N A:ILE186 4.5 64.8 1.0 CA A:ILE186 4.5 58.2 1.0 N A:VAL183 4.5 55.9 1.0 CA A:ALA181 4.5 72.0 1.0 C A:ASP182 4.6 62.1 1.0 N A:GLY187 4.6 58.8 1.0 CB A:ILE186 4.7 60.2 1.0 CA A:GLY187 4.7 62.9 1.0 OP2 P:DA513 4.8 57.4 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