Calcium in PDB 4yp3: Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion

All present enzymatic activity of Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion:
2.7.7.7;

The structure of Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion, PDB code: 4yp3 was solved by Y.Su, A.Patra, J.M.Harp, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.77 / 1.89
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.769, 98.769, 81.966, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 21.6

The binding sites of Calcium atom in the Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion (pdb code 4yp3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion, PDB code: 4yp3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:16.2 occ:1.00 OD2 A:ASP115 2.3 15.9 1.0 O1G A:DCP501 2.3 15.2 1.0 O A:MET14 2.3 14.0 1.0 O1B A:DCP501 2.3 15.6 1.0 O1A A:DCP501 2.4 18.5 1.0 OD2 A:ASP13 2.5 21.7 1.0 OD1 A:ASP13 2.6 21.0 1.0 CG A:ASP13 2.9 18.1 1.0 PB A:DCP501 3.4 14.9 1.0 CG A:ASP115 3.4 16.3 1.0 PG A:DCP501 3.5 16.5 1.0 PA A:DCP501 3.5 16.8 1.0 CA A:CA503 3.5 17.1 0.7 C A:MET14 3.5 13.8 1.0 O3A A:DCP501 3.7 18.3 1.0 O3B A:DCP501 3.8 15.7 1.0 OD1 A:ASP115 3.8 15.0 1.0 N A:MET14 3.9 13.1 1.0 O A:HOH830 4.0 30.4 1.0 O2G A:DCP501 4.0 14.3 1.0 C5' A:DCP501 4.2 16.8 1.0 NZ A:LYS231 4.2 22.6 1.0 C A:ASP13 4.3 13.7 1.0 CA A:MET14 4.3 13.9 1.0 CB A:ASP13 4.3 16.0 1.0 O5' A:DCP501 4.4 15.5 1.0 O A:HOH875 4.4 32.7 1.0 N A:ASP15 4.6 14.7 1.0 N A:CYS16 4.6 13.8 1.0 CA A:ASP15 4.7 16.2 1.0 CB A:ASP115 4.7 13.0 1.0 O A:ASP13 4.7 17.2 1.0 CA A:ASP13 4.8 13.8 1.0 O2A A:DCP501 4.8 18.2 1.0 O2B A:DCP501 4.8 15.9 1.0 O3G A:DCP501 4.8 17.3 1.0 C A:ASP15 4.8 16.3 1.0 CB A:MET14 4.8 15.9 1.0 N A:PHE17 4.8 14.7 1.0 CE A:LYS231 4.9 26.1 0.5 CB A:PHE17 4.9 13.8 1.0

Calcium binding site 2 out of 2 in the Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite An 8-Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:17.1 occ:0.72 OE2 A:GLU116 2.3 31.1 1.0 O A:HOH875 2.3 32.7 1.0 O1A A:DCP501 2.4 18.5 1.0 OD1 A:ASP115 2.4 15.0 1.0 OD1 A:ASP13 2.4 21.0 1.0 O3' P:DT8 2.5 22.1 1.0 C3' P:DT8 3.0 23.5 1.0 CG A:ASP115 3.2 16.3 1.0 OD2 A:ASP115 3.4 15.9 1.0 CD A:GLU116 3.4 28.6 1.0 CA A:CA502 3.5 16.2 1.0 PA A:DCP501 3.6 16.8 1.0 CG A:ASP13 3.6 18.1 1.0 OG A:SER113 3.8 20.7 1.0 O5' A:DCP501 4.0 15.5 1.0 C4' P:DT8 4.0 25.8 1.0 O2A A:DCP501 4.1 18.2 1.0 CB A:GLU116 4.1 20.3 1.0 CG A:GLU116 4.2 23.8 1.0 C5' A:DCP501 4.2 16.8 1.0 C2' P:DT8 4.3 26.6 1.0 OD2 A:ASP13 4.3 21.7 1.0 O A:HOH830 4.4 30.4 1.0 OE1 A:GLU116 4.4 29.6 1.0 O P:HOH118 4.5 14.7 0.4 CB A:ASP13 4.6 16.0 1.0 C5' P:DT8 4.6 31.6 1.0 C A:ASP115 4.6 16.1 1.0 CB A:ASP115 4.7 13.0 1.0 NZ A:LYS224 4.7 17.5 0.6 O A:ASP115 4.7 15.2 1.0 N A:GLU116 4.8 15.7 1.0 O1G A:DCP501 4.8 15.2 1.0 CB A:SER113 4.9 18.6 1.0 O3A A:DCP501 4.9 18.3 1.0

Y.Su, A.Patra, J.M.Harp, M.Egli, F.P.Guengerich. Roles of Residues Arg-61 and Gln-38 of Human Dna Polymerase Eta in Bypass of Deoxyguanosine and 7,8-Dihydro-8-Oxo-2'-Deoxyguanosine. J.Biol.Chem. 2015.
ISSN: ESSN 1083-351X
PubMed: 25947374
DOI: 10.1074/JBC.M115.653691