Calcium in PDB 4yr0: Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite An 8- Oxoguanine Lesion

All present enzymatic activity of Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite An 8- Oxoguanine Lesion:
2.7.7.7;

The structure of Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite An 8- Oxoguanine Lesion, PDB code: 4yr0 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)	42.75 / 1.78
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.727, 98.727, 82.446, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 21.3

The binding sites of Calcium atom in the Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite An 8- Oxoguanine Lesion (pdb code 4yr0). 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 R61M Inserting Dctp Opposite An 8- Oxoguanine Lesion, PDB code: 4yr0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Mutant Human Dna Polymerase Eta R61M 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 R61M Inserting Dctp Opposite An 8- Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:12.7 occ:1.00 O A:MET14 2.3 11.7 1.0 O3G A:DCP501 2.3 12.1 1.0 O2B A:DCP501 2.3 10.2 1.0 OD2 A:ASP115 2.3 14.8 1.0 O2A A:DCP501 2.4 13.5 1.0 OD2 A:ASP13 2.5 23.6 1.0 OD1 A:ASP13 2.7 19.8 1.0 CG A:ASP13 2.9 16.4 1.0 PB A:DCP501 3.4 11.9 1.0 CG A:ASP115 3.4 15.3 1.0 C A:MET14 3.5 12.3 1.0 PG A:DCP501 3.5 13.0 1.0 PA A:DCP501 3.5 12.9 1.0 CA A:CA503 3.6 10.3 0.6 O3A A:DCP501 3.7 13.9 1.0 OD1 A:ASP115 3.8 10.7 1.0 O A:HOH918 3.8 26.0 1.0 O3B A:DCP501 3.8 13.2 1.0 N A:MET14 3.9 13.7 1.0 O A:HOH861 4.0 24.4 1.0 O2G A:DCP501 4.1 12.9 1.0 C5' A:DCP501 4.1 10.0 1.0 CA A:MET14 4.2 14.4 1.0 C A:ASP13 4.3 12.4 1.0 O5' A:DCP501 4.3 12.9 1.0 CB A:ASP13 4.3 11.2 1.0 O A:HOH851 4.5 20.3 1.0 N A:ASP15 4.5 11.5 1.0 N A:CYS16 4.5 10.1 1.0 CA A:ASP15 4.6 12.6 1.0 O A:ASP13 4.7 13.2 1.0 C A:ASP15 4.7 10.8 1.0 CB A:ASP115 4.7 9.3 1.0 O1B A:DCP501 4.7 11.4 1.0 CB A:MET14 4.8 14.8 1.0 O1G A:DCP501 4.8 11.5 1.0 O1A A:DCP501 4.8 16.8 1.0 CA A:ASP13 4.8 14.0 1.0 N A:PHE17 4.8 11.5 1.0 CB A:PHE17 4.9 9.1 1.0

Calcium binding site 2 out of 2 in the Mutant Human Dna Polymerase Eta R61M 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 R61M Inserting Dctp Opposite An 8- Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:10.3 occ:0.64 OE1 A:GLU116 2.3 18.7 1.0 OD1 A:ASP13 2.3 19.8 1.0 O A:HOH851 2.3 20.3 1.0 OD1 A:ASP115 2.4 10.7 1.0 O2A A:DCP501 2.4 13.5 1.0 O3' P:DT8 2.4 17.1 0.5 O3' P:DT8 2.7 16.5 0.5 C3' P:DT8 3.2 18.0 0.5 CG A:ASP115 3.3 15.3 1.0 CD A:GLU116 3.4 22.4 1.0 C3' P:DT8 3.4 18.4 0.5 CG A:ASP13 3.5 16.4 1.0 OD2 A:ASP115 3.5 14.8 1.0 PA A:DCP501 3.6 12.9 1.0 CA A:CA502 3.6 12.7 1.0 OG A:SER113 3.9 14.0 1.0 O1A A:DCP501 4.1 16.8 1.0 O5' A:DCP501 4.1 12.9 1.0 OE2 A:GLU116 4.1 21.8 1.0 CB A:GLU116 4.2 18.0 1.0 OD2 A:ASP13 4.2 23.6 1.0 C4' P:DT8 4.2 18.9 0.5 C5' A:DCP501 4.2 10.0 1.0 CG A:GLU116 4.2 16.1 1.0 NZ A:LYS224 4.3 21.8 1.0 C4' P:DT8 4.3 18.5 0.5 C2' P:DT8 4.5 19.6 0.5 O A:HOH861 4.5 24.4 1.0 O P:HOH110 4.5 14.4 0.7 CB A:ASP13 4.5 11.2 1.0 C2' P:DT8 4.7 19.8 0.5 C5' P:DT8 4.7 22.2 0.5 C A:ASP115 4.7 14.0 1.0 CB A:ASP115 4.7 9.3 1.0 C5' P:DT8 4.7 18.5 0.5 O A:ASP115 4.8 13.8 1.0 O3G A:DCP501 4.9 12.1 1.0 N A:GLU116 4.9 11.5 1.0 O5' P:DT8 4.9 21.3 0.5 CB A:SER113 4.9 16.0 1.0 O3A A:DCP501 5.0 13.9 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