Calcium in PDB 4yr2: Mutant Human Dna Polymerase Eta R61M Inserting Datp Opposite An 8- Oxoguanine Lesion

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

The structure of Mutant Human Dna Polymerase Eta R61M Inserting Datp Opposite An 8- Oxoguanine Lesion, PDB code: 4yr2 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)	32.40 / 1.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.971, 98.971, 82.177, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 21.8

The binding sites of Calcium atom in the Mutant Human Dna Polymerase Eta R61M Inserting Datp Opposite An 8- Oxoguanine Lesion (pdb code 4yr2). 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 Datp Opposite An 8- Oxoguanine Lesion, PDB code: 4yr2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Mutant Human Dna Polymerase Eta R61M Inserting Datp 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 Datp Opposite An 8- Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:25.4 occ:1.00 O2B A:DTP501 2.2 22.3 1.0 O3G A:DTP501 2.2 27.7 1.0 OD1 A:ASP13 2.3 28.6 1.0 OD2 A:ASP115 2.3 25.8 1.0 O2A A:DTP501 2.3 32.6 1.0 O A:MET14 2.4 18.4 1.0 CA A:CA503 3.1 32.3 0.4 PB A:DTP501 3.3 27.0 1.0 CG A:ASP13 3.4 29.8 1.0 CG A:ASP115 3.4 29.5 1.0 PG A:DTP501 3.5 38.3 1.0 PA A:DTP501 3.5 39.7 1.0 C A:MET14 3.6 15.3 1.0 O3A A:DTP501 3.7 35.0 1.0 O A:HOH939 3.8 28.7 0.2 OD1 A:ASP115 3.8 25.0 1.0 O3B A:DTP501 3.8 28.3 1.0 C5' A:DTP501 3.8 29.2 1.0 OD2 A:ASP13 3.9 41.1 1.0 O A:HOH939 3.9 23.8 0.4 N A:MET14 4.1 17.2 1.0 O2G A:DTP501 4.1 22.7 1.0 O A:HOH914 4.1 24.6 1.0 O5' A:DTP501 4.2 35.8 1.0 C A:ASP13 4.3 13.6 1.0 CA A:MET14 4.3 17.8 1.0 N A:CYS16 4.5 17.6 1.0 N A:ASP15 4.6 14.9 1.0 CB A:ASP13 4.6 20.6 1.0 CB A:ASP115 4.6 19.6 1.0 CA A:ASP15 4.6 19.3 1.0 O1B A:DTP501 4.7 23.8 1.0 C A:ASP15 4.7 21.4 1.0 N A:PHE17 4.7 17.3 1.0 O A:HOH939 4.7 31.6 0.4 O1G A:DTP501 4.7 32.5 1.0 O A:ASP13 4.8 19.3 1.0 O1A A:DTP501 4.8 38.5 1.0 CA A:ASP13 4.8 18.1 1.0 CB A:MET14 4.8 17.1 1.0 CB A:PHE17 4.8 14.3 1.0 OE2 A:GLU116 4.9 44.0 1.0 O A:ASP115 4.9 22.8 1.0

Calcium binding site 2 out of 2 in the Mutant Human Dna Polymerase Eta R61M Inserting Datp 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 Datp Opposite An 8- Oxoguanine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:32.3 occ:0.41 O2A A:DTP501 2.2 32.6 1.0 OD1 A:ASP115 2.4 25.0 1.0 OE2 A:GLU116 2.4 44.0 1.0 O3' P:DT8 2.5 33.9 1.0 CG A:GLU116 2.7 28.9 1.0 O A:HOH939 2.8 28.7 0.2 CD A:GLU116 2.8 41.0 1.0 OD1 A:ASP13 2.9 28.6 1.0 CG A:ASP115 3.1 29.5 1.0 CA A:CA502 3.1 25.4 1.0 OD2 A:ASP115 3.2 25.8 1.0 C3' P:DT8 3.3 35.7 1.0 PA A:DTP501 3.4 39.7 1.0 OD2 A:ASP13 3.5 41.1 1.0 CG A:ASP13 3.5 29.8 1.0 O5' A:DTP501 3.8 35.8 1.0 C5' A:DTP501 3.9 29.2 1.0 OE1 A:GLU116 4.0 37.2 1.0 OG A:SER113 4.0 24.0 1.0 O1A A:DTP501 4.0 38.5 1.0 O A:HOH939 4.2 23.8 0.4 CB A:GLU116 4.2 21.7 1.0 C4' P:DT8 4.3 36.4 1.0 O3G A:DTP501 4.4 27.7 1.0 C2' P:DT8 4.5 34.5 1.0 C A:ASP115 4.5 24.8 1.0 O A:ASP115 4.5 22.8 1.0 CB A:ASP115 4.5 19.6 1.0 O A:HOH939 4.6 31.6 0.4 O2B A:DTP501 4.6 22.3 1.0 N A:GLU116 4.7 24.9 1.0 O3A A:DTP501 4.7 35.0 1.0 CB A:ASP13 4.8 20.6 1.0 NZ A:LYS224 4.8 29.2 0.6 C5' P:DT8 4.9 31.4 1.0 CA A:GLU116 4.9 18.1 1.0 CA A:ASP115 5.0 21.2 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