Calcium in PDB 4yr3: Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite Template G

All present enzymatic activity of Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite Template G:
2.7.7.7;

The structure of Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite Template G, PDB code: 4yr3 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)	49.36 / 2.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.710, 98.710, 81.953, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 21.9

The binding sites of Calcium atom in the Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite Template G (pdb code 4yr3). 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 Template G, PDB code: 4yr3:
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 Template G


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 Template G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:12.3 occ:1.00 O1A A:DCP501 2.3 13.2 1.0 O1G A:DCP501 2.3 12.4 1.0 O A:MET14 2.3 10.4 1.0 OD2 A:ASP115 2.3 13.2 1.0 O1B A:DCP501 2.3 10.4 1.0 OD2 A:ASP13 2.4 21.4 1.0 OD1 A:ASP13 2.7 17.1 1.0 CG A:ASP13 2.9 17.6 1.0 PB A:DCP501 3.4 11.2 1.0 CG A:ASP115 3.4 12.8 1.0 CA A:CA503 3.5 15.8 0.7 C A:MET14 3.5 12.5 1.0 PA A:DCP501 3.5 12.9 1.0 PG A:DCP501 3.5 12.0 1.0 O3A A:DCP501 3.7 13.2 1.0 OD1 A:ASP115 3.8 12.3 1.0 O3B A:DCP501 3.8 11.9 1.0 N A:MET14 4.0 12.7 1.0 O3G A:DCP501 4.0 12.8 1.0 NZ A:LYS231 4.1 21.2 0.9 C5' A:DCP501 4.1 13.3 1.0 O A:HOH690 4.1 31.6 1.0 C A:ASP13 4.3 13.3 1.0 CA A:MET14 4.3 13.1 0.6 CA A:MET14 4.3 13.1 0.4 CB A:ASP13 4.3 15.7 1.0 O5' A:DCP501 4.3 13.5 1.0 O A:HOH771 4.4 26.7 1.0 N A:ASP15 4.5 13.2 1.0 N A:CYS16 4.6 10.6 1.0 CA A:ASP15 4.7 13.7 1.0 O A:ASP13 4.7 13.7 1.0 CB A:ASP115 4.7 10.5 1.0 O2B A:DCP501 4.8 12.3 1.0 CA A:ASP13 4.8 14.0 1.0 C A:ASP15 4.8 15.1 1.0 O2G A:DCP501 4.8 13.4 1.0 CB A:MET14 4.8 13.6 0.6 O2A A:DCP501 4.8 12.9 1.0 CB A:MET14 4.8 13.5 0.4 N A:PHE17 4.9 10.6 1.0 CE A:LYS231 4.9 21.8 0.6 O A:ASP115 5.0 13.9 1.0 CB A:PHE17 5.0 10.6 1.0

Calcium binding site 2 out of 2 in the Mutant Human Dna Polymerase Eta R61M Inserting Dctp Opposite Template G


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 Template G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:15.8 occ:0.70 OE2 A:GLU116 2.3 26.4 1.0 OD1 A:ASP13 2.3 17.1 1.0 OD1 A:ASP115 2.3 12.3 1.0 O A:HOH771 2.4 26.7 1.0 O1A A:DCP501 2.5 13.2 1.0 O3' P:DT8 2.5 19.4 1.0 C3' P:DT8 3.2 20.7 1.0 CG A:ASP115 3.2 12.8 1.0 CD A:GLU116 3.3 24.7 1.0 OD2 A:ASP115 3.4 13.2 1.0 CA A:CA502 3.5 12.3 1.0 CG A:ASP13 3.5 17.6 1.0 PA A:DCP501 3.6 12.9 1.0 OG A:SER113 3.9 16.1 1.0 CB A:GLU116 4.1 18.2 1.0 CG A:GLU116 4.1 21.4 1.0 OE1 A:GLU116 4.1 24.9 1.0 O5' A:DCP501 4.1 13.5 1.0 O2A A:DCP501 4.1 12.9 1.0 C5' A:DCP501 4.1 13.3 1.0 OD2 A:ASP13 4.2 21.4 1.0 C4' P:DT8 4.2 23.1 1.0 C2' P:DT8 4.4 21.1 1.0 NZ A:LYS224 4.5 15.1 0.6 O P:HOH101 4.5 35.2 1.0 CB A:ASP13 4.5 15.7 1.0 C A:ASP115 4.6 14.3 1.0 O A:ASP115 4.6 13.9 1.0 CB A:ASP115 4.6 10.5 1.0 O A:HOH690 4.7 31.6 1.0 N A:GLU116 4.7 14.5 1.0 C5' P:DT8 4.8 26.7 1.0 O1G A:DCP501 4.8 12.4 1.0 O1B A:DCP501 4.9 10.4 1.0 O3A A:DCP501 5.0 13.2 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