Calcium in PDB 4yqw: Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite Template G

All present enzymatic activity of Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite Template G:
2.7.7.7;

The structure of Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite Template G, PDB code: 4yqw 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)	42.97 / 2.06
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.238, 99.238, 82.378, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 22.7

The binding sites of Calcium atom in the Mutant Human Dna Polymerase Eta Q38A/R61A Inserting Dctp Opposite Template G (pdb code 4yqw). 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 Template G, PDB code: 4yqw:
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 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 Q38A/R61A Inserting Dctp Opposite Template G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.0 occ:1.00 O1A A:DCP501 2.2 22.2 1.0 O1G A:DCP501 2.2 18.8 1.0 O1B A:DCP501 2.3 15.4 1.0 O A:MET14 2.3 14.2 1.0 OD2 A:ASP115 2.4 19.2 1.0 OD2 A:ASP13 2.5 24.1 1.0 OD1 A:ASP13 2.5 31.0 1.0 CG A:ASP13 2.8 19.4 1.0 PB A:DCP501 3.4 18.2 1.0 CA A:CA503 3.4 21.4 0.5 CG A:ASP115 3.4 18.9 1.0 PG A:DCP501 3.5 19.0 1.0 C A:MET14 3.5 14.4 1.0 PA A:DCP501 3.5 19.6 1.0 O3A A:DCP501 3.8 18.8 1.0 OD1 A:ASP115 3.8 18.4 1.0 O3B A:DCP501 3.8 18.7 1.0 O A:HOH858 4.0 36.4 0.9 N A:MET14 4.0 19.2 1.0 O A:HOH796 4.0 30.1 1.0 O2G A:DCP501 4.1 18.8 1.0 NZ A:LYS231 4.1 18.6 1.0 C5' A:DCP501 4.1 18.5 1.0 CB A:ASP13 4.3 22.4 1.0 CA A:MET14 4.3 17.8 0.2 CA A:MET14 4.3 17.9 0.8 C A:ASP13 4.3 16.4 1.0 O5' A:DCP501 4.4 20.6 1.0 N A:ASP15 4.5 15.2 1.0 N A:CYS16 4.7 18.3 1.0 O3G A:DCP501 4.7 20.5 1.0 O2A A:DCP501 4.7 18.9 1.0 CA A:ASP15 4.7 17.9 1.0 CB A:ASP115 4.7 12.2 1.0 O A:ASP13 4.7 19.3 1.0 O2B A:DCP501 4.8 17.7 1.0 CB A:MET14 4.8 17.6 0.2 CA A:ASP13 4.8 18.2 1.0 CB A:MET14 4.8 17.7 0.8 C A:ASP15 4.9 22.3 1.0 OE2 A:GLU116 4.9 34.1 1.0 CE A:LYS231 4.9 24.6 0.6 N A:PHE17 4.9 19.3 1.0

Calcium binding site 2 out of 2 in the Mutant Human Dna Polymerase Eta Q38A/R61A 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 Q38A/R61A Inserting Dctp Opposite Template G within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:21.4 occ:0.54 OE2 A:GLU116 2.2 34.1 1.0 OD2 A:ASP13 2.3 24.1 1.0 OD1 A:ASP115 2.4 18.4 1.0 O3' P:DT8 2.4 24.2 1.0 O A:HOH858 2.5 36.4 0.9 O1A A:DCP501 2.5 22.2 1.0 CD A:GLU116 2.7 29.4 1.0 CG A:GLU116 2.7 30.9 1.0 C3' P:DT8 2.8 20.7 1.0 CG A:ASP115 3.2 18.9 1.0 CA A:CA502 3.4 18.0 1.0 OD2 A:ASP115 3.4 19.2 1.0 CG A:ASP13 3.5 19.4 1.0 PA A:DCP501 3.6 19.6 1.0 OE1 A:GLU116 3.9 32.6 1.0 C4' P:DT8 3.9 21.8 1.0 OG A:SER113 3.9 22.7 1.0 C2' P:DT8 4.0 27.6 1.0 O5' A:DCP501 4.0 20.6 1.0 O2A A:DCP501 4.1 18.9 1.0 C5' A:DCP501 4.1 18.5 1.0 CB A:GLU116 4.2 22.1 1.0 OD1 A:ASP13 4.3 31.0 1.0 CB A:ASP13 4.5 22.4 1.0 C5' P:DT8 4.5 19.7 1.0 O A:HOH796 4.6 30.1 1.0 C A:ASP115 4.6 26.5 1.0 CB A:ASP115 4.7 12.2 1.0 O A:ASP115 4.7 20.2 1.0 O1G A:DCP501 4.7 18.8 1.0 N A:GLU116 4.7 24.8 1.0 O1B A:DCP501 4.8 15.4 1.0 O3A A:DCP501 5.0 18.8 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