Calcium in PDB 5dg7: Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion, PDB code: 5dg7 was solved by A.Patra, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.89 / 2.26
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.039, 99.039, 81.826, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 21.2

The binding sites of Calcium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion (pdb code 5dg7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion, PDB code: 5dg7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:18.1 occ:1.00 O1A A:TTP501 2.3 21.6 1.0 O1G A:TTP501 2.3 14.2 1.0 O A:MET14 2.4 15.9 1.0 OD2 A:ASP115 2.4 15.9 1.0 O1B A:TTP501 2.5 16.0 1.0 OD2 A:ASP13 2.6 29.5 1.0 OD1 A:ASP13 2.7 23.7 1.0 CG A:ASP13 3.0 18.9 1.0 CA A:CA503 3.3 25.0 0.3 PB A:TTP501 3.3 18.3 1.0 PA A:TTP501 3.4 19.9 1.0 CG A:ASP115 3.5 17.7 1.0 PG A:TTP501 3.5 17.6 1.0 C A:MET14 3.5 16.9 1.0 O3A A:TTP501 3.6 20.4 1.0 O3B A:TTP501 3.7 18.0 1.0 OD1 A:ASP115 3.8 16.9 1.0 O2G A:TTP501 4.0 17.9 1.0 N A:MET14 4.0 18.7 1.0 C5' A:TTP501 4.1 16.2 1.0 O5' A:TTP501 4.2 19.7 1.0 NZ A:LYS231 4.2 24.5 1.0 CA A:MET14 4.3 17.2 1.0 O A:HOH721 4.3 26.9 1.0 C A:ASP13 4.4 16.2 1.0 CB A:ASP13 4.4 19.1 1.0 N A:ASP15 4.6 12.8 1.0 O2A A:TTP501 4.6 13.9 1.0 N A:CYS16 4.6 14.2 1.0 O2B A:TTP501 4.6 21.6 1.0 O3G A:TTP501 4.6 19.7 1.0 CB A:MET14 4.7 18.8 1.0 CB A:ASP115 4.8 12.9 1.0 N A:PHE17 4.8 14.1 1.0 CA A:ASP15 4.8 15.2 1.0 O A:ASP13 4.8 15.0 1.0 CB A:PHE17 4.8 14.6 1.0 CA A:ASP13 4.9 15.0 1.0 C A:ASP15 4.9 15.5 1.0 OE2 A:GLU116 4.9 26.6 1.0 O A:ASP115 5.0 17.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Dna Polymerase Eta Inserting Dttp Across A Dna Template Containing 1,N6-Ethenodeoxyadenosine Lesion within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:25.0 occ:0.30 O3' P:DT8 2.2 21.4 1.0 OD1 A:ASP13 2.3 23.7 1.0 O1A A:TTP501 2.4 21.6 1.0 OE2 A:GLU116 2.4 26.6 1.0 OD1 A:ASP115 2.5 16.9 1.0 C3' P:DT8 2.7 21.6 1.0 CG A:GLU116 2.8 25.5 1.0 CD A:GLU116 2.9 28.4 1.0 CA A:CA502 3.3 18.1 1.0 CG A:ASP115 3.3 17.7 1.0 OD2 A:ASP115 3.5 15.9 1.0 PA A:TTP501 3.5 19.9 1.0 CG A:ASP13 3.5 18.9 1.0 C4' P:DT8 3.8 25.6 1.0 OG A:SER113 3.9 19.1 1.0 O2A A:TTP501 4.0 13.9 1.0 OE1 A:GLU116 4.0 25.2 1.0 C2' P:DT8 4.0 25.2 1.0 O5' A:TTP501 4.1 19.7 1.0 C5' A:TTP501 4.1 16.2 1.0 OD2 A:ASP13 4.2 29.5 1.0 CB A:GLU116 4.3 17.9 1.0 C5' P:DT8 4.4 24.1 1.0 O A:ASP115 4.6 17.7 1.0 CB A:ASP13 4.6 19.1 1.0 C A:ASP115 4.6 16.6 1.0 O A:HOH721 4.7 26.9 1.0 O1G A:TTP501 4.7 14.2 1.0 CB A:ASP115 4.8 12.9 1.0 N A:GLU116 4.8 18.7 1.0 O3A A:TTP501 4.8 20.4 1.0 O5' P:DT8 5.0 35.0 1.0 O4' P:DT8 5.0 25.6 1.0

A.Patra, Y.Su, Q.Zhang, K.M.Johnson, F.P.Guengerich, M.Egli. Structural and Kinetic Analysis of Miscoding Opposite the Dna Adduct 1,N6-Ethenodeoxyadenosine By Human Translesion Dna Polymerase Eta. J.Biol.Chem. V. 291 14134 2016.
ISSN: ESSN 1083-351X
PubMed: 27226627
DOI: 10.1074/JBC.M116.732487