Calcium in PDB 5jum: Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba)

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba):
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba), PDB code: 5jum was solved by A.Patra, D.A.Politica, M.P.Stone, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.56 / 2.60
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.117, 99.117, 81.690, 90.00, 90.00, 120.00
R / Rfree (%)	16.6 / 23.9

The binding sites of Calcium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba) (pdb code 5jum). 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 Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba), PDB code: 5jum:
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 Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba)


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 Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:26.6 occ:1.00 O A:MET14 2.3 19.5 1.0 OD1 A:ASP115 2.3 27.4 1.0 O1A A:DCP501 2.3 28.7 1.0 O1B A:DCP501 2.4 28.0 1.0 O1G A:DCP501 2.4 26.5 1.0 OD2 A:ASP13 2.5 31.2 1.0 OD1 A:ASP13 2.8 29.1 1.0 CG A:ASP13 2.9 29.8 1.0 CG A:ASP115 3.4 30.6 1.0 PB A:DCP501 3.4 30.6 1.0 C A:MET14 3.4 25.4 1.0 PG A:DCP501 3.6 25.6 1.0 PA A:DCP501 3.6 26.1 1.0 CA A:CA503 3.7 48.6 1.0 O3A A:DCP501 3.7 30.9 1.0 N A:MET14 3.8 27.3 1.0 O3B A:DCP501 3.8 31.1 1.0 OD2 A:ASP115 3.8 34.5 1.0 NZ A:LYS231 4.0 35.9 1.0 C5' A:DCP501 4.1 29.8 1.0 CA A:MET14 4.2 27.3 1.0 O3G A:DCP501 4.2 23.1 1.0 C A:ASP13 4.3 24.3 1.0 CB A:ASP13 4.3 26.4 1.0 O5' A:DCP501 4.4 34.3 1.0 N A:CYS16 4.5 25.9 1.0 N A:ASP15 4.5 24.7 1.0 CA A:ASP15 4.6 26.1 1.0 CB A:ASP115 4.7 24.6 1.0 CE A:LYS231 4.7 35.6 1.0 CA A:ASP13 4.7 24.4 1.0 C A:ASP15 4.7 25.9 1.0 CB A:MET14 4.7 24.9 1.0 O2G A:DCP501 4.8 27.4 1.0 N A:PHE17 4.8 22.8 1.0 O2B A:DCP501 4.8 25.3 1.0 O2A A:DCP501 4.8 30.9 1.0 O A:ASP13 4.8 27.1 1.0 CB A:PHE17 5.0 23.0 1.0 O A:ASP115 5.0 30.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba)


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 Dctp Opposite N-(2'-Deoxyguanosin-8- Yl)-3-Aminobenzanthrone (C8-Dg-Aba) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:48.6 occ:1.00 OE2 A:GLU116 2.4 31.8 1.0 OD1 A:ASP13 2.4 29.1 1.0 O1A A:DCP501 2.5 28.7 1.0 O3' P:DT8 2.7 37.2 1.0 C3' P:DT8 2.9 31.9 1.0 OD2 A:ASP115 2.9 34.5 1.0 CD A:GLU116 3.5 30.6 1.0 PA A:DCP501 3.5 26.1 1.0 CG A:ASP13 3.6 29.8 1.0 CA A:CA502 3.7 26.6 1.0 O2A A:DCP501 3.7 30.9 1.0 CG A:ASP115 3.8 30.6 1.0 C4' P:DT8 3.8 29.1 1.0 OD1 A:ASP115 3.8 27.4 1.0 CG A:GLU116 4.0 33.1 1.0 OG A:SER113 4.1 33.4 1.0 OD2 A:ASP13 4.1 31.2 1.0 C2' P:DT8 4.1 34.0 1.0 O5' A:DCP501 4.2 34.3 1.0 C5' P:DT8 4.2 35.1 1.0 CB A:GLU116 4.3 29.7 1.0 NZ A:LYS224 4.3 36.5 1.0 C5' A:DCP501 4.4 29.8 1.0 OE1 A:GLU116 4.4 37.4 1.0 CB A:ASP13 4.6 26.4 1.0 O5' P:DT8 4.7 44.5 1.0 O1G A:DCP501 4.8 26.5 1.0 O3A A:DCP501 4.8 30.9 1.0

A.Patra, D.A.Politica, A.Chatterjee, E.J.Tokarsky, Z.Suo, A.K.Basu, M.P.Stone, M.Egli. Mechanism of Error-Free Bypass of the Environmental Carcinogen N-(2'-Deoxyguanosin-8-Yl)-3-Aminobenzanthrone Adduct By Human Dna Polymerase Eta. Chembiochem V. 17 2033 2016.
ISSN: ESSN 1439-7633
PubMed: 27556902
DOI: 10.1002/CBIC.201600420