Calcium in PDB 5l1i: Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite O6-Methyl-2'-Deoxyguanosine

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite O6-Methyl-2'-Deoxyguanosine:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite O6-Methyl-2'-Deoxyguanosine, PDB code: 5l1i 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)	50.00 / 2.78
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.095, 99.095, 81.869, 90.00, 90.00, 120.00
R / Rfree (%)	16 / 22.8

The binding sites of Calcium atom in the Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite O6-Methyl-2'-Deoxyguanosine (pdb code 5l1i). 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 O6-Methyl-2'-Deoxyguanosine, PDB code: 5l1i:
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 O6-Methyl-2'-Deoxyguanosine


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 O6-Methyl-2'-Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:29.5 occ:1.00 O2B A:DCP501 2.2 28.8 1.0 O2G A:DCP501 2.2 24.7 1.0 O2A A:DCP501 2.2 29.9 1.0 O A:MET14 2.3 26.0 1.0 OD2 A:ASP115 2.3 31.1 1.0 OD2 A:ASP13 2.5 29.2 1.0 OD1 A:ASP13 2.6 27.3 1.0 CG A:ASP13 2.9 29.4 1.0 PB A:DCP501 3.2 27.9 1.0 O3A A:DCP501 3.3 31.3 1.0 PA A:DCP501 3.4 32.2 1.0 CG A:ASP115 3.4 33.2 1.0 PG A:DCP501 3.4 27.1 1.0 C A:MET14 3.5 29.4 1.0 CA A:CA503 3.6 48.4 1.0 O3B A:DCP501 3.6 27.2 1.0 OD1 A:ASP115 3.8 35.1 1.0 C5' A:DCP501 3.9 31.3 1.0 N A:MET14 3.9 30.0 1.0 O3G A:DCP501 4.0 23.9 1.0 O5' A:DCP501 4.1 31.3 1.0 O A:HOH650 4.2 32.2 1.0 CA A:MET14 4.3 30.6 1.0 CB A:ASP13 4.4 30.5 1.0 O A:HOH658 4.4 26.8 1.0 NZ A:LYS231 4.4 46.1 1.0 C A:ASP13 4.4 29.6 1.0 N A:ASP15 4.5 28.4 1.0 N A:CYS16 4.6 31.2 1.0 O1B A:DCP501 4.6 28.6 1.0 CB A:ASP115 4.7 33.0 1.0 O1G A:DCP501 4.7 24.4 1.0 O1A A:DCP501 4.7 28.5 1.0 CA A:ASP15 4.7 29.2 1.0 N A:PHE17 4.8 29.3 1.0 C A:ASP15 4.8 30.6 1.0 CB A:MET14 4.9 32.0 1.0 O A:ASP13 4.9 30.5 1.0 CA A:ASP13 4.9 30.0 1.0 CE A:LYS231 4.9 43.9 1.0 CB A:PHE17 4.9 27.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Eta Inserting Dctp Opposite O6-Methyl-2'-Deoxyguanosine


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 O6-Methyl-2'-Deoxyguanosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:48.4 occ:1.00 OP2 P:DC9 2.2 75.1 1.0 OD2 A:ASP13 2.3 29.2 1.0 OE2 A:GLU116 2.3 34.6 1.0 O A:HOH650 2.4 32.2 1.0 O2A A:DCP501 2.4 29.9 1.0 OD1 A:ASP115 2.5 35.1 1.0 O3' P:DT8 3.2 67.3 1.0 P P:DC9 3.3 73.0 1.0 CG A:ASP115 3.4 33.2 1.0 CG A:ASP13 3.5 29.4 1.0 CD A:GLU116 3.5 35.2 1.0 OD2 A:ASP115 3.5 31.1 1.0 CA A:CA502 3.6 29.5 1.0 PA A:DCP501 3.6 32.2 1.0 OG A:SER113 3.7 29.7 1.0 CB A:GLU116 4.0 32.6 1.0 CG A:GLU116 4.1 33.3 1.0 OP1 P:DC9 4.2 57.7 1.0 O1A A:DCP501 4.2 28.5 1.0 O5' A:DCP501 4.2 31.3 1.0 C5' A:DCP501 4.3 31.3 1.0 C3' P:DT8 4.3 73.8 1.0 OD1 A:ASP13 4.3 27.3 1.0 CB A:ASP13 4.4 30.5 1.0 O5' P:DC9 4.5 73.4 1.0 OE1 A:GLU116 4.5 39.8 1.0 C A:ASP115 4.7 31.9 1.0 O A:ASP115 4.7 33.0 1.0 N A:GLU116 4.7 32.0 1.0 CB A:ASP115 4.8 33.0 1.0 O A:HOH696 4.8 46.2 1.0 CB A:SER113 4.8 28.8 1.0 O2G A:DCP501 4.8 24.7 1.0 O A:HOH658 4.9 26.8 1.0 C4' P:DT8 4.9 77.3 1.0 O3A A:DCP501 4.9 31.3 1.0

A.Patra, Q.Zhang, F.P.Guengerich, M.Egli. Mechanisms of Insertion of Dctp and Dttp Opposite the Dna Lesion O6-Methyl-2'-Deoxyguanosine By Human Dna Polymerase Eta. J.Biol.Chem. V. 291 24304 2016.
ISSN: ESSN 1083-351X
PubMed: 27694439
DOI: 10.1074/JBC.M116.755462