Magnesium in PDB 9chw: Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template

All present enzymatic activity of Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template:
2.7.7.7;

The structure of Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template, PDB code: 9chw was solved by R.Tomar, M.P.Stone, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.90 / 2.16
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.686, 98.686, 82.062, 90, 90, 120
R / Rfree (%)	14.3 / 21

The binding sites of Magnesium atom in the Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template (pdb code 9chw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template, PDB code: 9chw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:10.9 occ:1.00 O3G A:DZ4501 2.0 7.6 1.0 O1B A:DZ4501 2.1 7.6 1.0 OD1 A:ASP13 2.1 10.5 1.0 O A:MET14 2.1 11.0 1.0 OD2 A:ASP115 2.1 8.5 1.0 O1A A:DZ4501 2.2 9.0 1.0 CG A:ASP13 3.1 6.9 1.0 PB A:DZ4501 3.1 9.1 1.0 CG A:ASP115 3.2 8.6 1.0 PG A:DZ4501 3.2 10.5 1.0 C A:MET14 3.3 7.6 1.0 PA A:DZ4501 3.4 11.5 1.0 OD2 A:ASP13 3.5 9.3 1.0 O3B A:DZ4501 3.5 10.7 1.0 MG A:MG503 3.5 9.4 1.0 N3A A:DZ4501 3.6 8.2 1.0 OD1 A:ASP115 3.7 7.6 1.0 O A:HOH673 3.7 12.2 1.0 NZ A:LYS231 3.7 7.3 1.0 N A:MET14 3.9 7.3 1.0 O1G A:DZ4501 4.0 10.4 1.0 C5' A:DZ4501 4.1 7.0 1.0 CA A:MET14 4.1 9.5 1.0 C A:ASP13 4.2 10.5 1.0 O5' A:DZ4501 4.2 12.1 1.0 O A:HOH716 4.3 7.7 1.0 N A:ASP15 4.3 7.9 1.0 CB A:ASP13 4.4 9.2 1.0 O2G A:DZ4501 4.4 13.7 1.0 CE A:LYS231 4.4 12.3 1.0 O2B A:DZ4501 4.4 9.3 1.0 CB A:ASP115 4.5 8.5 1.0 CA A:ASP15 4.5 8.3 1.0 N A:CYS16 4.6 9.0 1.0 O2A A:DZ4501 4.6 11.4 1.0 O A:ASP13 4.6 8.3 1.0 CB A:MET14 4.7 13.2 1.0 C A:ASP15 4.7 10.4 1.0 N A:PHE17 4.8 9.2 1.0 CA A:ASP13 4.8 10.5 1.0 CB A:PHE17 4.8 7.3 1.0 O A:ASP115 5.0 9.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Polymerase Eta with Incoming Dampnpp Nucleotide Opposite Threofuranosyl Thymidine in Dna Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:9.4 occ:1.00 OD1 A:ASP115 2.1 7.6 1.0 OD2 A:ASP13 2.1 9.3 1.0 OE1 A:GLU116 2.1 7.7 1.0 O A:HOH716 2.2 7.7 1.0 O3' P:DT8 2.2 11.2 1.0 O1A A:DZ4501 2.2 9.0 1.0 CG A:ASP115 3.0 8.6 1.0 CG A:ASP13 3.1 6.9 1.0 C3' P:DT8 3.1 8.8 1.0 CD A:GLU116 3.2 16.8 1.0 PA A:DZ4501 3.3 11.5 1.0 OD2 A:ASP115 3.3 8.5 1.0 OD1 A:ASP13 3.4 10.5 1.0 MG A:MG502 3.5 10.9 1.0 O2A A:DZ4501 3.6 11.4 1.0 OG A:SER113 3.8 11.9 1.0 O5' A:DZ4501 3.8 12.1 1.0 OE2 A:GLU116 3.9 16.6 1.0 C4' P:DT8 4.0 12.3 1.0 O A:HOH673 4.0 12.2 1.0 C5' A:DZ4501 4.1 7.0 1.0 O P:HOH106 4.2 10.5 1.0 CG A:GLU116 4.2 10.0 1.0 CB A:GLU116 4.2 12.0 1.0 NZ A:LYS224 4.3 11.4 1.0 C2' P:DT8 4.4 10.2 1.0 CB A:ASP115 4.4 8.5 1.0 CB A:ASP13 4.4 9.2 1.0 O3G A:DZ4501 4.7 7.6 1.0 C A:ASP115 4.7 9.9 1.0 N3A A:DZ4501 4.7 8.2 1.0 O1B A:DZ4501 4.7 7.6 1.0 O A:ASP115 4.7 9.4 1.0 CB A:SER113 4.8 12.6 1.0 C5' P:DT8 4.8 11.5 1.0 N A:GLU116 5.0 8.2 1.0

R.Tomar, P.P.Ghodke, A.Patra, E.Smyth, A.Pontarelli, W.Copp, F.P.Guengerich, J.J.Chaput, C.J.Wilds, M.P.Stone, M.Egli. Dna Replication Across Alpha-L-(3'-2')-Threofuranosyl Nucleotides Mediated By Human Dna Polymerase Eta. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39259676
DOI: 10.1021/ACS.BIOCHEM.4C00387