Manganese in PDB 2hhw: Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation

All present enzymatic activity of Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation:
2.7.7.7;

The structure of Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation, PDB code: 2hhw was solved by J.J.Warren, L.J.Forsberg, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.834, 108.897, 150.111, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.5

The binding sites of Manganese atom in the Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation (pdb code 2hhw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation, PDB code: 2hhw:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn878 b:21.2 occ:1.00 O2G A:23T881 2.0 23.7 1.0 OD2 A:ASP830 2.1 20.5 1.0 OD1 A:ASP653 2.1 25.5 1.0 O2B A:23T881 2.1 20.5 1.0 O A:TYR654 2.2 21.7 1.0 O1A A:23T881 2.2 17.5 1.0 CG A:ASP653 3.1 26.2 1.0 CG A:ASP830 3.1 20.8 1.0 PB A:23T881 3.3 21.8 1.0 C A:TYR654 3.4 22.7 1.0 PA A:23T881 3.4 21.0 1.0 PG A:23T881 3.5 24.4 1.0 OD2 A:ASP653 3.5 25.3 1.0 OD1 A:ASP830 3.5 20.0 1.0 O A:HOH1098 3.7 27.3 1.0 O3B A:23T881 3.7 23.9 1.0 O3A A:23T881 3.8 21.4 1.0 N A:TYR654 3.9 23.9 1.0 O A:HOH933 4.1 25.3 1.0 CA A:TYR654 4.1 23.4 1.0 O A:HOH936 4.2 25.6 1.0 O1G A:23T881 4.3 25.9 1.0 N A:SER655 4.4 23.9 1.0 C5' A:23T881 4.4 19.5 1.0 O5' A:23T881 4.4 19.5 1.0 C A:ASP653 4.4 24.9 1.0 CB A:ASP653 4.4 24.6 1.0 CB A:ASP830 4.4 19.3 1.0 O3G A:23T881 4.5 25.2 1.0 CB A:TYR654 4.5 23.3 1.0 N A:GLN656 4.5 24.1 1.0 CA A:SER655 4.5 24.3 1.0 CG2 A:ILE657 4.6 22.1 1.0 O2A A:23T881 4.6 21.6 1.0 O A:ASP830 4.6 21.5 1.0 C A:SER655 4.7 24.5 1.0 O1B A:23T881 4.8 19.1 1.0 N A:ILE657 4.8 23.9 1.0 CA A:ASP653 4.9 25.0 1.0 CB A:ILE657 4.9 23.7 1.0 O A:ASP653 4.9 25.3 1.0

Manganese binding site 2 out of 2 in the Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ddttp:O6-Methyl-Guanine Pair in the Polymerase Active Site, in the Closed Conformation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn878 b:10.1 occ:1.00 O2G D:23T880 2.0 13.3 1.0 O1B D:23T880 2.1 11.6 1.0 OD2 D:ASP830 2.1 10.5 1.0 O1A D:23T880 2.2 12.0 1.0 O D:TYR654 2.2 11.4 1.0 OD1 D:ASP653 2.2 14.0 1.0 CG D:ASP830 3.2 11.6 1.0 CG D:ASP653 3.2 14.9 1.0 PB D:23T880 3.3 11.8 1.0 C D:TYR654 3.4 10.0 1.0 PG D:23T880 3.4 14.2 1.0 PA D:23T880 3.4 11.5 1.0 OD1 D:ASP830 3.6 9.5 1.0 OD2 D:ASP653 3.6 17.2 1.0 O3B D:23T880 3.7 14.1 1.0 O D:HOH960 3.8 18.7 1.0 O3A D:23T880 3.8 12.1 1.0 N D:TYR654 4.0 9.6 1.0 O D:HOH1025 4.1 20.2 1.0 CA D:TYR654 4.2 10.1 1.0 O D:HOH987 4.2 18.3 1.0 O1G D:23T880 4.3 12.6 1.0 C5' D:23T880 4.3 10.1 1.0 N D:SER655 4.3 11.2 1.0 O5' D:23T880 4.4 10.6 1.0 O3G D:23T880 4.4 15.1 1.0 CB D:ASP830 4.4 9.3 1.0 N D:GLN656 4.5 9.2 1.0 C D:ASP653 4.5 11.0 1.0 CA D:SER655 4.5 11.3 1.0 CB D:ASP653 4.6 14.2 1.0 CG2 D:ILE657 4.6 8.6 1.0 O2B D:23T880 4.6 12.1 1.0 CB D:TYR654 4.6 8.4 1.0 O2A D:23T880 4.6 11.5 1.0 N D:ILE657 4.7 10.1 1.0 C D:SER655 4.7 10.9 1.0 O D:ASP830 4.8 9.7 1.0 CB D:ILE657 4.9 10.0 1.0 CA D:ASP653 4.9 10.7 1.0

J.J.Warren, L.J.Forsberg, L.S.Beese. The Structural Basis For the Mutagenicity of O6-Methyl-Guanine Lesions. Proc.Natl.Acad.Sci.Usa V. 103 19701 2006.
ISSN: ISSN 0027-8424
PubMed: 17179038
DOI: 10.1073/PNAS.0609580103