Magnesium in PDB 2hvi: Ddctp:G Pair in the Polymerase Active Site (0 Position)

All present enzymatic activity of Ddctp:G Pair in the Polymerase Active Site (0 Position):
2.7.7.7;

The structure of Ddctp:G Pair in the Polymerase Active Site (0 Position), PDB code: 2hvi 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 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.795, 108.492, 149.403, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.1

The binding sites of Magnesium atom in the Ddctp:G Pair in the Polymerase Active Site (0 Position) (pdb code 2hvi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ddctp:G Pair in the Polymerase Active Site (0 Position), PDB code: 2hvi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ddctp:G Pair in the Polymerase Active Site (0 Position)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ddctp:G Pair in the Polymerase Active Site (0 Position) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg878 b:24.9 occ:1.00 O2G A:DCT201 1.9 32.9 1.0 OD2 A:ASP830 2.1 26.4 1.0 O2A A:DCT201 2.1 26.3 1.0 O A:TYR654 2.2 24.6 1.0 O2B A:DCT201 2.2 26.1 1.0 OD1 A:ASP653 2.4 38.2 1.0 OD2 A:ASP653 2.7 39.7 1.0 CG A:ASP653 2.9 37.2 1.0 CG A:ASP830 3.1 27.8 1.0 C A:TYR654 3.4 26.2 1.0 PB A:DCT201 3.4 29.7 1.0 PG A:DCT201 3.4 32.7 1.0 PA A:DCT201 3.5 29.0 1.0 OD1 A:ASP830 3.5 28.4 1.0 O A:HOH3262 3.7 36.8 1.0 O3B A:DCT201 3.8 31.3 1.0 O3A A:DCT201 3.9 29.1 1.0 O A:HOH3244 4.0 36.9 1.0 N A:TYR654 4.0 27.6 1.0 O A:HOH3253 4.2 43.4 1.0 CA A:TYR654 4.2 27.2 1.0 C5' A:DCT201 4.3 26.9 1.0 O3G A:DCT201 4.3 32.9 1.0 N A:SER655 4.3 27.9 1.0 CB A:ASP653 4.4 32.2 1.0 O5' A:DCT201 4.4 27.9 1.0 O1G A:DCT201 4.4 31.6 1.0 CB A:ASP830 4.5 25.3 1.0 CA A:SER655 4.5 27.6 1.0 C A:ASP653 4.5 28.7 1.0 N A:GLN656 4.6 28.1 1.0 O1A A:DCT201 4.6 29.6 1.0 CB A:TYR654 4.7 27.4 1.0 O1B A:DCT201 4.7 30.0 1.0 O A:ASP830 4.7 26.6 1.0 C A:SER655 4.8 27.9 1.0 CG2 A:ILE657 4.8 28.2 1.0 N A:ILE657 4.9 29.6 1.0 CA A:ASP653 5.0 29.8 1.0 O A:ASP653 5.0 27.7 1.0

Magnesium binding site 2 out of 2 in the Ddctp:G Pair in the Polymerase Active Site (0 Position)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ddctp:G Pair in the Polymerase Active Site (0 Position) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg878 b:20.9 occ:1.00 OD2 D:ASP830 2.0 20.6 1.0 O2G D:DCT202 2.0 35.3 1.0 O2B D:DCT202 2.1 29.3 1.0 O D:TYR654 2.2 20.6 1.0 O2A D:DCT202 2.2 21.2 1.0 CG D:ASP830 3.2 22.9 1.0 C D:TYR654 3.4 20.6 1.0 PB D:DCT202 3.4 26.9 1.0 PG D:DCT202 3.5 33.3 1.0 PA D:DCT202 3.6 23.1 1.0 OD1 D:ASP830 3.8 20.8 1.0 OD2 D:ASP653 3.9 34.6 1.0 O3B D:DCT202 3.9 32.3 1.0 O3A D:DCT202 3.9 27.0 1.0 O D:HOH3133 4.1 39.9 1.0 O3G D:DCT202 4.2 34.2 1.0 N D:SER655 4.3 19.2 1.0 N D:TYR654 4.3 20.5 1.0 C5' D:DCT202 4.3 22.5 1.0 CA D:SER655 4.3 20.3 1.0 CB D:ASP830 4.3 19.3 1.0 CA D:TYR654 4.4 21.2 1.0 N D:GLN656 4.4 19.4 1.0 O5' D:DCT202 4.4 23.8 1.0 O1G D:DCT202 4.5 30.6 1.0 O D:HOH3182 4.6 44.4 1.0 O D:HOH3126 4.6 30.9 1.0 CB D:ASP653 4.6 26.1 1.0 CG2 D:ILE657 4.6 20.0 1.0 O1B D:DCT202 4.7 28.2 1.0 O1A D:DCT202 4.7 23.1 1.0 C D:SER655 4.7 19.0 1.0 CG D:ASP653 4.7 30.6 1.0 CB D:TYR654 4.8 18.4 1.0 O D:ASP830 4.8 19.9 1.0 C D:ASP653 4.9 22.4 1.0 N D:ILE657 4.9 20.8 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