Magnesium in PDB 1bpy: Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp:
2.7.7.7;

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp, PDB code: 1bpy was solved by M.R.Sawaya, H.Pelletier, R.Prasad, S.H.Wilson, J.Kraut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.543, 79.817, 54.942, 90.00, 107.11, 90.00
R / Rfree (%)	23.2 / 33

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp (pdb code 1bpy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp, PDB code: 1bpy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg339 b:45.8 occ:1.00 O1A A:DCT338 1.9 43.1 1.0 OD1 A:ASP190 2.0 46.0 1.0 OD2 A:ASP192 2.0 39.0 1.0 O A:HOH530 2.0 49.4 1.0 O1G A:DCT338 2.0 44.1 1.0 O2B A:DCT338 2.1 39.1 1.0 CG A:ASP190 3.0 38.9 1.0 CG A:ASP192 3.0 32.4 1.0 PB A:DCT338 3.1 44.5 1.0 PA A:DCT338 3.2 46.2 1.0 PG A:DCT338 3.2 48.1 1.0 MG A:MG340 3.4 49.6 1.0 O3A A:DCT338 3.4 33.5 1.0 O3B A:DCT338 3.5 57.3 1.0 OD1 A:ASP192 3.5 43.7 1.0 OD2 A:ASP190 3.5 44.1 1.0 O A:ASP190 3.9 55.1 1.0 O2G A:DCT338 4.0 40.5 1.0 O A:HOH609 4.0 58.2 1.0 C5' A:DCT338 4.1 40.2 1.0 C A:ASP190 4.1 49.5 1.0 O5' A:DCT338 4.1 45.9 1.0 N A:ASP190 4.2 45.7 1.0 OG A:SER180 4.2 64.2 1.0 CB A:ASP190 4.2 45.4 1.0 O2A A:DCT338 4.3 27.9 1.0 CB A:ASP192 4.4 30.7 1.0 CA A:ASP190 4.4 41.6 1.0 CA A:GLY179 4.4 35.8 1.0 O3G A:DCT338 4.4 42.7 1.0 N A:SER180 4.5 44.1 1.0 O A:HOH593 4.5 53.0 1.0 O1B A:DCT338 4.6 55.6 1.0 N A:MET191 4.8 51.5 1.0 N A:ASP192 4.8 52.7 1.0 C A:GLY179 4.9 48.6 1.0 C A:MET191 5.0 52.6 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg340 b:49.6 occ:1.00 OD1 A:ASP192 2.2 43.7 1.0 OD2 A:ASP190 2.2 44.1 1.0 O1A A:DCT338 2.4 43.1 1.0 OD2 A:ASP256 2.6 48.4 1.0 OD1 A:ASP190 2.7 46.0 1.0 CG A:ASP190 2.8 38.9 1.0 CG A:ASP192 3.1 32.4 1.0 OD2 A:ASP192 3.3 39.0 1.0 MG A:MG339 3.4 45.8 1.0 PA A:DCT338 3.5 46.2 1.0 C3' P:DOC10 3.7 56.8 1.0 CG A:ASP256 3.8 44.8 1.0 O2A A:DCT338 4.0 27.9 1.0 O5' A:DCT338 4.1 45.9 1.0 CB A:ASP190 4.1 45.4 1.0 O A:HOH609 4.2 58.2 1.0 CB A:ASP256 4.3 51.0 1.0 C5' A:DCT338 4.3 40.2 1.0 O A:MET191 4.3 48.7 1.0 O1G A:DCT338 4.4 44.1 1.0 CB A:ASP192 4.4 30.7 1.0 C5' P:DOC10 4.6 48.3 1.0 C4' P:DOC10 4.6 53.1 1.0 OD1 A:ASP256 4.8 46.6 1.0 C A:MET191 4.8 52.6 1.0 OP1 P:DOC10 4.8 51.1 1.0 C2' P:DOC10 4.8 51.6 1.0 O3A A:DCT338 4.9 33.5 1.0 CA A:ASP192 4.9 41.8 1.0 O2B A:DCT338 5.0 39.1 1.0

M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier. Crystal Structures of Human Dna Polymerase Beta Complexed with Gapped and Nicked Dna: Evidence For An Induced Fit Mechanism. Biochemistry V. 36 11205 1997.
ISSN: ISSN 0006-2960
PubMed: 9287163
DOI: 10.1021/BI9703812