Magnesium in PDB 2pfo: Dna Polymerase Lambda in Complex with Dna and Dupnpp

All present enzymatic activity of Dna Polymerase Lambda in Complex with Dna and Dupnpp:
2.7.7.7;

The structure of Dna Polymerase Lambda in Complex with Dna and Dupnpp, PDB code: 2pfo was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.094, 61.411, 140.314, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.2

The structure of Dna Polymerase Lambda in Complex with Dna and Dupnpp also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Sodium	(Na)	4 atoms

The binding sites of Magnesium atom in the Dna Polymerase Lambda in Complex with Dna and Dupnpp (pdb code 2pfo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Lambda in Complex with Dna and Dupnpp, PDB code: 2pfo:

Magnesium binding site 1 out of 1 in the Dna Polymerase Lambda in Complex with Dna and Dupnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Lambda in Complex with Dna and Dupnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg950 b:20.3 occ:1.00 O2B A:DUP952 1.9 20.1 1.0 O2A A:DUP952 2.0 16.5 1.0 OD2 A:ASP427 2.1 20.3 1.0 O3G A:DUP952 2.1 23.5 1.0 OD2 A:ASP429 2.1 20.9 1.0 O A:HOH2812 2.3 28.3 1.0 PB A:DUP952 2.9 24.2 1.0 PA A:DUP952 3.1 22.2 1.0 N3A A:DUP952 3.1 22.8 1.0 CG A:ASP427 3.2 21.5 1.0 CG A:ASP429 3.2 22.1 1.0 PG A:DUP952 3.2 24.9 1.0 O3B A:DUP952 3.4 25.1 1.0 MN A:MN951 3.5 22.5 1.0 OD1 A:ASP427 3.5 24.0 1.0 OD1 A:ASP429 3.6 18.9 1.0 O A:HOH2948 3.8 26.4 1.0 O2G A:DUP952 3.8 23.8 1.0 C5' A:DUP952 4.0 22.9 1.0 O5' A:DUP952 4.0 20.7 1.0 O A:ASP427 4.1 21.4 1.0 O1A A:DUP952 4.2 20.6 1.0 O1B A:DUP952 4.3 25.2 1.0 OG A:SER417 4.3 23.6 1.0 N A:SER417 4.3 25.9 1.0 O1G A:DUP952 4.4 25.1 1.0 O A:HOH2816 4.4 16.9 1.0 C A:ASP427 4.4 22.5 1.0 N A:ASP427 4.4 23.1 1.0 CB A:ASP427 4.5 21.2 1.0 CA A:GLY416 4.5 27.0 1.0 CB A:ASP429 4.5 22.9 1.0 O A:HOH2807 4.5 15.1 1.0 CA A:ASP427 4.7 21.2 1.0 N A:ASP429 4.9 22.0 1.0 CB A:SER417 4.9 24.6 1.0 C A:GLY416 5.0 27.8 1.0

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel. Role of the Catalytic Metal During Polymerization By Dna Polymerase Lambda. Dna Repair V. 6 1333 2007.
ISSN: ISSN 1568-7864
PubMed: 17475573
DOI: 10.1016/J.DNAREP.2007.03.005