Magnesium in PDB 2pfn: Na in the Active Site of Dna Polymerase Lambda

All present enzymatic activity of Na in the Active Site of Dna Polymerase Lambda:
2.7.7.7;

The structure of Na in the Active Site of Dna Polymerase Lambda, PDB code: 2pfn 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 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.082, 61.557, 140.532, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.2

The structure of Na in the Active Site of Dna Polymerase Lambda also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Magnesium atom in the Na in the Active Site of Dna Polymerase Lambda (pdb code 2pfn). 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 Na in the Active Site of Dna Polymerase Lambda, PDB code: 2pfn:

Magnesium binding site 1 out of 1 in the Na in the Active Site of Dna Polymerase Lambda


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Na in the Active Site of Dna Polymerase Lambda within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg950 b:25.6 occ:1.00 OD2 A:ASP427 1.9 26.7 1.0 O2B A:DUP952 2.0 21.8 1.0 OD2 A:ASP429 2.1 24.8 1.0 O2A A:DUP952 2.1 20.0 1.0 O A:HOH1052 2.1 29.0 1.0 O3G A:DUP952 2.2 22.9 1.0 CG A:ASP427 3.0 29.1 1.0 CG A:ASP429 3.0 24.3 1.0 PB A:DUP952 3.1 25.4 1.0 PA A:DUP952 3.3 21.7 1.0 PG A:DUP952 3.3 27.6 1.0 OD1 A:ASP429 3.4 19.5 1.0 N3A A:DUP952 3.4 24.0 1.0 NA A:NA951 3.4 29.2 1.0 OD1 A:ASP427 3.4 30.3 1.0 O3B A:DUP952 3.6 25.5 1.0 O2G A:DUP952 3.9 26.3 1.0 O A:ASP427 3.9 24.9 1.0 O A:HOH961 3.9 30.9 1.0 C5' A:DUP952 4.2 23.6 1.0 C A:ASP427 4.2 26.6 1.0 O A:HOH960 4.2 24.5 1.0 N A:ASP427 4.2 25.2 1.0 O5' A:DUP952 4.2 21.4 1.0 CB A:ASP427 4.3 26.8 1.0 OG A:SER417 4.3 24.1 1.0 O1A A:DUP952 4.4 23.2 1.0 CB A:ASP429 4.4 23.8 1.0 O1B A:DUP952 4.4 25.5 1.0 CA A:ASP427 4.5 25.3 1.0 O1G A:DUP952 4.5 27.1 1.0 N A:SER417 4.5 27.3 1.0 CA A:GLY416 4.7 27.7 1.0 O A:HOH1045 4.7 36.0 1.0 N A:ASP429 4.8 25.2 1.0 N A:VAL428 4.8 26.2 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