Sodium in PDB 3mgi: Ternary Complex of A Dna Polymerase Lambda Loop Mutant

All present enzymatic activity of Ternary Complex of A Dna Polymerase Lambda Loop Mutant:
2.7.7.7;

The structure of Ternary Complex of A Dna Polymerase Lambda Loop Mutant, PDB code: 3mgi was solved by M.Garcia-Diaz, K.Bebenek, R.Z.Zhou, L.F.Povirk, T.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.11 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.177, 63.235, 140.382, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 27

The structure of Ternary Complex of A Dna Polymerase Lambda Loop Mutant also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Ternary Complex of A Dna Polymerase Lambda Loop Mutant (pdb code 3mgi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Ternary Complex of A Dna Polymerase Lambda Loop Mutant, PDB code: 3mgi:

Sodium binding site 1 out of 1 in the Ternary Complex of A Dna Polymerase Lambda Loop Mutant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of A Dna Polymerase Lambda Loop Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na578 b:36.0 occ:1.00 O A:SER339 2.9 26.6 1.0 OP1 P:DA5 2.9 21.4 1.0 O A:HOH4 3.0 35.6 1.0 O A:ALA344 3.0 22.6 1.0 O P:HOH95 3.1 27.0 1.0 O A:ILE341 3.1 22.6 1.0 O P:HOH15 3.3 24.9 1.0 O A:HOH13 3.5 25.3 1.0 C A:ILE341 3.7 22.3 1.0 C A:SER339 3.7 26.1 1.0 OP2 P:DA5 3.8 15.0 1.0 P P:DA5 3.8 19.5 1.0 C A:ASN340 4.0 18.9 1.0 N A:ILE341 4.1 22.7 1.0 CA A:ASN340 4.1 20.2 1.0 C A:ALA344 4.2 20.3 1.0 CA A:TRP342 4.2 22.5 1.0 N A:TRP342 4.2 23.9 1.0 N A:ASN340 4.3 24.9 1.0 N A:ALA344 4.5 16.9 1.0 O A:ASN340 4.6 20.5 1.0 CA A:ILE341 4.6 20.3 1.0 N A:GLY343 4.6 20.5 1.0 CA A:SER339 4.7 30.4 1.0 C A:TRP342 4.8 17.9 1.0 O3' P:DT4 4.9 15.6 1.0 CA A:ALA344 4.9 16.3 1.0 O5' P:DA5 5.0 19.3 1.0

K.Bebenek, M.Garcia-Diaz, R.Z.Zhou, L.F.Povirk, T.A.Kunkel. Loop 1 Modulates the Fidelity of Dna Polymerase Lambda Nucleic Acids Res. V. 38 5419 2010.
ISSN: ISSN 0305-1048
PubMed: 20435673
DOI: 10.1093/NAR/GKQ261