Sodium in PDB 2bcs: Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp

All present enzymatic activity of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp:
2.7.7.7;

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp, PDB code: 2bcs 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)	26.90 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.968, 62.542, 140.817, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.1

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp (pdb code 2bcs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp, PDB code: 2bcs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na600 b:18.8 occ:1.00 O A:ALA344 2.3 22.8 1.0 OP1 P:DA5 2.3 20.9 1.0 O A:SER339 2.4 24.8 1.0 O A:ILE341 2.4 21.7 1.0 O P:HOH52 2.5 40.4 1.0 O P:HOH180 2.5 31.9 1.0 C A:ALA344 3.3 22.0 1.0 C A:ILE341 3.3 22.5 1.0 P P:DA5 3.4 23.0 1.0 C A:SER339 3.5 24.5 1.0 N A:ALA344 3.5 19.2 1.0 OP2 P:DA5 3.6 21.3 1.0 N A:GLY343 3.8 23.0 1.0 CA A:TRP342 3.9 22.7 1.0 CA A:ALA344 4.0 22.1 1.0 N A:ILE341 4.0 25.2 1.0 N A:TRP342 4.0 21.3 1.0 O A:HOH1079 4.0 60.4 1.0 C A:TRP342 4.2 21.9 1.0 CA A:SER339 4.2 26.9 1.0 O3' P:DT4 4.2 22.7 1.0 O P:HOH203 4.2 50.6 1.0 C A:ASN340 4.3 25.4 1.0 CA A:ILE341 4.4 24.2 1.0 N A:ASN340 4.4 23.2 1.0 N A:GLY345 4.4 22.3 1.0 CB A:ALA344 4.5 18.6 1.0 C A:GLY343 4.5 22.1 1.0 CA A:ASN340 4.5 24.8 1.0 O5' P:DA5 4.6 24.3 1.0 CA A:GLY345 4.7 23.8 1.0 CA A:GLY343 4.8 21.7 1.0 CB A:SER339 4.8 27.2 1.0 O A:ASN340 4.9 24.0 1.0 O A:HOH996 5.0 38.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dcmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na620 b:44.4 occ:1.00 O T:HOH44 2.3 34.1 1.0 O A:SER463 2.3 31.8 1.0 O A:HOH993 2.4 32.7 1.0 O T:HOH39 2.5 41.8 1.0 O A:HOH954 2.6 33.4 1.0 O A:HOH1002 2.7 39.7 1.0 C A:SER463 3.5 32.6 1.0 O T:HOH41 3.8 34.4 1.0 OP1 T:DT11 3.9 28.3 1.0 N A:GLU465 4.2 38.8 1.0 N A:GLN464 4.3 33.8 1.0 CA A:GLN464 4.3 37.3 1.0 CA A:SER463 4.4 31.4 1.0 CB A:SER463 4.4 31.7 1.0 O A:HOH990 4.4 49.1 1.0 OE2 A:GLU466 4.4 62.3 1.0 OE1 A:GLU466 4.5 62.0 1.0 OP2 T:DT11 4.6 31.4 1.0 N A:SER463 4.6 28.4 1.0 OE2 A:GLU465 4.7 43.4 1.0 P T:DT11 4.8 30.5 1.0 C A:GLN464 4.8 37.5 1.0 CD A:GLU466 4.9 60.6 1.0

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel. Structural Analysis of Strand Misalignment During Dna Synthesis By A Human Dna Polymerase Cell(Cambridge,Mass.) V. 124 331 2006.
ISSN: ISSN 0092-8674
PubMed: 16439207
DOI: 10.1016/J.CELL.2005.10.039