Sodium in PDB 2bcq: Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp

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

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp, PDB code: 2bcq 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)	41.74 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.044, 62.539, 139.644, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp 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 Dtmp (pdb code 2bcq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp, PDB code: 2bcq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp


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 Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:15.3 occ:1.00 O A:HOH2815 2.3 24.8 1.0 O A:SER339 2.3 16.2 1.0 O A:ALA344 2.3 15.6 1.0 O A:ILE341 2.4 15.4 1.0 OP1 P:DA5 2.4 15.2 1.0 O P:HOH37 2.7 23.0 1.0 C A:ILE341 3.3 15.1 1.0 C A:SER339 3.4 15.9 1.0 C A:ALA344 3.5 14.4 1.0 P P:DA5 3.5 14.3 1.0 OP2 P:DA5 3.7 13.8 1.0 N A:ALA344 3.7 14.1 1.0 N A:ILE341 3.9 14.9 1.0 CA A:TRP342 3.9 14.3 1.0 N A:GLY343 3.9 13.7 1.0 O P:HOH346 4.0 34.0 1.0 N A:TRP342 4.0 15.2 1.0 O A:HOH2943 4.0 42.0 1.0 C A:ASN340 4.1 14.6 1.0 CA A:ALA344 4.1 15.2 1.0 CA A:SER339 4.2 15.9 1.0 N A:ASN340 4.2 15.5 1.0 CA A:ASN340 4.3 14.5 1.0 C A:TRP342 4.3 16.0 1.0 CA A:ILE341 4.3 14.2 1.0 O3' P:DT4 4.4 13.4 1.0 N A:GLY345 4.5 13.8 1.0 O P:HOH440 4.5 41.6 1.0 CB A:ALA344 4.6 15.6 1.0 O A:ASN340 4.7 15.4 1.0 O5' P:DA5 4.7 14.3 1.0 C A:GLY343 4.7 13.9 1.0 CA A:GLY345 4.7 14.4 1.0 CB A:SER339 4.8 16.7 1.0 CA A:GLY343 4.9 13.8 1.0 O A:PHE338 5.0 14.7 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp


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 Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na4 b:27.8 occ:1.00 O A:SER463 2.3 18.1 1.0 O A:HOH2927 2.4 35.7 1.0 O T:HOH25 2.4 30.1 1.0 O A:HOH2875 2.4 40.1 1.0 O A:HOH3042 2.6 33.4 1.0 O A:HOH2833 2.7 25.9 1.0 C A:SER463 3.5 18.5 1.0 O T:HOH74 3.7 42.3 1.0 OP1 T:DT11 3.9 17.4 1.0 OE2 A:GLU466 4.0 43.0 1.0 NA A:NA712 4.0 59.1 1.0 O T:HOH58 4.1 40.3 1.0 N A:GLU465 4.3 23.7 1.0 N A:GLN464 4.3 17.5 1.0 O A:HOH3228 4.4 62.8 1.0 CA A:SER463 4.4 17.8 1.0 CA A:GLN464 4.4 20.0 1.0 CB A:SER463 4.4 17.2 1.0 O A:HOH3126 4.4 49.6 1.0 OE1 A:GLU466 4.4 38.9 1.0 O A:HOH3069 4.5 41.7 1.0 OP2 T:DT11 4.5 18.2 1.0 N A:SER463 4.6 16.0 1.0 CD A:GLU466 4.7 41.6 1.0 OE2 A:GLU465 4.7 28.0 1.0 P T:DT11 4.8 18.0 1.0 C A:GLN464 4.9 22.0 1.0 OG A:SER463 5.0 19.3 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na712 b:59.1 occ:1.00 O T:HOH55 2.2 57.7 1.0 O A:HOH3228 2.3 62.8 1.0 O T:HOH80 2.4 51.3 1.0 O A:HOH2833 2.4 25.9 1.0 O T:HOH58 2.5 40.3 1.0 O A:HOH3042 3.3 33.4 1.0 OE2 A:GLU466 3.9 43.0 1.0 OE1 A:GLU466 3.9 38.9 1.0 O T:HOH79 4.0 44.1 1.0 NA A:NA4 4.0 27.8 1.0 CD A:GLU466 4.1 41.6 1.0 O T:HOH25 4.1 30.1 1.0 OP2 T:DT11 4.5 18.2 1.0 O A:HOH3148 4.5 39.2 1.0 O T:HOH38 4.5 33.6 1.0 OP2 T:DG12 4.6 23.9 1.0 O A:HOH2927 4.7 35.7 1.0 O T:HOH48 4.7 49.4 1.0 O A:HOH3093 5.0 48.2 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