Sodium in PDB 2bcu: Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp and A T:T Mismatch

All present enzymatic activity of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp and A T:T Mismatch:
2.7.7.7;

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp and A T:T Mismatch, PDB code: 2bcu 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)	40.03 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.998, 62.667, 140.494, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24.7

The binding sites of Sodium atom in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp and A T:T Mismatch (pdb code 2bcu). 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 Damp and A T:T Mismatch, PDB code: 2bcu:
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 Damp and A T:T Mismatch


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 Damp and A T:T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na576 b:30.5 occ:1.00 O12 A:PPV579 2.3 33.0 1.0 OD1 A:ASP427 2.3 31.1 1.0 O A:HOH601 2.4 31.4 1.0 OD2 A:ASP429 2.5 26.7 1.0 OP1 P:DG7 2.7 21.8 1.0 O A:HOH603 2.7 29.2 1.0 O22 A:PPV579 2.9 42.0 1.0 P2 A:PPV579 3.0 35.6 1.0 CG A:ASP427 3.1 30.1 1.0 CG A:ASP429 3.4 27.6 1.0 OD2 A:ASP427 3.4 27.6 1.0 OD1 A:ASP429 3.6 24.5 1.0 O11 A:PPV579 3.6 39.8 1.0 P P:DG7 3.8 25.7 1.0 OPP A:PPV579 4.0 42.2 1.0 O5' P:DG7 4.1 26.1 1.0 C5' P:DG7 4.1 23.5 1.0 O A:ASP427 4.1 32.3 1.0 O A:HOH664 4.3 50.1 1.0 P1 A:PPV579 4.3 47.4 1.0 N A:ASP427 4.4 31.3 1.0 N A:SER417 4.4 27.4 1.0 CA A:GLY416 4.4 27.4 1.0 OG A:SER417 4.4 27.7 1.0 O32 A:PPV579 4.4 37.7 1.0 O31 A:PPV579 4.5 47.6 1.0 C A:ASP427 4.5 30.1 1.0 OP2 P:DG7 4.5 26.7 1.0 CB A:ASP427 4.5 27.9 1.0 O A:HOH583 4.6 23.5 1.0 CB A:ASP429 4.7 27.0 1.0 CA A:ASP427 4.7 29.7 1.0 C A:GLY416 4.9 28.8 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp and A T:T Mismatch


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 Damp and A T:T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na577 b:23.8 occ:1.00 O A:ALA344 2.2 22.9 1.0 OP1 P:DT5 2.3 26.0 1.0 O A:ILE341 2.4 21.3 1.0 O A:SER339 2.5 25.6 1.0 O A:HOH611 2.6 29.7 1.0 O P:HOH95 2.7 37.9 1.0 C A:ALA344 3.3 24.3 1.0 P P:DT5 3.4 25.7 1.0 C A:ILE341 3.4 20.1 1.0 C A:SER339 3.5 27.3 1.0 N A:ALA344 3.6 21.3 1.0 OP2 P:DT5 3.7 26.5 1.0 N A:GLY343 3.9 22.6 1.0 O A:HOH632 3.9 42.0 1.0 CA A:ALA344 4.0 22.9 1.0 CA A:TRP342 4.0 22.0 1.0 N A:ILE341 4.0 21.3 1.0 O P:HOH154 4.0 43.1 1.0 N A:TRP342 4.1 21.6 1.0 C A:TRP342 4.2 21.9 1.0 CA A:SER339 4.3 28.2 1.0 O3' P:DT4 4.3 24.1 1.0 C A:ASN340 4.3 24.3 1.0 N A:GLY345 4.3 24.6 1.0 CA A:ILE341 4.4 21.4 1.0 N A:ASN340 4.5 26.0 1.0 C A:GLY343 4.5 21.7 1.0 CB A:ALA344 4.5 20.5 1.0 OG A:SER339 4.5 40.6 1.0 CA A:ASN340 4.6 24.4 1.0 O5' P:DT5 4.6 26.8 1.0 CA A:GLY345 4.6 25.3 1.0 CA A:GLY343 4.8 21.5 1.0 O A:PHE338 5.0 23.6 1.0 O A:ASN340 5.0 24.0 1.0 O A:HOH599 5.0 40.9 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp and A T:T Mismatch


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 Damp and A T:T Mismatch within 5.0Å range: probe atom residue distance (Å) B Occ A:Na578 b:55.4 occ:1.00 O A:SER463 2.2 41.6 1.0 O T:HOH24 2.3 34.5 1.0 O T:HOH41 2.7 65.5 1.0 O A:HOH692 2.8 58.8 1.0 C A:SER463 3.2 42.8 1.0 OP1 T:DT11 3.5 39.4 1.0 N A:GLN464 4.1 44.9 1.0 OE1 A:GLU466 4.1 71.8 1.0 CA A:GLN464 4.1 48.2 1.0 CA A:SER463 4.2 40.8 1.0 N A:SER463 4.3 36.3 1.0 N A:GLU465 4.3 51.5 1.0 CB A:SER463 4.4 38.9 1.0 O T:HOH35 4.4 52.0 1.0 P T:DT11 4.6 41.6 1.0 OE2 A:GLU466 4.6 71.8 1.0 OP2 T:DT11 4.6 42.3 1.0 CD A:GLU466 4.8 70.9 1.0 C A:GLN464 4.8 49.8 1.0 OE2 A:GLU465 4.9 53.6 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