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

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

The structure of Dna Polymerase Lambda in Complex with Dttp and A Dna Duplex Containing An Unpaired Dtmp, PDB code: 2bcv 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)	31.19 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.140, 62.988, 141.936, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.2

The structure of Dna Polymerase Lambda in Complex with Dttp and 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 Dttp and A Dna Duplex Containing An Unpaired Dtmp (pdb code 2bcv). 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 Dttp and A Dna Duplex Containing An Unpaired Dtmp, PDB code: 2bcv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Lambda in Complex with Dttp and 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 Dttp and A Dna Duplex Containing An Unpaired Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na577 b:24.1 occ:1.00 O A:ALA344 2.4 21.8 1.0 OP1 P:DA5 2.5 17.0 1.0 O A:SER339 2.5 25.1 1.0 O A:ILE341 2.6 16.7 1.0 O P:HOH109 2.7 37.7 1.0 O A:HOH581 2.7 31.1 1.0 C A:ILE341 3.4 19.4 1.0 C A:SER339 3.5 23.3 1.0 P P:DA5 3.5 19.4 1.0 C A:ALA344 3.5 20.1 1.0 OP2 P:DA5 3.7 17.0 1.0 N A:ALA344 3.7 18.7 1.0 N A:ILE341 3.9 20.3 1.0 N A:GLY343 3.9 21.6 1.0 CA A:TRP342 4.0 19.4 1.0 N A:TRP342 4.1 20.6 1.0 O P:HOH271 4.1 52.0 1.0 C A:ASN340 4.1 22.7 1.0 O A:HOH735 4.1 47.6 1.0 CA A:ALA344 4.1 20.5 1.0 N A:ASN340 4.2 23.1 1.0 CA A:SER339 4.3 22.5 1.0 CA A:ASN340 4.3 23.0 1.0 C A:TRP342 4.3 21.0 1.0 O3' P:DT4 4.3 17.3 1.0 CA A:ILE341 4.4 20.0 1.0 N A:GLY345 4.6 18.8 1.0 CB A:ALA344 4.6 15.9 1.0 O A:ASN340 4.7 23.9 1.0 C A:GLY343 4.7 19.4 1.0 O P:HOH250 4.7 51.0 1.0 O5' P:DA5 4.8 20.1 1.0 CA A:GLY345 4.8 20.8 1.0 CA A:GLY343 4.9 18.8 1.0 CB A:SER339 4.9 22.1 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Lambda in Complex with Dttp and 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 Dttp and A Dna Duplex Containing An Unpaired Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na578 b:36.4 occ:1.00 O T:HOH61 2.3 36.9 1.0 O A:SER463 2.5 28.2 1.0 O A:HOH721 2.5 41.2 1.0 O T:HOH46 2.6 40.6 1.0 O A:HOH754 2.7 40.8 1.0 O T:HOH28 3.0 32.2 1.0 C A:SER463 3.5 27.2 1.0 OP1 T:DT11 3.7 25.1 1.0 O T:HOH42 3.8 40.8 1.0 O T:HOH45 4.0 44.5 1.0 OE2 A:GLU466 4.3 49.1 1.0 N A:GLN464 4.4 28.0 1.0 N A:GLU465 4.4 30.9 1.0 CA A:SER463 4.4 26.2 1.0 CA A:GLN464 4.4 29.4 1.0 CB A:SER463 4.4 26.0 1.0 OP2 T:DT11 4.5 25.7 1.0 N A:SER463 4.5 23.1 1.0 P T:DT11 4.6 25.4 1.0 OE2 A:GLU465 4.9 31.6 1.0 C A:GLN464 5.0 29.2 1.0 OG A:SER463 5.0 27.1 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Lambda in Complex with Dttp and 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 Dttp and A Dna Duplex Containing An Unpaired Dtmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na579 b:27.2 occ:1.00 OD1 A:ASP429 2.4 19.3 1.0 OD1 A:ASP427 2.4 23.4 1.0 OD1 A:ASP490 2.5 21.9 1.0 O1A A:TTP580 2.6 19.4 1.0 O P:HOH45 2.7 27.8 1.0 CG A:ASP427 3.3 24.8 1.0 CG A:ASP490 3.3 19.8 1.0 CB A:ASP490 3.3 18.0 1.0 OD2 A:ASP427 3.3 25.1 1.0 CG A:ASP429 3.4 22.0 1.0 PA A:TTP580 3.5 22.4 1.0 MG A:MG576 3.6 29.6 1.0 O5' A:TTP580 3.6 22.6 1.0 C3' P:O2C6 3.7 20.3 1.0 OD2 A:ASP429 3.8 20.4 1.0 C5' A:TTP580 3.8 19.5 1.0 O A:HOH587 3.9 25.9 1.0 O2A A:TTP580 4.0 22.3 1.0 O A:HOH632 4.1 37.2 1.0 C4' P:O2C6 4.1 20.7 1.0 C5' P:O2C6 4.2 21.7 1.0 OD2 A:ASP490 4.5 21.3 1.0 CB A:ASP427 4.7 21.7 1.0 CB A:ASP429 4.7 20.1 1.0 O3G A:TTP580 4.8 27.7 1.0 CA A:ASP490 4.8 20.4 1.0 O1P P:O2C6 4.8 19.3 1.0 O3A A:TTP580 4.9 23.4 1.0 O5' P:O2C6 4.9 21.7 1.0 CE2 A:PHE506 4.9 21.9 1.0 C2' P:O2C6 4.9 22.0 1.0 O2' P:O2C6 4.9 21.6 1.0 O1B A:TTP580 5.0 20.1 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