Sodium in PDB 3mdc: Dna Polymerase Lambda in Complex with Dfdctp

All present enzymatic activity of Dna Polymerase Lambda in Complex with Dfdctp:
2.7.7.7;

The structure of Dna Polymerase Lambda in Complex with Dfdctp, PDB code: 3mdc was solved by M.Garcia-Diaz, M.Murray, T.Kunkel, K.M.Chou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.68 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.206, 59.773, 142.008, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 26.6

The structure of Dna Polymerase Lambda in Complex with Dfdctp also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Sodium atom in the Dna Polymerase Lambda in Complex with Dfdctp (pdb code 3mdc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Dna Polymerase Lambda in Complex with Dfdctp, PDB code: 3mdc:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Dna Polymerase Lambda in Complex with Dfdctp


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 Dfdctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na11 b:52.9 occ:1.00 O A:CYS300 2.9 49.6 1.0 OP1 D:DC3 3.0 38.3 1.0 O A:ILE305 3.1 47.0 1.0 O A:HOH153 3.2 43.9 1.0 O A:ILE302 3.5 47.6 1.0 OP2 D:DC3 3.8 38.7 1.0 P D:DC3 3.8 42.5 1.0 C A:ILE305 3.9 38.9 1.0 C A:CYS300 4.1 48.3 1.0 C A:ILE302 4.3 49.2 1.0 O D:HOH138 4.3 40.1 1.0 CA A:GLY306 4.5 40.9 1.0 N A:ILE305 4.5 40.0 1.0 N A:GLY306 4.6 36.5 1.0 N A:ILE302 4.7 38.0 1.0 CA A:PRO303 4.8 48.9 1.0 CA A:CYS300 4.8 47.3 1.0 N A:PRO303 4.8 48.8 1.0 CA A:ILE305 4.8 43.7 1.0 N A:GLY304 4.8 44.9 1.0 O3' D:DC2 4.9 43.6 1.0 C A:SER301 4.9 45.2 1.0 O5' D:DC3 5.0 28.6 1.0

Sodium binding site 2 out of 4 in the Dna Polymerase Lambda in Complex with Dfdctp


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 Dfdctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:24.9 occ:1.00 OP1 P:DA5 2.4 13.9 1.0 O A:ILE341 2.5 11.8 1.0 O A:SER339 2.5 14.9 1.0 O P:HOH7 2.5 20.0 1.0 O A:ALA344 2.6 14.9 1.0 O P:HOH86 3.0 28.7 1.0 C A:ILE341 3.4 20.2 1.0 P P:DA5 3.5 14.4 1.0 C A:SER339 3.6 19.0 1.0 C A:ALA344 3.6 16.4 1.0 OP2 P:DA5 3.7 16.6 1.0 N A:ALA344 3.8 17.0 1.0 N A:GLY343 3.8 15.7 1.0 O A:HOH101 3.9 30.1 1.0 N A:ILE341 3.9 20.6 1.0 CA A:TRP342 3.9 16.7 1.0 N A:TRP342 4.0 19.7 1.0 C A:ASN340 4.1 13.2 1.0 C A:TRP342 4.2 15.0 1.0 CA A:ALA344 4.3 15.9 1.0 O P:HOH244 4.3 35.3 1.0 CA A:ILE341 4.3 16.8 1.0 O3' P:DT4 4.4 13.7 1.0 CA A:ASN340 4.4 22.4 1.0 N A:ASN340 4.4 18.7 1.0 CA A:SER339 4.4 19.8 1.0 O P:HOH235 4.5 40.4 1.0 N A:GLY345 4.6 13.3 1.0 O A:ASN340 4.7 20.8 1.0 O5' P:DA5 4.7 15.3 1.0 C A:GLY343 4.7 19.4 1.0 O A:HOH655 4.8 33.5 1.0 CB A:ALA344 4.8 13.3 1.0 CA A:GLY345 4.8 17.2 1.0 CA A:GLY343 4.8 16.3 1.0 O A:PHE338 5.0 17.6 1.0

Sodium binding site 3 out of 4 in the Dna Polymerase Lambda in Complex with Dfdctp


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 Dfdctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na577 b:55.1 occ:1.00 O A:SER463 2.9 27.4 1.0 O A:HOH159 3.0 43.0 1.0 O T:HOH88 3.1 39.7 1.0 O A:HOH55 3.3 29.7 1.0 O A:HOH595 3.4 41.9 1.0 O T:HOH199 3.8 41.3 1.0 C A:SER463 4.1 25.0 1.0 O A:HOH642 4.4 48.4 1.0 OP1 T:DT10 4.4 19.7 1.0 O T:HOH196 4.7 48.3 1.0 CB A:SER463 4.7 27.7 1.0 CA A:SER463 4.8 29.4 1.0 OE2 A:GLU466 4.9 60.0 1.0 OE2 A:GLU465 4.9 37.3 1.0 O A:HOH638 4.9 42.5 1.0 N A:SER463 5.0 19.6 1.0 OE1 A:GLU466 5.0 40.2 1.0 N A:GLU465 5.0 34.0 1.0

Sodium binding site 4 out of 4 in the Dna Polymerase Lambda in Complex with Dfdctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dna Polymerase Lambda in Complex with Dfdctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na580 b:36.6 occ:1.00 OD1 A:ASP382 2.6 32.7 1.0 ND1 A:HIS486 2.8 25.9 1.0 O A:HOH234 2.9 34.6 1.0 O A:HOH172 3.0 39.2 1.0 O A:HOH20 3.0 27.2 1.0 NH2 A:ARG485 3.0 29.3 1.0 CG A:ASP382 3.4 27.7 1.0 CZ A:ARG485 3.6 32.0 1.0 CE1 A:HIS486 3.7 21.7 1.0 N A:HIS486 3.7 21.5 1.0 OD2 A:ASP382 3.7 28.4 1.0 CG A:HIS486 3.9 23.8 1.0 NE A:ARG485 3.9 32.8 1.0 CB A:HIS486 4.1 20.7 1.0 NH1 A:ARG485 4.4 34.5 1.0 CA A:ARG485 4.4 28.2 1.0 CA A:HIS486 4.5 23.2 1.0 C A:ARG485 4.5 31.0 1.0 ND1 A:HIS379 4.6 19.0 1.0 NH1 A:ARG478 4.6 31.3 1.0 O A:HOH648 4.7 46.9 1.0 CB A:ASP382 4.7 18.3 1.0 O A:HOH56 4.8 22.8 1.0 NE2 A:HIS486 4.9 27.5 1.0 O A:ARG484 4.9 32.6 1.0 CE1 A:HIS379 4.9 26.8 1.0 CD2 A:HIS486 5.0 22.5 1.0 CD A:ARG485 5.0 30.4 1.0

M.Garcia-Diaz, M.S.Murray, T.A.Kunkel, K.M.Chou. Interaction Between Dna Polymerase Lambda and Anticancer Nucleoside Analogs. J.Biol.Chem. V. 285 16874 2010.
ISSN: ISSN 0021-9258
PubMed: 20348107
DOI: 10.1074/JBC.M109.094391