Sodium in PDB 2pfo: Dna Polymerase Lambda in Complex with Dna and Dupnpp

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

The structure of Dna Polymerase Lambda in Complex with Dna and Dupnpp, PDB code: 2pfo 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)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.094, 61.411, 140.314, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.2

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

Magnesium	(Mg)	1 atom
Manganese	(Mn)	1 atom

The binding sites of Sodium atom in the Dna Polymerase Lambda in Complex with Dna and Dupnpp (pdb code 2pfo). 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 Dna and Dupnpp, PDB code: 2pfo:
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 Dna and Dupnpp


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 Dna and Dupnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na600 b:41.5 occ:1.00 O A:SER463 2.3 26.2 1.0 O T:HOH157 2.3 42.7 1.0 O T:HOH241 2.6 56.1 1.0 O T:HOH117 2.6 35.8 1.0 O A:HOH2905 2.7 43.9 1.0 O A:HOH2848 3.0 42.7 1.0 C A:SER463 3.4 27.0 1.0 OP1 T:DT10 3.6 27.0 1.0 O A:HOH2965 4.1 42.2 1.0 CA A:SER463 4.2 26.3 1.0 N A:GLN464 4.3 27.6 1.0 OE1 A:GLU466 4.3 59.6 1.0 CB A:SER463 4.3 25.9 1.0 N A:SER463 4.3 24.5 1.0 CA A:GLN464 4.4 30.6 1.0 N A:GLU465 4.5 35.1 1.0 OP2 T:DT10 4.6 28.5 1.0 P T:DT10 4.6 31.0 1.0 OE2 A:GLU466 4.6 60.1 1.0 CD A:GLU466 4.9 58.2 1.0 OE2 A:GLU465 5.0 38.4 1.0

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


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 Dna and Dupnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:21.7 occ:1.00 OP1 P:DA5 2.3 15.1 1.0 O A:ALA344 2.3 18.6 1.0 O A:SER339 2.3 17.4 1.0 O P:HOH152 2.5 23.3 1.0 O A:ILE341 2.5 18.1 1.0 O P:HOH80 2.7 25.7 1.0 C A:ALA344 3.3 16.9 1.0 C A:SER339 3.3 20.3 1.0 P P:DA5 3.4 17.2 1.0 NA A:NA602 3.4 46.4 1.0 C A:ILE341 3.5 19.6 1.0 OP2 P:DA5 3.6 17.4 1.0 N A:ALA344 3.6 15.7 1.0 N A:GLY343 3.9 17.0 1.0 CA A:ALA344 4.0 15.5 1.0 CA A:SER339 4.0 20.8 1.0 N A:ILE341 4.1 19.0 1.0 CA A:TRP342 4.1 17.9 1.0 O P:HOH217 4.1 29.8 1.0 N A:TRP342 4.2 17.6 1.0 N A:GLY345 4.3 17.9 1.0 N A:ASN340 4.3 20.7 1.0 C A:ASN340 4.3 19.0 1.0 C A:TRP342 4.3 17.4 1.0 O3' P:DT4 4.4 15.7 1.0 CA A:ILE341 4.5 19.0 1.0 O5' P:DA5 4.5 17.1 1.0 CA A:ASN340 4.5 20.1 1.0 CA A:GLY345 4.5 17.5 1.0 CB A:ALA344 4.5 14.2 1.0 C A:GLY343 4.6 16.7 1.0 CB A:SER339 4.6 20.3 1.0 O A:HOH2822 4.8 35.0 1.0 CA A:GLY343 4.9 16.2 1.0 O P:HOH195 4.9 40.4 1.0 O A:ASN340 4.9 21.4 1.0 O A:PHE338 4.9 20.2 1.0 O A:HOH2895 5.0 35.7 1.0

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


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 Dna and Dupnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:46.4 occ:1.00 O A:HOH2895 2.4 35.7 1.0 O P:HOH80 2.5 25.7 1.0 O A:HOH3013 2.6 55.0 1.0 O P:HOH152 2.7 23.3 1.0 O P:HOH217 2.7 29.8 1.0 O A:SER339 2.8 17.4 1.0 NA A:NA601 3.4 21.7 1.0 C A:SER339 3.8 20.3 1.0 O A:HOH2917 4.0 28.5 1.0 OD1 A:ASN340 4.2 22.9 1.0 O P:HOH195 4.2 40.4 1.0 CA A:ASN340 4.2 20.1 1.0 N A:ASN340 4.5 20.7 1.0 O A:HOH2822 4.7 35.0 1.0 OP1 P:DA5 4.7 15.1 1.0 O A:HOH2899 4.7 30.2 1.0 OP2 P:DA5 4.8 17.4 1.0 CB A:SER339 4.8 20.3 1.0 CA A:SER339 4.9 20.8 1.0 C A:ASN340 4.9 19.0 1.0 OG A:SER339 5.0 28.7 1.0

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


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 Dna and Dupnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:39.9 occ:0.50 O A:ILE302 1.7 65.6 1.0 O A:HOH2978 2.0 60.2 1.0 O A:CYS300 2.1 73.5 1.0 C A:ILE302 2.6 66.1 1.0 O A:SER301 3.1 71.6 1.0 O A:ILE305 3.2 57.6 1.0 C A:CYS300 3.2 73.8 1.0 N A:PRO303 3.2 64.9 1.0 OP1 D:DC3 3.3 48.5 1.0 C A:SER301 3.3 70.7 1.0 CA A:PRO303 3.3 64.3 1.0 N A:ILE302 3.6 68.7 1.0 CA A:ILE302 3.6 67.1 1.0 O A:HOH3021 3.7 52.2 1.0 N A:GLY304 3.9 61.3 1.0 N A:ILE305 4.0 58.2 1.0 C A:PRO303 4.0 62.9 1.0 N A:SER301 4.1 72.7 1.0 C A:ILE305 4.1 57.1 1.0 CA A:SER301 4.1 71.8 1.0 CA A:CYS300 4.2 74.2 1.0 O A:ALA299 4.3 76.3 1.0 P D:DC3 4.4 48.4 1.0 CA A:ILE305 4.5 57.1 1.0 OP2 D:DC3 4.5 48.5 1.0 CD A:PRO303 4.6 64.2 1.0 CB A:PRO303 4.6 64.1 1.0 CB A:ILE305 4.6 56.5 1.0 CB A:ILE302 4.6 66.0 1.0

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, L.C.Pedersen, T.A.Kunkel. Role of the Catalytic Metal During Polymerization By Dna Polymerase Lambda. Dna Repair V. 6 1333 2007.
ISSN: ISSN 1568-7864
PubMed: 17475573
DOI: 10.1016/J.DNAREP.2007.03.005