Sodium in PDB 2bcr: Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp

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

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp, PDB code: 2bcr 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)	41.87 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.076, 62.925, 139.364, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.1

The structure of Dna Polymerase Lambda in Complex with A Dna Duplex Containing An Unpaired Damp 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 Damp (pdb code 2bcr). 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, PDB code: 2bcr:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:25.3 occ:1.00 O A:SER463 2.4 18.2 1.0 O T:HOH98 2.4 27.5 1.0 O A:HOH945 2.4 31.9 1.0 O T:HOH54 2.4 32.0 1.0 O T:HOH40 2.5 27.5 1.0 O A:HOH946 2.8 40.2 1.0 O T:HOH60 3.5 40.0 1.0 C A:SER463 3.5 19.1 1.0 OP1 T:DT11 3.9 17.3 1.0 OE1 A:GLU466 4.2 44.3 1.0 O A:HOH1076 4.3 42.9 1.0 O A:HOH922 4.3 43.6 1.0 N A:GLU465 4.3 24.0 1.0 N A:GLN464 4.4 20.1 1.0 CA A:GLN464 4.4 21.1 1.0 CA A:SER463 4.5 18.5 1.0 OP2 T:DT11 4.5 18.3 1.0 CB A:SER463 4.5 19.6 1.0 N A:SER463 4.7 16.7 1.0 P T:DT11 4.7 18.8 1.0 OE2 A:GLU465 4.8 29.0 1.0 OE2 A:GLU466 4.9 46.3 1.0 C A:GLN464 5.0 22.1 1.0 CD A:GLU466 5.0 42.7 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:14.8 occ:1.00 O A:ALA344 2.3 15.2 1.0 O A:SER339 2.3 15.6 0.5 O A:SER339 2.4 16.3 0.5 OP1 P:DA5 2.4 14.4 1.0 O P:HOH251 2.4 24.4 1.0 O A:ILE341 2.5 14.1 1.0 O P:HOH45 2.7 20.6 1.0 C A:ILE341 3.4 15.0 1.0 P P:DA5 3.4 14.5 1.0 C A:ALA344 3.5 14.5 1.0 C A:SER339 3.5 15.1 0.5 O A:HOH991 3.5 36.9 1.0 C A:SER339 3.5 15.6 0.5 OP2 P:DA5 3.7 13.8 1.0 N A:ALA344 3.7 13.8 1.0 CA A:TRP342 3.9 15.5 1.0 N A:ILE341 3.9 15.8 1.0 N A:GLY343 3.9 13.4 1.0 N A:TRP342 4.0 15.6 1.0 O P:HOH242 4.1 35.6 1.0 CA A:ALA344 4.1 14.6 1.0 C A:ASN340 4.1 15.8 1.0 C A:TRP342 4.3 15.3 1.0 CA A:SER339 4.3 16.1 0.5 O3' P:DT4 4.3 14.2 1.0 N A:ASN340 4.4 14.4 1.0 CA A:ASN340 4.4 14.7 1.0 CA A:SER339 4.4 16.9 0.5 CA A:ILE341 4.4 14.7 1.0 OG A:SER339 4.4 20.5 0.5 N A:GLY345 4.5 13.2 1.0 CB A:ALA344 4.5 12.3 1.0 O P:HOH347 4.7 41.9 1.0 O5' P:DA5 4.7 11.1 1.0 C A:GLY343 4.7 15.8 1.0 O A:ASN340 4.7 14.7 1.0 CA A:GLY345 4.8 14.8 1.0 O A:HOH1149 4.8 48.0 1.0 O A:HOH915 4.9 29.8 1.0 CA A:GLY343 4.9 15.2 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:42.8 occ:1.00 O A:ILE305 2.4 41.1 1.0 O A:CYS300 2.4 51.8 1.0 O A:ILE302 2.5 46.9 1.0 O D:HOH406 2.6 45.8 1.0 O A:HOH1105 2.7 53.6 1.0 OP1 D:DC3 3.1 31.1 1.0 C A:ILE302 3.2 47.8 1.0 C A:CYS300 3.3 51.5 1.0 C A:ILE305 3.5 40.6 1.0 N A:ILE302 3.7 49.4 1.0 N A:ILE305 3.9 41.9 1.0 CA A:CYS300 3.9 52.0 1.0 OP2 D:DC3 4.0 29.0 1.0 N A:PRO303 4.0 47.4 1.0 P D:DC3 4.0 29.9 1.0 CA A:ILE302 4.0 48.7 1.0 C A:SER301 4.1 50.1 1.0 CA A:PRO303 4.1 46.9 1.0 CA A:ILE305 4.1 41.7 1.0 O A:ALA299 4.2 56.0 1.0 N A:SER301 4.2 51.0 1.0 O D:HOH316 4.2 39.7 1.0 N A:GLY304 4.2 44.8 1.0 O D:HOH474 4.4 53.4 1.0 CA A:SER301 4.4 50.9 1.0 CB A:ILE305 4.5 42.6 1.0 N A:GLY306 4.6 40.9 1.0 C A:PRO303 4.6 46.2 1.0 O A:SER301 4.7 50.1 1.0 CA A:GLY306 4.8 42.0 1.0 O3' D:DC2 4.9 27.4 1.0 CB A:ILE302 4.9 49.4 1.0 CB A:CYS300 4.9 50.5 1.0 C A:GLY304 5.0 41.8 1.0 N A:CYS300 5.0 53.7 1.0 C A:ALA299 5.0 55.6 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