Sodium in PDB 1xsn: Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp

All present enzymatic activity of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp:
2.7.7.7;

The structure of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp, PDB code: 1xsn was solved by M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.84 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.043, 62.551, 139.830, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.5

The structure of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp (pdb code 1xsn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp, PDB code: 1xsn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na577 b:25.8 occ:1.00 O A:ALA344 2.3 23.3 1.0 O A:SER339 2.4 26.7 1.0 O P:HOH2807 2.4 29.9 1.0 O A:HOH582 2.5 25.4 1.0 O A:ILE341 2.5 23.5 1.0 OP1 P:DA5 2.6 25.4 1.0 C A:SER339 3.4 25.8 1.0 C A:ILE341 3.4 24.4 1.0 C A:ALA344 3.5 23.7 1.0 P P:DA5 3.6 27.9 1.0 OP2 P:DA5 3.7 25.4 1.0 N A:ALA344 3.7 23.5 1.0 N A:GLY343 3.9 24.1 1.0 N A:ILE341 4.0 22.3 1.0 CA A:TRP342 4.0 24.9 1.0 O P:HOH2809 4.1 35.0 1.0 N A:TRP342 4.1 24.6 1.0 CA A:ALA344 4.2 23.4 1.0 C A:ASN340 4.2 24.1 1.0 CA A:SER339 4.2 27.0 1.0 N A:ASN340 4.3 26.6 1.0 O A:HOH770 4.3 54.9 1.0 CA A:ASN340 4.3 26.6 1.0 C A:TRP342 4.3 24.1 1.0 O3' P:DT4 4.4 21.3 1.0 CA A:ILE341 4.4 21.6 1.0 N A:GLY345 4.5 21.7 1.0 O P:HOH2835 4.5 64.4 1.0 CB A:ALA344 4.6 22.7 1.0 C A:GLY343 4.7 24.8 1.0 O P:HOH2824 4.7 47.5 1.0 O A:ASN340 4.8 24.8 1.0 CA A:GLY345 4.8 24.0 1.0 CB A:SER339 4.8 29.1 1.0 CA A:GLY343 4.9 25.2 1.0 O5' P:DA5 4.9 24.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Dna Polymerase Lambda in Complex with A One Nucleotide Dna Gap and Ddttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na578 b:49.7 occ:1.00 O A:SER463 2.3 40.8 1.0 O T:HOH190 2.4 51.5 1.0 O A:HOH617 2.6 46.1 1.0 O A:HOH722 2.7 57.9 1.0 O A:HOH721 2.8 50.7 1.0 C A:SER463 3.4 41.5 1.0 OP1 T:DT10 3.8 37.2 1.0 OE1 A:GLU466 4.1 70.3 1.0 CA A:SER463 4.3 39.5 1.0 O A:HOH685 4.3 64.8 1.0 N A:GLN464 4.3 43.5 1.0 CB A:SER463 4.3 38.5 1.0 N A:GLU465 4.3 50.0 1.0 CA A:GLN464 4.4 46.0 1.0 N A:SER463 4.5 35.8 1.0 O T:HOH224 4.6 68.6 1.0 OP2 T:DT10 4.6 41.3 1.0 P T:DT10 4.7 40.0 1.0 OE2 A:GLU465 4.8 53.0 1.0 C A:GLN464 4.9 47.9 1.0 OG A:SER463 5.0 37.6 1.0

M.Garcia-Diaz, K.Bebenek, J.M.Krahn, T.A.Kunkel, L.C.Pedersen. A Closed Conformation For the Pol Lambda Catalytic Cycle. Nat.Struct.Mol.Biol. V. 12 97 2005.
ISSN: ISSN 1545-9993
PubMed: 15608652
DOI: 10.1038/NSMB876