Sodium in PDB 1d3y: Structure of the Dna Topoisomerase VI A Subunit

All present enzymatic activity of Structure of the Dna Topoisomerase VI A Subunit:
5.99.1.3;

The structure of Structure of the Dna Topoisomerase VI A Subunit, PDB code: 1d3y was solved by M.D.Nichols, K.A.Deangelis, J.L.Keck, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.510, 59.040, 87.260, 90.00, 94.05, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of Structure of the Dna Topoisomerase VI A Subunit also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Sodium atom in the Structure of the Dna Topoisomerase VI A Subunit (pdb code 1d3y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of the Dna Topoisomerase VI A Subunit, PDB code: 1d3y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of the Dna Topoisomerase VI A Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Dna Topoisomerase VI A Subunit within 5.0Å range: probe atom residue distance (Å) B Occ A:Na370 b:16.3 occ:1.00 O A:HOH435 3.1 23.7 1.0 N A:ASP114 3.1 22.1 1.0 OE1 A:GLN78 3.3 23.4 1.0 NZ A:LYS74 3.4 38.0 1.0 CG A:ASP114 3.5 24.8 1.0 OD2 A:ASP114 3.6 25.7 1.0 CB A:ALA118 3.7 19.4 1.0 CB A:ASP114 3.7 25.3 1.0 OD1 A:ASP114 3.7 25.1 1.0 CA A:PHE113 3.8 21.1 1.0 C A:PHE113 3.9 22.1 1.0 CA A:ASP114 4.0 23.1 1.0 O A:ARG112 4.0 20.6 1.0 CD2 A:PHE113 4.0 19.4 1.0 CE A:LYS74 4.2 36.2 1.0 CD A:GLN78 4.2 22.2 1.0 NE2 A:GLN78 4.3 20.6 1.0 CD A:LYS74 4.3 34.1 1.0 CB A:PHE113 4.5 18.6 1.0 CG A:PHE113 4.7 18.4 1.0 N A:PHE113 4.8 19.6 1.0 C A:ARG112 4.9 22.3 1.0 CE2 A:PHE113 4.9 20.0 1.0

Sodium binding site 2 out of 2 in the Structure of the Dna Topoisomerase VI A Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Dna Topoisomerase VI A Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Na373 b:12.4 occ:1.00 O B:HOH410 3.1 16.6 1.0 N B:ASP114 3.2 19.4 1.0 OE1 B:GLN78 3.5 23.9 1.0 NZ B:LYS74 3.5 36.4 1.0 CG B:ASP114 3.8 30.1 1.0 CB B:ASP114 3.8 25.1 1.0 CB B:ALA118 3.8 12.7 1.0 OD2 B:ASP114 3.8 32.3 1.0 CA B:PHE113 3.8 17.1 1.0 CE B:LYS74 4.0 36.4 1.0 C B:PHE113 4.0 17.1 1.0 CA B:ASP114 4.1 20.7 1.0 CD2 B:PHE113 4.1 16.2 1.0 O B:ARG112 4.2 17.4 1.0 NE2 B:GLN78 4.3 15.8 1.0 CD B:GLN78 4.3 21.0 1.0 OD1 B:ASP114 4.3 28.4 1.0 CB B:PHE113 4.4 16.9 1.0 CD B:LYS74 4.7 33.1 1.0 CG B:PHE113 4.7 15.5 1.0 N B:ASP115 4.8 19.1 1.0 N B:PHE113 4.9 17.1 1.0 C B:ARG112 4.9 18.4 1.0

M.D.Nichols, K.Deangelis, J.L.Keck, J.M.Berger. Structure and Function of An Archaeal Topoisomerase VI Subunit with Homology to the Meiotic Recombination Factor SPO11. Embo J. V. 18 6177 1999.
ISSN: ISSN 0261-4189
PubMed: 10545127
DOI: 10.1093/EMBOJ/18.21.6177