Sodium in PDB 4fpv: Crystal Structure of D. Rerio TDP2 Complexed with Single Strand Dna Product

The structure of Crystal Structure of D. Rerio TDP2 Complexed with Single Strand Dna Product, PDB code: 4fpv was solved by K.Shi, K.Kurahashi, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.15 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.070, 95.021, 104.506, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 20.2

The structure of Crystal Structure of D. Rerio TDP2 Complexed with Single Strand Dna Product also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of D. Rerio TDP2 Complexed with Single Strand Dna Product (pdb code 4fpv). 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 D. Rerio TDP2 Complexed with Single Strand Dna Product, PDB code: 4fpv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of D. Rerio TDP2 Complexed with Single Strand Dna Product


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 D. Rerio TDP2 Complexed with Single Strand Dna Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:47.4 occ:1.00 OD2 A:ASP341 2.4 41.8 1.0 O A:HOH722 2.4 49.0 1.0 OG1 A:THR366 2.5 21.5 1.0 NZ A:LYS122 3.3 56.7 1.0 CG A:ASP341 3.4 40.5 1.0 CD A:LYS122 3.4 46.0 1.0 CB A:THR366 3.4 19.8 1.0 CB A:ASP341 3.6 28.5 1.0 CE A:LYS122 3.8 52.4 1.0 CG2 A:THR366 3.8 21.2 1.0 CB A:HIS342 3.9 31.5 0.9 CB A:HIS342 3.9 30.2 0.1 N A:HIS342 4.3 23.9 0.9 N A:HIS342 4.3 25.4 0.1 OD1 A:ASP341 4.5 49.1 1.0 C A:ASP341 4.7 27.0 1.0 CA A:HIS342 4.7 26.0 0.9 CG A:LYS122 4.8 40.9 1.0 CA A:HIS342 4.8 25.2 0.1 CA A:ASP341 4.8 25.6 1.0 CA A:THR366 4.8 20.7 1.0 CG A:HIS342 4.9 33.7 0.9 CG A:HIS342 4.9 33.8 0.1

Sodium binding site 2 out of 2 in the Crystal Structure of D. Rerio TDP2 Complexed with Single Strand Dna Product


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 D. Rerio TDP2 Complexed with Single Strand Dna Product within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:43.4 occ:1.00 OD1 B:ASP341 2.3 28.6 1.0 O B:HOH713 2.4 38.3 1.0 O B:HOH741 2.6 43.8 1.0 ND2 B:ASN368 3.1 17.9 1.0 CG B:ASP341 3.2 32.1 1.0 CA B:ASP341 3.3 13.8 1.0 CB B:ASP341 3.4 17.2 1.0 OD1 B:ASN368 3.4 19.8 1.0 O B:HOH521 3.5 23.2 1.0 CG B:ASN368 3.7 15.8 1.0 O B:ASP341 3.8 17.6 1.0 C B:ASP341 4.0 16.9 1.0 OD2 B:ASP341 4.4 38.9 1.0 O B:PRO340 4.4 17.1 1.0 N B:ASP341 4.5 16.5 1.0 NZ B:LYS122 4.9 47.1 1.0 C B:PRO340 4.9 19.7 1.0 O B:HOH681 5.0 52.4 1.0

K.Shi, K.Kurahashi, R.Gao, S.E.Tsutakawa, J.A.Tainer, Y.Pommier, H.Aihara. Structural Basis For Recognition of 5'-Phosphotyrosine Adducts By TDP2. Nat.Struct.Mol.Biol. V. 19 1372 2012.
ISSN: ISSN 1545-9993
PubMed: 23104058
DOI: 10.1038/NSMB.2423