Sodium in PDB 4i2f: Binary Complex of Mouse Tdt with Ssdna

All present enzymatic activity of Binary Complex of Mouse Tdt with Ssdna:
2.7.7.31;

The structure of Binary Complex of Mouse Tdt with Ssdna, PDB code: 4i2f was solved by J.Gouge, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.61 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.166, 84.428, 114.404, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.8

The structure of Binary Complex of Mouse Tdt with Ssdna also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Sodium atom in the Binary Complex of Mouse Tdt with Ssdna (pdb code 4i2f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Binary Complex of Mouse Tdt with Ssdna, PDB code: 4i2f:

Sodium binding site 1 out of 1 in the Binary Complex of Mouse Tdt with Ssdna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Complex of Mouse Tdt with Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:43.7 occ:1.00 O A:HOH1049 2.3 54.4 1.0 O A:THR253 2.3 34.7 1.0 OP1 C:DA3 2.4 0.1 1.0 O A:VAL258 2.5 32.2 1.0 O A:VAL255 2.7 27.5 1.0 C A:THR253 3.3 35.2 1.0 P C:DA3 3.4 0.7 1.0 C A:VAL258 3.5 32.8 1.0 OP2 C:DA3 3.5 0.7 1.0 C A:VAL255 3.7 28.1 1.0 CA A:THR253 3.8 29.9 1.0 N A:VAL258 3.8 28.2 1.0 CA A:VAL258 4.1 27.7 1.0 O C:HOH102 4.1 59.5 1.0 CB A:THR253 4.2 35.4 1.0 N A:GLY257 4.2 28.2 1.0 N A:VAL255 4.3 29.5 1.0 CA A:PHE256 4.3 24.9 1.0 N A:PHE256 4.4 23.6 1.0 N A:SER254 4.4 32.9 1.0 CB A:VAL258 4.5 28.7 1.0 O3' C:DA2 4.5 0.5 1.0 O5' C:DA3 4.5 0.6 1.0 N A:GLY259 4.6 32.5 1.0 C A:SER254 4.6 35.8 1.0 C A:PHE256 4.7 30.5 1.0 CA A:VAL255 4.7 27.9 1.0 C A:GLY257 4.8 32.3 1.0 CA A:SER254 4.9 32.5 1.0 O A:PHE252 5.0 29.4 1.0 CA A:GLY259 5.0 33.0 1.0

J.Gouge, S.Rosario, F.Romain, P.Beguin, M.Delarue. Structures of Intermediates Along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism. J.Mol.Biol. V. 425 4334 2013.
ISSN: ISSN 0022-2836
PubMed: 23856622
DOI: 10.1016/J.JMB.2013.07.009