Zinc in PDB 4i28: Binary Complex of Mouse Tdt with Ssdna and Zn++

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

The structure of Binary Complex of Mouse Tdt with Ssdna and Zn++, PDB code: 4i28 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)	16.73 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.824, 84.799, 115.773, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.6

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

Magnesium	(Mg)	1 atom
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Binary Complex of Mouse Tdt with Ssdna and Zn++ (pdb code 4i28). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Binary Complex of Mouse Tdt with Ssdna and Zn++, PDB code: 4i28:

Zinc binding site 1 out of 1 in the Binary Complex of Mouse Tdt with Ssdna and Zn++


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Binary Complex of Mouse Tdt with Ssdna and Zn++ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:30.5 occ:1.00 OD1 A:ASP345 2.0 32.4 1.0 OD2 A:ASP434 2.0 27.7 1.0 OD2 A:ASP343 2.0 28.5 1.0 OP1 C:DA5 2.0 53.4 1.0 CG A:ASP343 2.8 26.6 1.0 CG A:ASP345 2.9 31.8 1.0 O3' C:DA4 3.0 54.6 1.0 CG A:ASP434 3.0 29.3 1.0 OD1 A:ASP343 3.0 27.2 1.0 P C:DA5 3.0 53.2 1.0 OD2 A:ASP345 3.2 37.7 1.0 CB A:ASP434 3.6 24.8 1.0 MG A:MG603 3.8 32.7 1.0 OD1 A:ASP434 4.0 27.5 1.0 O5' C:DA5 4.1 52.4 1.0 C3' C:DA4 4.1 54.4 1.0 C5' C:DA4 4.1 53.2 1.0 OP2 C:DA5 4.1 53.1 1.0 C4' C:DA4 4.2 54.2 1.0 CB A:ASP343 4.2 22.1 1.0 C5' C:DA5 4.2 61.4 0.5 C5' C:DA5 4.3 51.3 0.5 CB A:ASP345 4.3 19.3 1.0 CZ3 A:TRP450 4.5 26.4 1.0 NH2 A:ARG432 4.5 23.7 1.0 CE1 A:HIS342 4.5 35.4 1.0 CA A:ASP345 4.8 18.2 1.0 CA A:ASP434 4.8 24.5 1.0 O A:VAL344 4.9 19.2 1.0 N A:ASP434 4.9 24.7 1.0 OP1 C:DA4 4.9 50.5 1.0 N A:ASP345 4.9 19.3 1.0 C A:VAL344 4.9 21.9 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