Magnesium in PDB 4i2b: Ternary Complex of Mouse Tdt with Ssdna and Ampcpp

All present enzymatic activity of Ternary Complex of Mouse Tdt with Ssdna and Ampcpp:
2.7.7.31;

The structure of Ternary Complex of Mouse Tdt with Ssdna and Ampcpp, PDB code: 4i2b 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)	47.90 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.039, 84.491, 116.290, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.7

The structure of Ternary Complex of Mouse Tdt with Ssdna and Ampcpp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Ternary Complex of Mouse Tdt with Ssdna and Ampcpp (pdb code 4i2b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of Mouse Tdt with Ssdna and Ampcpp, PDB code: 4i2b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Mouse Tdt with Ssdna and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Mouse Tdt with Ssdna and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:33.2 occ:1.00 O2G A:APC603 2.1 46.3 1.0 O2B A:APC603 2.2 36.6 1.0 OD1 A:ASP343 2.2 35.4 1.0 O2A A:APC603 2.2 41.1 1.0 O A:HOH911 2.2 27.2 1.0 OD2 A:ASP345 2.3 41.6 1.0 PB A:APC603 3.1 41.1 1.0 PA A:APC603 3.3 45.4 1.0 PG A:APC603 3.3 50.3 1.0 CG A:ASP343 3.3 35.7 1.0 CG A:ASP345 3.3 36.8 1.0 C3A A:APC603 3.5 42.2 1.0 O3B A:APC603 3.6 45.3 1.0 OD1 A:ASP345 3.7 37.2 1.0 OD2 A:ASP343 3.8 36.8 1.0 C5' A:APC603 3.8 62.5 1.0 MG A:MG604 3.8 40.3 1.0 O5' A:APC603 4.0 52.4 1.0 O A:HOH790 4.1 28.5 1.0 O A:HOH726 4.1 41.1 1.0 N A:GLY333 4.1 25.8 1.0 O A:ASP343 4.1 28.4 1.0 O A:HOH948 4.2 49.5 1.0 O3G A:APC603 4.2 49.6 1.0 CA A:GLY332 4.3 25.5 1.0 O1B A:APC603 4.5 45.7 1.0 C A:ASP343 4.5 32.4 1.0 O1G A:APC603 4.5 56.1 1.0 O1A A:APC603 4.5 48.4 1.0 CB A:ASP343 4.6 31.9 1.0 CB A:ASP345 4.6 30.5 1.0 C A:GLY332 4.8 27.8 1.0 O A:HOH1025 4.8 62.6 1.0 N A:ASP343 4.9 30.2 1.0 CA A:ASP343 4.9 30.2 1.0 N A:ASP345 5.0 31.8 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Mouse Tdt with Ssdna and Ampcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Mouse Tdt with Ssdna and Ampcpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:40.3 occ:1.00 O A:HOH1025 1.9 62.6 1.0 OD2 A:ASP343 2.0 36.8 1.0 OD2 A:ASP434 2.2 45.7 1.0 O2A A:APC603 2.2 41.1 1.0 OD1 A:ASP345 2.2 37.2 1.0 O A:HOH947 2.3 34.7 1.0 CG A:ASP343 3.0 35.7 1.0 CG A:ASP345 3.1 36.8 1.0 OD1 A:ASP343 3.3 35.4 1.0 PA A:APC603 3.3 45.4 1.0 OD2 A:ASP345 3.4 41.6 1.0 CG A:ASP434 3.4 39.7 1.0 O1A A:APC603 3.5 48.4 1.0 O5' A:APC603 3.7 52.4 1.0 MG A:MG602 3.8 33.2 1.0 CB A:ASP434 4.0 32.7 1.0 O A:HOH948 4.2 49.5 1.0 CB A:ASP343 4.3 31.9 1.0 CB A:ASP345 4.4 30.5 1.0 C5' A:APC603 4.4 62.5 1.0 OD1 A:ASP434 4.4 37.1 1.0 O2G A:APC603 4.7 46.3 1.0 CZ3 A:TRP450 4.7 42.8 1.0 NH2 A:ARG432 4.8 60.2 1.0 C3A A:APC603 4.9 42.2 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