Magnesium in PDB 4qza: Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair

All present enzymatic activity of Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair:
2.7.7.31;

The structure of Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qza 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)	26.71 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.885, 74.780, 127.147, 90.00, 99.14, 90.00
R / Rfree (%)	18.9 / 21.1

The structure of Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair (pdb code 4qza). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qza:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:41.4 occ:1.00 OD1 A:ASP343 2.1 41.1 1.0 O2B A:DCT604 2.2 36.6 1.0 O3G A:DCT604 2.3 51.6 1.0 O A:HOH773 2.3 44.3 1.0 O2A A:DCT604 2.3 45.5 1.0 OD2 A:ASP345 2.4 39.0 1.0 PB A:DCT604 3.3 43.3 1.0 CG A:ASP343 3.3 42.1 1.0 PA A:DCT604 3.4 43.3 1.0 CG A:ASP345 3.4 43.5 1.0 O3A A:DCT604 3.5 45.4 1.0 PG A:DCT604 3.5 49.9 1.0 O3B A:DCT604 3.7 48.5 1.0 OD1 A:ASP345 3.7 46.1 1.0 MG A:MG602 3.8 54.7 1.0 OD2 A:ASP343 3.8 40.5 1.0 ND1 A:HIS342 4.0 42.5 1.0 CE1 A:HIS342 4.0 42.0 1.0 O A:ASP343 4.1 42.6 1.0 C5' A:DCT604 4.1 34.2 1.0 O5' A:DCT604 4.3 39.3 1.0 O2G A:DCT604 4.3 52.0 1.0 O A:HOH702 4.3 31.7 1.0 N A:GLY333 4.4 35.4 1.0 CA A:GLY332 4.4 34.1 1.0 C A:ASP343 4.4 43.0 1.0 O A:HOH759 4.5 48.8 1.0 O1A A:DCT604 4.5 48.2 1.0 O1B A:DCT604 4.5 38.7 1.0 CB A:ASP343 4.5 37.0 1.0 N A:ASP343 4.6 36.5 1.0 O1G A:DCT604 4.7 54.7 1.0 CB A:ASP345 4.7 37.5 1.0 CA A:ASP343 4.8 36.5 1.0 C A:GLY332 5.0 37.5 1.0 N A:ASP345 5.0 37.0 1.0

Magnesium binding site 2 out of 2 in the Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mouse Tdt in Complex with A Dsb Substrate, C-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:54.7 occ:1.00 OD2 A:ASP343 1.9 40.5 1.0 OD1 A:ASP345 1.9 46.1 1.0 OD2 A:ASP434 2.2 53.5 1.0 O2A A:DCT604 2.8 45.5 1.0 CG A:ASP343 2.9 42.1 1.0 CG A:ASP345 2.9 43.5 1.0 C3' U:DC6 3.1 59.5 1.0 OD1 A:ASP343 3.2 41.1 1.0 OD2 A:ASP345 3.3 39.0 1.0 CG A:ASP434 3.4 49.7 1.0 C4' U:DC6 3.4 58.2 1.0 C5' U:DC6 3.6 55.5 1.0 MG A:MG601 3.8 41.4 1.0 CB A:ASP434 4.1 42.5 1.0 PA A:DCT604 4.1 43.3 1.0 CE1 A:HIS342 4.1 42.0 1.0 O5' A:DCT604 4.1 39.3 1.0 C5' A:DCT604 4.1 34.2 1.0 CB A:ASP343 4.2 37.0 1.0 CB A:ASP345 4.2 37.5 1.0 C2' U:DC6 4.3 60.7 1.0 OD1 A:ASP434 4.4 52.9 1.0 CZ3 A:TRP450 4.4 38.6 1.0 O5' U:DC6 4.4 54.9 1.0 NE2 A:HIS342 4.5 42.5 1.0 OP1 U:DC6 4.6 54.0 1.0 NH2 A:ARG432 4.8 45.1 1.0 O1A A:DCT604 4.8 48.2 1.0 O4' U:DC6 4.8 58.5 1.0

J.Gouge, S.Rosario, F.Romain, F.Poitevin, P.Beguin, M.Delarue. Structural Basis For A Novel Mechanism of Dna Bridging and Alignment in Eukaryotic Dsb Dna Repair. Embo J. V. 34 1126 2015.
ISSN: ISSN 0261-4189
PubMed: 25762590
DOI: 10.15252/EMBJ.201489643