Magnesium in PDB 4qz9: Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair

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

The structure of Mouse Tdt in Complex with A Dsb Substrate, C-A Base Pair, PDB code: 4qz9 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)	39.06 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.936, 74.720, 126.357, 90.00, 100.06, 90.00
R / Rfree (%)	18.4 / 20.4

The structure of Mouse Tdt in Complex with A Dsb Substrate, C-A 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-A Base Pair (pdb code 4qz9). 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-A Base Pair, PDB code: 4qz9:
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-A 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-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:36.6 occ:1.00 OD1 A:ASP343 2.0 36.2 1.0 O2B A:DCT604 2.1 35.4 1.0 O2G A:DCT604 2.1 44.8 1.0 O2A A:DCT604 2.1 41.1 1.0 O A:HOH849 2.2 34.4 1.0 OD2 A:ASP345 2.2 36.1 1.0 CG A:ASP343 3.1 40.2 1.0 PB A:DCT604 3.2 37.6 1.0 CG A:ASP345 3.3 41.0 1.0 PA A:DCT604 3.3 39.1 1.0 PG A:DCT604 3.4 44.4 1.0 O3A A:DCT604 3.5 39.6 1.0 OD2 A:ASP343 3.6 46.2 1.0 O3B A:DCT604 3.7 39.6 1.0 OD1 A:ASP345 3.7 44.6 1.0 CE1 A:HIS342 4.0 41.6 1.0 ND1 A:HIS342 4.0 42.6 1.0 O3G A:DCT604 4.0 49.9 1.0 O A:ASP343 4.1 33.6 1.0 MG A:MG602 4.1 63.6 1.0 C5' A:DCT604 4.1 35.4 1.0 O A:HOH708 4.2 30.1 1.0 O5' A:DCT604 4.3 37.4 1.0 C A:ASP343 4.3 35.7 1.0 N A:GLY333 4.4 29.6 1.0 O1A A:DCT604 4.4 41.7 1.0 CB A:ASP343 4.4 33.6 1.0 CA A:GLY332 4.5 28.2 1.0 O1B A:DCT604 4.5 35.3 1.0 N A:ASP343 4.6 33.5 1.0 CB A:ASP345 4.6 35.2 1.0 O1G A:DCT604 4.6 48.5 1.0 CA A:ASP343 4.7 32.9 1.0 N A:ASP345 4.9 33.6 1.0 N A:VAL344 4.9 32.8 1.0 C A:GLY332 5.0 31.2 1.0

Magnesium binding site 2 out of 2 in the Mouse Tdt in Complex with A Dsb Substrate, C-A 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-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:63.6 occ:1.00 OD2 A:ASP434 2.2 53.1 1.0 OD2 A:ASP343 2.2 46.2 1.0 OD1 A:ASP345 2.5 44.6 1.0 O2A A:DCT604 2.8 41.1 1.0 C3' U:DC6 2.8 72.5 1.0 C4' U:DC6 3.1 71.2 1.0 C5' U:DC6 3.2 68.7 1.0 CG A:ASP343 3.3 40.2 1.0 CG A:ASP434 3.4 48.0 1.0 CG A:ASP345 3.4 41.0 1.0 O5' A:DCT604 3.7 37.4 1.0 PA A:DCT604 3.7 39.1 1.0 OD1 A:ASP343 3.7 36.2 1.0 OD2 A:ASP345 3.8 36.1 1.0 C5' A:DCT604 4.0 35.4 1.0 C2' U:DC6 4.0 73.7 1.0 CE1 A:HIS342 4.1 41.6 1.0 O5' U:DC6 4.1 66.8 1.0 MG A:MG601 4.1 36.6 1.0 OP1 U:DC6 4.2 65.3 1.0 CB A:ASP434 4.2 36.9 1.0 O1A A:DCT604 4.2 41.7 1.0 CZ3 A:TRP450 4.2 38.2 1.0 NE2 A:HIS342 4.3 42.1 1.0 OD1 A:ASP434 4.4 49.1 1.0 O4' U:DC6 4.5 71.2 1.0 CB A:ASP343 4.6 33.6 1.0 NH2 A:ARG432 4.7 43.7 1.0 CB A:ASP345 4.7 35.2 1.0 P U:DC6 4.8 64.7 1.0 C1' U:DC6 5.0 72.9 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