Magnesium in PDB 4qzd: Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair

All present enzymatic activity of Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair:
2.7.7.31;

The structure of Mouse Tdt, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qzd 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)	43.56 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	55.933, 74.920, 125.633, 90.00, 98.43, 90.00
R / Rfree (%)	20 / 24.5

The structure of Mouse Tdt, F405A Mutant, 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, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair (pdb code 4qzd). 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, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair, PDB code: 4qzd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mouse Tdt, F405A Mutant, 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, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:63.2 occ:1.00 OD1 A:ASP343 2.0 74.4 1.0 O3G A:DCT604 2.1 65.4 1.0 O2B A:DCT604 2.2 55.8 1.0 O A:HOH724 2.2 72.4 1.0 OD2 A:ASP345 2.4 66.0 1.0 O2A A:DCT604 2.5 60.5 1.0 CG A:ASP343 3.1 79.7 1.0 CG A:ASP345 3.1 71.7 1.0 PB A:DCT604 3.4 52.2 1.0 MG A:MG602 3.4 59.7 1.0 OD1 A:ASP345 3.5 78.5 1.0 PG A:DCT604 3.6 65.8 1.0 PA A:DCT604 3.6 54.4 1.0 O A:ASP343 3.6 71.1 1.0 O3A A:DCT604 3.6 58.5 1.0 OD2 A:ASP343 3.7 0.7 1.0 O A:HOH737 3.8 61.6 1.0 O3B A:DCT604 3.9 56.4 1.0 C A:ASP343 4.0 70.3 1.0 C5' A:DCT604 4.2 46.3 1.0 CB A:ASP343 4.3 64.9 1.0 CB A:ASP345 4.3 63.9 1.0 O1G A:DCT604 4.4 70.6 1.0 N A:GLY333 4.4 55.9 1.0 CA A:GLY332 4.4 58.0 1.0 O1B A:DCT604 4.5 45.1 1.0 O5' A:DCT604 4.5 45.2 1.0 CA A:ASP343 4.5 65.1 1.0 O1A A:DCT604 4.6 61.7 1.0 N A:ASP345 4.6 64.2 1.0 O2G A:DCT604 4.6 63.7 1.0 O U:HOH101 4.6 61.5 1.0 N A:ASP343 4.6 65.7 1.0 N A:VAL344 4.6 65.8 1.0 CA A:VAL344 4.9 66.0 1.0 C A:VAL344 4.9 70.0 1.0 C A:GLY332 5.0 60.6 1.0

Magnesium binding site 2 out of 2 in the Mouse Tdt, F405A Mutant, 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, F405A Mutant, in Complex with A Dsb Substrate, C-C Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:59.7 occ:1.00 OD1 A:ASP345 2.1 78.5 1.0 O U:HOH101 2.2 61.5 1.0 OD2 A:ASP434 2.2 0.4 1.0 O2A A:DCT604 2.5 60.5 1.0 OD1 A:ASP343 2.5 74.4 1.0 OD2 A:ASP343 2.7 0.7 1.0 CG A:ASP343 2.7 79.7 1.0 OP1 U:DC5 2.9 0.4 1.0 CG A:ASP345 2.9 71.7 1.0 OD2 A:ASP345 3.0 66.0 1.0 CG A:ASP434 3.3 89.8 1.0 MG A:MG601 3.4 63.2 1.0 O5' U:DC5 3.7 0.6 1.0 PA A:DCT604 3.8 54.4 1.0 CB A:ASP343 3.8 64.9 1.0 P U:DC5 3.8 0.3 1.0 CB A:ASP434 4.1 77.0 1.0 O5' A:DCT604 4.2 45.2 1.0 OD1 A:ASP434 4.3 90.0 1.0 CB A:ASP345 4.3 63.9 1.0 O1A A:DCT604 4.4 61.7 1.0 O3G A:DCT604 4.4 65.4 1.0 C5' A:DCT604 4.5 46.3 1.0 OP2 U:DC5 4.5 0.6 1.0 NH2 A:ARG432 4.6 94.7 1.0 O3A A:DCT604 5.0 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