Magnesium in PDB 4qzh: Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair

All present enzymatic activity of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair:
2.7.7.31;

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair, PDB code: 4qzh 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)	41.50 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.309, 75.009, 125.611, 90.00, 97.64, 90.00
R / Rfree (%)	19.6 / 22.1

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair (pdb code 4qzh). 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, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair, PDB code: 4qzh:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-T 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, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:79.3 occ:1.00 OD2 A:ASP343 2.3 83.0 1.0 O2A A:DCT604 2.6 59.8 1.0 OD2 A:ASP434 2.6 99.4 1.0 OP1 U:DC6 3.1 0.7 1.0 PA A:DCT604 3.1 51.6 1.0 OD1 A:ASP345 3.2 73.9 1.0 O1A A:DCT604 3.2 47.1 1.0 CG A:ASP343 3.3 72.7 1.0 O5' A:DCT604 3.3 41.9 1.0 OD1 A:ASP343 3.6 70.6 1.0 CE1 A:HIS342 3.7 66.4 0.5 CG A:ASP434 3.9 87.8 1.0 CG A:ASP345 4.1 67.0 1.0 C5' A:DCT604 4.1 40.1 1.0 NE2 A:HIS342 4.1 67.3 0.5 OD2 A:ASP345 4.2 58.4 1.0 MG A:MG602 4.4 61.3 1.0 P U:DC6 4.4 0.9 1.0 O5' U:DC6 4.5 0.6 1.0 NH2 A:ARG432 4.6 70.0 1.0 CB A:ASP343 4.6 64.9 1.0 O3A A:DCT604 4.7 59.3 1.0 OD1 A:ASP434 4.7 89.2 1.0 CB A:ASP434 4.7 71.8 1.0 ND1 A:HIS342 4.8 67.8 0.5 O2G A:DCT604 4.8 73.0 1.0

Magnesium binding site 2 out of 2 in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-T 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, F401A Mutant, in Complex with A Dsb Substrate, C-T Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:61.3 occ:1.00 OD1 A:ASP343 1.9 70.6 1.0 O2G A:DCT604 2.0 73.0 1.0 O2A A:DCT604 2.2 59.8 1.0 O2B A:DCT604 2.4 58.3 1.0 OD2 A:ASP345 2.5 58.4 1.0 CG A:ASP343 3.1 72.7 1.0 PG A:DCT604 3.2 72.7 1.0 O3G A:DCT604 3.2 71.9 1.0 PB A:DCT604 3.3 60.0 1.0 CG A:ASP345 3.4 67.0 1.0 O A:ASP343 3.5 71.0 1.0 PA A:DCT604 3.6 51.6 1.0 O A:HOH703 3.6 63.6 1.0 O3B A:DCT604 3.7 67.3 1.0 OD1 A:ASP345 3.7 73.9 1.0 OD2 A:ASP343 3.8 83.0 1.0 O3A A:DCT604 3.8 59.3 1.0 C A:ASP343 4.0 68.8 1.0 CB A:ASP343 4.3 64.9 1.0 ND1 A:HIS342 4.3 67.8 0.5 N A:GLY333 4.3 58.7 1.0 C5' A:DCT604 4.3 40.1 1.0 N A:ASP343 4.3 64.9 1.0 MG A:MG601 4.4 79.3 1.0 CA A:ASP343 4.4 64.4 1.0 CE1 A:HIS342 4.4 66.4 0.5 O1G A:DCT604 4.5 71.9 1.0 O1A A:DCT604 4.5 47.1 1.0 O5' A:DCT604 4.6 41.9 1.0 CA A:GLY332 4.6 60.5 1.0 O1B A:DCT604 4.7 57.9 1.0 N A:VAL344 4.7 64.0 1.0 CB A:ASP345 4.7 60.8 1.0 N A:ASP345 4.9 61.9 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