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

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

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-A Base Pair, PDB code: 4qzf 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)	43.70 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.426, 74.955, 125.629, 90.00, 97.78, 90.00
R / Rfree (%)	22.8 / 25.6

The structure of Mouse Tdt, F401A Mutant, 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, F401A Mutant, in Complex with A Dsb Substrate, C-A Base Pair (pdb code 4qzf). 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-A Base Pair, PDB code: 4qzf:
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-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, F401A Mutant, in Complex with A Dsb Substrate, C-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:58.0 occ:1.00 OD1 A:ASP343 1.9 75.0 1.0 O2G A:DCT604 2.3 57.7 1.0 O2A A:DCT604 2.3 49.4 1.0 O2B A:DCT604 2.3 49.4 1.0 OD1 A:ASP345 2.4 46.6 1.0 CG A:ASP343 2.9 68.2 1.0 O A:HOH741 3.3 57.6 1.0 OD2 A:ASP343 3.3 67.6 1.0 O A:ASP343 3.3 57.9 1.0 PG A:DCT604 3.4 59.9 1.0 PB A:DCT604 3.5 49.4 1.0 CG A:ASP345 3.5 55.5 1.0 O3G A:DCT604 3.6 62.2 1.0 PA A:DCT604 3.7 41.7 1.0 C A:ASP343 3.8 56.0 1.0 O3A A:DCT604 3.8 47.9 1.0 O3B A:DCT604 3.9 55.2 1.0 OD2 A:ASP345 4.1 60.0 1.0 CB A:ASP343 4.1 54.2 1.0 CE1 A:HIS342 4.2 64.4 1.0 ND1 A:HIS342 4.3 65.4 1.0 CA A:ASP343 4.3 53.4 1.0 N A:ASP343 4.3 55.1 1.0 C5' A:DCT604 4.4 26.9 1.0 N A:GLY333 4.5 51.9 1.0 N A:VAL344 4.5 49.9 1.0 MG A:MG602 4.6 64.8 1.0 O5' A:DCT604 4.6 29.2 1.0 CA A:GLY332 4.7 56.0 1.0 N A:ASP345 4.7 50.0 1.0 CB A:ASP345 4.7 49.5 1.0 O1A A:DCT604 4.7 40.0 1.0 O1G A:DCT604 4.8 59.8 1.0 O1B A:DCT604 4.8 45.4 1.0 CA A:VAL344 4.8 50.2 1.0 C A:VAL344 5.0 55.0 1.0

Magnesium binding site 2 out of 2 in the Mouse Tdt, F401A Mutant, 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, F401A Mutant, in Complex with A Dsb Substrate, C-A Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:64.8 occ:1.00 OD2 A:ASP434 2.4 72.2 1.0 OD2 A:ASP343 2.5 67.6 1.0 O2A A:DCT604 2.9 49.4 1.0 O5' U:DC6 3.1 0.0 1.0 OD2 A:ASP345 3.2 60.0 1.0 C3' U:DC6 3.3 0.4 1.0 PA A:DCT604 3.4 41.7 1.0 O1A A:DCT604 3.5 40.0 1.0 CG A:ASP343 3.5 68.2 1.0 CG A:ASP434 3.6 70.2 1.0 O5' A:DCT604 3.7 29.2 1.0 C5' U:DC6 3.9 0.2 1.0 OP1 U:DC6 4.0 0.4 1.0 OD1 A:ASP343 4.0 75.0 1.0 CE1 A:HIS342 4.0 64.4 1.0 NE2 A:HIS342 4.1 64.8 1.0 CG A:ASP345 4.1 55.5 1.0 C4' U:DC6 4.2 0.8 1.0 P U:DC6 4.2 0.9 1.0 C2' U:DC6 4.3 0.4 1.0 OD1 A:ASP345 4.3 46.6 1.0 NH2 A:ARG432 4.3 72.1 1.0 OD1 A:ASP434 4.4 72.5 1.0 C5' A:DCT604 4.5 26.9 1.0 CB A:ASP434 4.6 62.0 1.0 MG A:MG601 4.6 58.0 1.0 CB A:ASP343 4.7 54.2 1.0 O3' U:DA5 4.8 0.6 1.0 O3A A:DCT604 4.9 47.9 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