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

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

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-G Base Pair, PDB code: 4qze 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)	40.84 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.033, 71.608, 113.948, 90.00, 95.19, 90.00
R / Rfree (%)	19.2 / 21.8

The structure of Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-G 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-G Base Pair (pdb code 4qze). 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-G Base Pair, PDB code: 4qze:
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-G 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-G Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:39.0 occ:1.00 O2B A:DCT604 2.0 45.1 1.0 O2A A:DCT604 2.0 44.6 1.0 OD1 A:ASP343 2.1 44.3 1.0 O A:HOH784 2.2 45.8 1.0 O2G A:DCT604 2.2 40.6 1.0 OD2 A:ASP345 2.3 44.8 1.0 PB A:DCT604 3.0 43.7 1.0 PA A:DCT604 3.2 42.1 1.0 CG A:ASP343 3.2 44.2 1.0 O3A A:DCT604 3.2 43.5 1.0 PG A:DCT604 3.3 45.1 1.0 CG A:ASP345 3.5 45.4 1.0 O3B A:DCT604 3.6 47.2 1.0 MG A:MG602 3.6 51.9 1.0 O3G A:DCT604 3.7 49.6 1.0 OD2 A:ASP343 3.7 49.2 1.0 OD1 A:ASP345 4.0 46.0 1.0 C5' A:DCT604 4.0 37.7 1.0 ND1 A:HIS342 4.0 49.6 1.0 O A:ASP343 4.1 47.5 1.0 O5' A:DCT604 4.1 41.6 1.0 CE1 A:HIS342 4.2 48.3 1.0 O1B A:DCT604 4.3 40.5 1.0 N A:GLY333 4.4 37.7 1.0 O1A A:DCT604 4.4 42.9 1.0 C A:ASP343 4.4 46.6 1.0 CB A:ASP343 4.4 44.9 1.0 O A:HOH725 4.4 41.3 1.0 N A:ASP343 4.6 43.5 1.0 CA A:GLY332 4.6 38.7 1.0 CB A:ASP345 4.7 41.8 1.0 CA A:ASP343 4.7 43.8 1.0 O1G A:DCT604 4.8 53.1 1.0 N A:ASP345 5.0 43.3 1.0 N A:VAL344 5.0 41.6 1.0

Magnesium binding site 2 out of 2 in the Mouse Tdt, F401A Mutant, in Complex with A Dsb Substrate, C-G 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-G Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:51.9 occ:1.00 OD2 A:ASP343 2.0 49.2 1.0 OD1 A:ASP345 2.1 46.0 1.0 OD2 A:ASP434 2.3 52.5 1.0 O2A A:DCT604 2.4 44.6 1.0 CG A:ASP345 2.9 45.4 1.0 CG A:ASP343 2.9 44.2 1.0 C3' U:DC6 3.0 88.5 1.0 OD2 A:ASP345 3.1 44.8 1.0 C5' U:DC6 3.2 83.0 1.0 C4' U:DC6 3.2 87.0 1.0 OD1 A:ASP343 3.2 44.3 1.0 PA A:DCT604 3.4 42.1 1.0 CG A:ASP434 3.4 50.9 1.0 MG A:MG601 3.6 39.0 1.0 O1A A:DCT604 3.8 42.9 1.0 O5' A:DCT604 3.8 41.6 1.0 C5' A:DCT604 4.0 37.7 1.0 CE1 A:HIS342 4.1 48.3 1.0 CB A:ASP434 4.1 45.0 1.0 CB A:ASP343 4.3 44.9 1.0 O A:HOH786 4.3 42.4 1.0 CB A:ASP345 4.4 41.8 1.0 OD1 A:ASP434 4.4 53.9 1.0 C2' U:DC6 4.4 90.3 1.0 O5' U:DC6 4.6 80.3 1.0 O4' U:DC6 4.7 89.5 1.0 O3A A:DCT604 4.7 43.5 1.0 NE2 A:HIS342 4.8 48.8 1.0 NH2 A:ARG432 4.8 49.4 1.0 OP1 U:DC6 4.9 74.5 1.0 ND1 A:HIS342 5.0 49.6 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