Magnesium in PDB 5d49: Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination

The structure of Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination, PDB code: 5d49 was solved by J.Loc'h, S.Rosario, M.Delarue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.02 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.550, 74.250, 126.150, 90.00, 101.84, 90.00
R / Rfree (%)	19.7 / 24.5

The structure of Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination (pdb code 5d49). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination, PDB code: 5d49:

Magnesium binding site 1 out of 1 in the Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:30.0 occ:1.00 OP1 C:DC8 1.9 33.9 1.0 OD2 A:ASP345 2.1 31.0 1.0 O4 A:SO4603 2.1 31.0 0.8 OD1 A:ASP343 2.2 35.7 1.0 O A:HOH720 2.2 27.7 1.0 O A:HOH852 2.3 30.2 1.0 CG A:ASP345 3.1 28.1 1.0 CG A:ASP343 3.3 33.7 1.0 S A:SO4603 3.3 34.1 0.8 P C:DC8 3.3 32.9 1.0 OD1 A:ASP345 3.4 29.0 1.0 O1 A:SO4603 3.5 38.0 0.8 OD2 A:ASP343 3.7 41.0 1.0 O A:HOH777 3.7 51.0 1.0 O5' C:DC8 3.9 30.9 1.0 O3 A:SO4603 4.0 34.6 0.8 C5' C:DC8 4.1 30.1 1.0 O A:HOH736 4.2 31.5 1.0 OP2 C:DC8 4.2 32.3 1.0 O A:ASP343 4.2 30.8 1.0 N A:GLY333 4.3 29.8 1.0 O3' C:DG7 4.3 33.5 1.0 O2 A:SO4603 4.4 35.2 0.8 CB A:ASP345 4.4 24.8 1.0 CA A:GLY332 4.4 28.9 1.0 C A:ASP343 4.5 31.4 1.0 CB A:ASP343 4.5 30.2 1.0 O C:HOH122 4.6 40.3 1.0 N A:ASP343 4.7 29.3 1.0 CA A:ASP343 4.8 28.9 1.0 N A:ASP345 4.8 26.2 1.0 C A:GLY332 4.9 31.8 1.0

J.Loc'h, S.Rosario, M.Delarue. Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination. Structure V. 24 1452 2016.
ISSN: ISSN 0969-2126
PubMed: 27499438
DOI: 10.1016/J.STR.2016.06.014