Magnesium in PDB 5d4b: 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: 5d4b 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)	49.23 / 2.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.730, 71.450, 198.170, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.7

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)

2 atoms

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 5d4b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structural Basis For A New Templated Activity By Terminal Deoxynucleotidyl Transferase: Implications For V(D)J Recombination, PDB code: 5d4b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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:67.5 occ:1.00 OD1 A:ASP343 2.0 72.8 1.0 O2 C:SO4401 2.3 66.3 1.0 OP1 C:DC6 2.4 76.9 1.0 OD2 A:ASP345 2.6 66.7 1.0 CG A:ASP343 3.1 70.2 1.0 O1 C:SO4401 3.2 73.7 1.0 S C:SO4401 3.3 72.1 1.0 O A:ASP343 3.5 59.8 1.0 CG A:ASP345 3.5 61.6 1.0 OD2 A:ASP343 3.6 74.5 1.0 OD1 A:ASP345 3.8 63.4 1.0 P C:DC6 3.8 76.8 1.0 O A:HOH732 3.9 60.6 1.0 O4 C:SO4401 4.1 75.6 1.0 C A:ASP343 4.2 59.7 1.0 CB A:ASP343 4.4 58.0 1.0 O A:HOH703 4.4 47.8 1.0 N A:ASP343 4.4 58.6 1.0 O3 C:SO4401 4.4 71.7 1.0 N A:GLY333 4.4 48.2 1.0 O5' C:DC6 4.5 77.8 1.0 CA A:ASP343 4.6 57.0 1.0 OP2 C:DC6 4.6 76.4 1.0 C5' C:DC6 4.6 78.8 1.0 CA A:GLY332 4.6 48.2 1.0 O3' C:DA5 4.8 77.6 1.0 CB A:ASP345 4.9 47.7 1.0 N A:ASP345 5.0 46.8 1.0

Magnesium binding site 2 out of 2 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 2 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 B:Mg601 b:50.3 occ:1.00 OD1 B:ASP343 2.0 49.0 1.0 O4 B:SO4603 2.0 72.9 1.0 OP1 D:DC6 2.1 49.0 1.0 O B:HOH702 2.3 50.7 1.0 OD2 B:ASP345 2.6 57.0 1.0 S B:SO4603 3.1 73.1 1.0 O3 B:SO4603 3.1 74.5 1.0 CG B:ASP343 3.1 50.5 1.0 CG B:ASP345 3.5 54.3 1.0 P D:DC6 3.6 49.8 1.0 OD2 B:ASP343 3.6 56.8 1.0 O B:ASP343 3.6 48.1 1.0 OD1 B:ASP345 3.7 56.1 1.0 O1 B:SO4603 3.8 76.2 1.0 O B:HOH711 4.2 35.5 1.0 O5' D:DC6 4.2 50.0 1.0 O2 B:SO4603 4.2 69.5 1.0 C B:ASP343 4.3 47.5 1.0 CB B:ASP343 4.4 43.9 1.0 C5' D:DC6 4.4 50.2 1.0 O B:HOH733 4.4 61.6 1.0 N B:ASP343 4.4 46.1 1.0 OP2 D:DC6 4.4 50.1 1.0 N B:GLY333 4.5 46.5 1.0 O3' D:DA5 4.5 52.2 1.0 CA B:ASP343 4.6 43.7 1.0 CA B:GLY332 4.7 47.6 1.0 CB B:ASP345 4.9 45.0 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