Magnesium in PDB 7v3a: Crystal Structure of Apo-Np Exonuclease C409A

The structure of Crystal Structure of Apo-Np Exonuclease C409A, PDB code: 7v3a was solved by Y.Y.Hsiao, K.W.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.79 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	127.324, 59.431, 71.533, 90, 90, 90
R / Rfree (%)	20.3 / 24

The structure of Crystal Structure of Apo-Np Exonuclease C409A also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Apo-Np Exonuclease C409A (pdb code 7v3a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Apo-Np Exonuclease C409A, PDB code: 7v3a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Apo-Np Exonuclease C409A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Apo-Np Exonuclease C409A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:33.8 occ:1.00 OD1 A:ASP389 2.1 35.3 1.0 O A:HOH757 2.1 32.2 1.0 O A:HOH771 2.1 36.9 1.0 O A:HOH701 2.2 34.6 1.0 O A:HOH804 2.2 32.0 1.0 O A:HOH848 2.2 34.1 1.0 CG A:ASP389 3.1 32.6 1.0 OD2 A:ASP389 3.4 33.7 1.0 O A:GLN462 3.9 31.0 1.0 OD2 A:ASP466 3.9 42.1 1.0 O A:HOH851 4.0 40.8 1.0 O A:ILE390 4.0 26.6 1.0 O A:HOH744 4.1 32.5 1.0 O A:HOH856 4.1 59.2 1.0 CB A:ASP389 4.4 26.5 1.0 OD1 A:ASP466 4.5 40.9 1.0 N A:ILE390 4.5 24.2 1.0 O A:HOH837 4.5 46.3 1.0 CG A:ASP466 4.6 40.9 1.0 CA A:ASP389 4.8 26.0 1.0 O A:HOH709 4.8 33.9 1.0 O A:GLY463 4.9 35.5 1.0 O A:HOH784 5.0 29.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Apo-Np Exonuclease C409A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Apo-Np Exonuclease C409A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:40.1 occ:1.00 OD1 B:ASP389 2.0 38.2 1.0 O B:HOH702 2.0 35.3 1.0 O B:HOH729 2.1 36.4 1.0 O B:HOH736 2.1 38.2 1.0 O B:HOH851 2.2 47.4 1.0 O B:HOH751 2.3 35.7 1.0 CG B:ASP389 3.0 35.0 1.0 OD2 B:ASP389 3.4 36.0 1.0 O B:GLN462 3.8 38.5 1.0 OD2 B:ASP466 3.9 52.2 1.0 O B:ILE390 4.0 33.1 1.0 O B:HOH711 4.2 33.9 1.0 OD1 B:ASP466 4.2 51.4 1.0 O B:HOH852 4.3 37.1 1.0 N B:ILE390 4.3 25.3 1.0 CB B:ASP389 4.3 31.1 1.0 CG B:ASP466 4.5 50.2 1.0 O B:HOH832 4.6 51.6 1.0 CA B:ASP389 4.6 29.1 1.0 O B:HOH756 4.7 33.3 1.0 O B:GLY463 4.8 42.7 1.0 O B:HOH725 5.0 37.8 1.0 C B:ILE390 5.0 30.2 1.0

K.W.Huang, J.W.Chen, T.Y.Hua, Y.Y.Chu, T.Y.Chiu, J.Y.Liu, C.I.Tu, K.C.Hsu, Y.T.Kao, J.W.Chu, Y.Y.Hsiao. Targeted Covalent Inhibitors Allosterically Deactivate the Deddhlassa Fever Virus Np Exonuclease From Alternative Distal Site. Jacs Au 2021.
ISSN: ESSN 2691-3704