Magnesium in PDB 7v3c: Crystal Structure of Np Exonuclease C409A-Pcmb Complex

The structure of Crystal Structure of Np Exonuclease C409A-Pcmb Complex, PDB code: 7v3c 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)	26.44 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.851, 58.809, 68.845, 90, 90, 90
R / Rfree (%)	18.7 / 22.2

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

Zinc	(Zn)	2 atoms
Mercury	(Hg)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Np Exonuclease C409A-Pcmb Complex (pdb code 7v3c). 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 Np Exonuclease C409A-Pcmb Complex, PDB code: 7v3c:
Jump to Magnesium binding site number: 1; 2;

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


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 Np Exonuclease C409A-Pcmb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:46.5 occ:1.00 OD2 A:ASP533 2.0 38.3 1.0 O A:HOH764 2.1 39.8 1.0 O A:HOH709 2.3 45.5 1.0 OD2 A:ASP389 2.3 39.7 1.0 O A:HOH759 2.3 41.5 1.0 O A:HOH703 3.0 55.8 1.0 CG A:ASP389 3.1 36.1 1.0 CG A:ASP533 3.1 35.9 1.0 OD1 A:ASP389 3.2 37.4 1.0 O A:HOH704 3.6 47.2 1.0 CB A:ASP533 3.7 25.3 1.0 OE2 A:GLU391 4.0 41.1 1.0 O A:HOH702 4.0 53.3 1.0 NH2 A:ARG492 4.1 45.7 1.0 O A:HOH794 4.1 46.8 1.0 OD1 A:ASP533 4.2 33.8 1.0 CZ A:PHE537 4.3 29.4 1.0 CE2 A:PHE537 4.3 28.5 1.0 O A:ILE390 4.5 28.6 1.0 CB A:ASP389 4.6 20.5 1.0

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


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 Np Exonuclease C409A-Pcmb Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:41.4 occ:1.00 O B:HOH709 1.9 35.4 1.0 OD2 B:ASP533 2.0 36.7 1.0 O B:HOH701 2.0 42.2 1.0 O B:HOH729 2.1 34.7 1.0 O B:HOH768 2.2 43.5 1.0 OD2 B:ASP389 2.3 49.9 1.0 CG B:ASP533 3.1 32.8 1.0 CG B:ASP389 3.3 41.5 1.0 OE2 B:GLU391 3.3 45.0 1.0 OD1 B:ASP389 3.6 45.1 1.0 CB B:ASP533 3.7 26.6 1.0 NH2 B:ARG492 4.1 45.1 1.0 OD1 B:ASP533 4.1 34.0 1.0 O B:ILE390 4.2 28.7 1.0 CD B:GLU391 4.5 39.8 1.0 CB B:ASP389 4.6 24.5 1.0 O B:CYS529 4.6 25.1 1.0 CZ B:PHE537 4.7 34.2 1.0 CE2 B:PHE537 4.7 33.3 1.0 CB B:HIS528 4.7 31.4 1.0 CA B:ALA530 4.8 25.2 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
DOI: 10.1021/JACSAU.1C00420