Zinc in PDB 7v38: Crystal Structure of Np Exonuclease-Pcmps Complex

The structure of Crystal Structure of Np Exonuclease-Pcmps Complex, PDB code: 7v38 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 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.227, 74.012, 140.807, 90, 90, 90
R / Rfree (%)	21.3 / 26.2

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

Mercury

(Hg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Np Exonuclease-Pcmps Complex (pdb code 7v38). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Np Exonuclease-Pcmps Complex, PDB code: 7v38:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Np Exonuclease-Pcmps Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Np Exonuclease-Pcmps Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:47.5 occ:1.00 OE2 A:GLU399 2.1 45.4 1.0 NE2 A:HIS509 2.1 45.4 1.0 SG A:CYS506 2.3 45.4 1.0 SG A:CYS529 2.4 48.4 1.0 CD2 A:HIS509 2.9 47.9 1.0 CD A:GLU399 2.9 51.1 1.0 OE1 A:GLU399 3.1 50.8 1.0 CB A:CYS529 3.2 43.7 1.0 CE1 A:HIS509 3.3 45.9 1.0 CB A:CYS506 3.4 51.9 1.0 CA A:CYS529 3.8 43.5 1.0 NE2 A:HIS412 4.0 48.4 1.0 CG A:HIS509 4.1 46.3 1.0 CE1 A:HIS412 4.2 50.8 1.0 CZ A:PHE414 4.2 51.8 1.0 ND1 A:HIS509 4.3 43.7 1.0 N A:ALA530 4.3 50.3 1.0 CG A:GLU399 4.3 51.1 1.0 CE2 A:PHE414 4.4 54.6 1.0 C A:CYS529 4.5 49.8 1.0 CA A:CYS506 4.8 60.6 1.0 N A:LEU531 4.9 38.3 1.0 CB A:MET508 4.9 54.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Np Exonuclease-Pcmps Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Np Exonuclease-Pcmps Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:45.2 occ:1.00 OE2 B:GLU399 2.1 44.1 1.0 NE2 B:HIS509 2.1 43.2 1.0 SG B:CYS506 2.2 42.4 1.0 SG B:CYS529 2.4 44.9 1.0 CD2 B:HIS509 2.9 43.0 1.0 CD B:GLU399 3.0 47.6 1.0 CE1 B:HIS509 3.2 41.3 1.0 OE1 B:GLU399 3.2 48.3 1.0 CB B:CYS529 3.3 35.4 1.0 CB B:CYS506 3.4 53.5 1.0 CA B:CYS529 3.9 35.3 1.0 NE2 B:HIS412 3.9 41.2 1.0 CE1 B:HIS412 4.1 40.7 1.0 CG B:HIS509 4.2 46.3 1.0 CZ B:PHE414 4.2 52.5 1.0 ND1 B:HIS509 4.2 44.9 1.0 N B:ALA530 4.3 46.8 1.0 CE2 B:PHE414 4.3 51.4 1.0 CG B:GLU399 4.4 46.0 1.0 C B:CYS529 4.5 42.1 1.0 CA B:CYS506 4.8 56.6 1.0 N B:LEU531 4.8 48.9 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