Zinc in PDB 5zn8: Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis

The structure of Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis, PDB code: 5zn8 was solved by F.Shang, J.Chen, L.Wang, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.91 / 2.00
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	90.037, 90.037, 86.181, 90.00, 90.00, 120.00
R / Rfree (%)	15.4 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis (pdb code 5zn8). 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 Nicotinamidase Pnca From Bacillus Subtilis, PDB code: 5zn8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis


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 Nicotinamidase Pnca From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:52.5 occ:1.00 OE2 A:GLU64 1.8 55.0 1.0 NE2 A:HIS55 1.9 41.5 1.0 OD2 A:ASP53 2.2 57.9 1.0 NE2 A:HIS71 2.2 55.5 1.0 CD A:GLU64 2.7 53.7 1.0 CD2 A:HIS55 2.7 54.1 1.0 HD2 A:HIS55 2.8 65.0 1.0 O A:HOH381 3.0 58.7 1.0 OE1 A:GLU64 3.0 41.5 1.0 CE1 A:HIS55 3.1 50.1 1.0 CG A:ASP53 3.1 45.0 1.0 CE1 A:HIS71 3.1 54.1 1.0 O A:HOH375 3.2 46.7 1.0 HE1 A:HIS71 3.2 64.9 1.0 CD2 A:HIS71 3.3 54.0 1.0 HE1 A:HIS55 3.4 60.1 1.0 OD1 A:ASP53 3.5 45.2 1.0 HD2 A:HIS71 3.5 64.9 1.0 HG2 A:GLU64 3.9 67.2 1.0 CG A:HIS55 3.9 59.1 1.0 CG A:GLU64 4.0 56.0 1.0 ND1 A:HIS55 4.1 45.1 1.0 HZ A:PHE14 4.1 58.5 1.0 ND1 A:HIS71 4.3 58.6 1.0 HB3 A:ASP53 4.3 46.4 1.0 CB A:ASP53 4.3 38.7 1.0 CG A:HIS71 4.4 60.1 1.0 HE1 A:TYR106 4.5 31.9 1.0 O A:HOH320 4.5 55.2 1.0 HG3 A:GLU64 4.6 67.2 1.0 HE1 A:HIS62 4.6 54.5 1.0 HB2 A:ASP53 4.7 46.4 1.0 HB3 A:GLU64 4.7 65.9 1.0 CB A:GLU64 4.8 54.9 1.0 HB2 A:GLU64 4.8 65.9 1.0 HD22 A:ASN72 4.9 59.4 1.0 CZ A:PHE14 5.0 48.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Nicotinamidase Pnca From Bacillus Subtilis


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 Nicotinamidase Pnca From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:35.3 occ:1.00 O B:HOH311 1.6 32.4 1.0 NE2 B:HIS55 2.0 29.5 1.0 OE1 B:GLU64 2.1 34.9 1.0 OD2 B:ASP53 2.2 35.6 1.0 NE2 B:HIS71 2.2 36.8 1.0 CD2 B:HIS55 2.8 32.8 1.0 CG B:ASP53 2.9 30.9 1.0 OD1 B:ASP53 2.9 32.7 1.0 HD2 B:HIS55 2.9 39.4 1.0 CE1 B:HIS71 3.0 37.3 1.0 CE1 B:HIS55 3.1 38.5 1.0 HE1 B:HIS71 3.1 44.8 1.0 CD B:GLU64 3.1 33.9 1.0 CD2 B:HIS71 3.2 35.8 1.0 HE1 B:HIS55 3.4 46.2 1.0 OE2 B:GLU64 3.4 33.3 1.0 HD2 B:HIS71 3.5 42.9 1.0 HZ B:PHE14 3.9 51.8 1.0 ND1 B:HIS71 4.0 38.5 1.0 CG B:HIS55 4.0 29.3 1.0 ND1 B:HIS55 4.1 34.8 1.0 CG B:HIS71 4.2 39.1 1.0 HD22 B:ASN72 4.2 50.4 1.0 O B:HOH360 4.2 32.7 1.0 HB2 B:ASN72 4.3 43.8 1.0 CB B:ASP53 4.3 33.3 1.0 HB3 B:GLU64 4.4 43.7 1.0 CG B:GLU64 4.5 34.8 1.0 O B:HOH383 4.5 39.9 1.0 HB2 B:GLU64 4.5 43.7 1.0 HB3 B:ASP53 4.5 39.9 1.0 HB2 B:ASP53 4.6 39.9 1.0 CB B:GLU64 4.7 36.5 1.0 CZ B:PHE14 4.8 43.2 1.0 O B:HOH368 4.8 35.5 1.0 HE1 B:HIS62 4.8 37.0 1.0 HG2 B:GLU64 4.9 41.8 1.0 O B:HOH315 5.0 32.0 1.0

F.Shang, J.Chen, L.Wang, L.Jin, L.Zou, T.Bu, Y.Dong, N.C.Ha, K.H.Nam, C.Quan, Y.Xu. Crystal Structure of the Nicotinamidase/Pyrazinamidase Pnca From Bacillus Subtilis. Biochem.Biophys.Res.Commun. V. 503 2906 2018.
ISSN: ESSN 1090-2104
PubMed: 30107912
DOI: 10.1016/J.BBRC.2018.08.067