Zinc in PDB 6b9v: Crystal Structure of A New Diphosphatase From the Phnp Family

The structure of Crystal Structure of A New Diphosphatase From the Phnp Family, PDB code: 6b9v was solved by Q.Li, S.D.Bruner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.28 / 1.88
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.780, 41.364, 96.034, 90.00, 95.20, 90.00
R / Rfree (%)	15.9 / 19.6

The structure of Crystal Structure of A New Diphosphatase From the Phnp Family also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of A New Diphosphatase From the Phnp Family (pdb code 6b9v). 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 A New Diphosphatase From the Phnp Family, PDB code: 6b9v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A New Diphosphatase From the Phnp Family


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 A New Diphosphatase From the Phnp Family within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn304 b:20.1 occ:1.00 ND1 A:HIS234 2.0 29.1 1.0 SG A:CYS28 2.3 19.1 1.0 SG A:CYS23 2.3 21.0 1.0 SG A:CYS25 2.3 19.5 1.0 CE1 A:HIS234 3.0 22.7 1.0 CG A:HIS234 3.1 21.1 1.0 CB A:CYS28 3.2 18.6 1.0 CB A:CYS23 3.3 21.8 1.0 CB A:CYS25 3.4 22.0 1.0 CB A:HIS234 3.5 16.1 1.0 N A:CYS25 4.1 22.4 1.0 N A:CYS28 4.1 17.6 1.0 NE2 A:HIS234 4.1 29.3 1.0 CD2 A:HIS234 4.2 19.0 1.0 CA A:CYS28 4.3 15.6 1.0 CA A:CYS25 4.3 19.6 1.0 CA A:CYS23 4.6 20.4 1.0 C A:CYS23 4.6 22.3 1.0 CB A:THR20 4.8 29.4 1.0 O A:CYS23 4.8 26.2 1.0 C A:CYS25 4.8 20.1 1.0 O A:HOH610 4.9 46.3 1.0 O A:CYS25 4.9 21.4 1.0 N A:THR20 5.0 17.6 1.0 CA A:HIS234 5.0 15.2 1.0 OG1 A:THR20 5.0 28.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A New Diphosphatase From the Phnp Family


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 A New Diphosphatase From the Phnp Family within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:21.6 occ:1.00 SG B:CYS28 2.3 19.4 1.0 ND1 B:HIS234 2.3 31.1 1.0 SG B:CYS23 2.3 20.1 1.0 SG B:CYS25 2.4 21.7 1.0 CB B:CYS28 3.2 15.5 1.0 CB B:CYS23 3.2 21.3 1.0 CG B:HIS234 3.2 28.4 1.0 CE1 B:HIS234 3.3 33.6 1.0 CB B:CYS25 3.3 27.8 1.0 CB B:HIS234 3.5 16.3 1.0 N B:CYS25 4.0 24.9 1.0 N B:CYS28 4.1 20.5 1.0 CA B:CYS25 4.2 30.7 1.0 CA B:CYS28 4.2 19.3 1.0 NE2 B:HIS234 4.4 28.8 1.0 CD2 B:HIS234 4.4 25.0 1.0 CA B:CYS23 4.5 19.3 1.0 C B:CYS23 4.6 20.9 1.0 C B:CYS25 4.7 26.3 1.0 O B:CYS25 4.7 21.0 1.0 O B:CYS23 4.8 24.6 1.0 CA B:HIS234 4.9 20.8 1.0 N B:ASP24 5.0 21.7 1.0

G.A.W.Beaudoin, Q.Li, S.D.Bruner, A.D.Hanson. An Unusual Diphosphatase From the Phnp Family Cleaves Reactive Fad Photoproducts. Biochem.J. V. 475 261 2018.
ISSN: ESSN 1470-8728
PubMed: 29229761
DOI: 10.1042/BCJ20170817