Zinc in PDB 3zu0: Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn)

All present enzymatic activity of Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn):
3.1.3.5;

The structure of Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn), PDB code: 3zu0 was solved by S.Garavaglia, S.Bruzzone, C.Cassani, L.Canella, G.Allegrone, L.Sturla, E.Mannino, E.Millo, A.De Flora, M.Rizzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.707 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.626, 104.051, 119.601, 90.00, 90.00, 90.00
R / Rfree (%)	21.49 / 24.69

The binding sites of Zinc atom in the Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn) (pdb code 3zu0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn), PDB code: 3zu0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1595 b:28.5 occ:1.00 O2 A:PO41597 2.0 31.7 1.0 NE2 A:HIS227 2.0 23.9 1.0 OD1 A:ASN126 2.1 25.0 1.0 OD2 A:ASP94 2.1 26.8 1.0 OD1 A:ASP250 2.1 29.0 1.0 CG A:ASP94 2.9 24.8 1.0 CD2 A:HIS227 3.0 21.8 1.0 CE1 A:HIS227 3.0 24.6 1.0 CG A:ASN126 3.1 28.2 1.0 CG A:ASP250 3.2 27.3 1.0 OD1 A:ASP94 3.3 25.6 1.0 ZN A:ZN1596 3.3 28.0 1.0 P A:PO41597 3.3 45.7 1.0 CB A:ASP250 3.5 26.6 1.0 O3 A:PO41597 3.5 33.7 1.0 OD1 A:ASP44 3.5 23.8 1.0 CA A:ASP250 3.6 24.6 1.0 ND2 A:ASN126 3.6 29.1 1.0 CD2 A:HIS127 4.0 29.7 1.0 N A:ASN126 4.1 26.8 1.0 ND1 A:HIS227 4.1 23.4 1.0 CB A:ASP94 4.2 24.0 1.0 CG A:HIS227 4.2 22.4 1.0 O1 A:PO41597 4.2 43.1 1.0 O A:ASP250 4.3 33.9 1.0 OD2 A:ASP250 4.3 31.7 1.0 O4 A:PO41597 4.3 44.4 1.0 N A:ASP250 4.4 23.4 1.0 CB A:ASN126 4.4 25.8 1.0 C A:ASP250 4.4 29.1 1.0 CG A:ASP44 4.7 27.2 1.0 NE2 A:HIS127 4.7 33.5 1.0 N A:HIS127 4.8 27.3 1.0 CA A:ASN126 4.8 26.7 1.0 NE2 A:HIS46 4.9 29.2 1.0 NE2 A:HIS252 5.0 29.0 1.0

Zinc binding site 2 out of 4 in the Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1596 b:28.0 occ:1.00 OD1 A:ASP44 2.1 23.8 1.0 NE2 A:HIS252 2.1 29.0 1.0 NE2 A:HIS46 2.1 29.2 1.0 O2 A:PO41597 2.2 31.7 1.0 OD2 A:ASP94 2.4 26.8 1.0 O4 A:PO41597 3.0 44.4 1.0 CE1 A:HIS252 3.0 30.9 1.0 CE1 A:HIS46 3.1 30.0 1.0 CG A:ASP44 3.1 27.2 1.0 P A:PO41597 3.1 45.7 1.0 CD2 A:HIS252 3.1 27.7 1.0 CD2 A:HIS46 3.1 26.6 1.0 ZN A:ZN1595 3.3 28.5 1.0 CG A:ASP94 3.4 24.8 1.0 CB A:ASP44 3.6 20.8 1.0 CB A:ASP94 3.6 24.0 1.0 O1 A:PO41597 4.0 43.1 1.0 OD2 A:ASP44 4.1 26.9 1.0 ND1 A:HIS252 4.2 27.3 1.0 ND1 A:HIS46 4.2 31.4 1.0 CG A:HIS252 4.2 26.5 1.0 CG A:HIS46 4.3 30.6 1.0 O3 A:PO41597 4.3 33.7 1.0 CD2 A:HIS127 4.4 29.7 1.0 NE2 A:HIS227 4.4 23.9 1.0 CE1 A:HIS227 4.4 24.6 1.0 CA A:ASP44 4.4 24.1 1.0 OD1 A:ASP94 4.5 25.6 1.0 CA A:ASP250 4.5 24.6 1.0 O A:ASP250 4.6 33.9 1.0 O3B A:A121598 4.6 51.0 1.0 OD1 A:ASP250 4.7 29.0 1.0 C A:ASP250 4.8 29.1 1.0 NE2 A:HIS127 4.9 33.5 1.0 OD1 A:ASN126 5.0 25.0 1.0

Zinc binding site 3 out of 4 in the Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1588 b:27.7 occ:1.00 OD1 B:ASN126 2.0 27.2 1.0 NE2 B:HIS227 2.0 24.1 1.0 O B:HOH2007 2.1 27.6 1.0 OD2 B:ASP94 2.2 27.0 1.0 OD1 B:ASP250 2.2 25.5 1.0 CE1 B:HIS227 3.0 26.4 1.0 CG B:ASP94 3.0 27.8 1.0 CD2 B:HIS227 3.0 25.5 1.0 CG B:ASN126 3.1 27.6 1.0 ZN B:ZN1589 3.2 27.7 1.0 CG B:ASP250 3.2 28.9 1.0 OD1 B:ASP94 3.4 26.8 1.0 O B:HOH2058 3.4 27.1 1.0 CA B:ASP250 3.5 27.3 1.0 OD2 B:ASP44 3.6 26.0 1.0 CB B:ASP250 3.6 25.4 1.0 ND2 B:ASN126 3.7 26.2 1.0 ND1 B:HIS227 4.1 27.3 1.0 CD2 B:HIS127 4.1 24.9 1.0 CG B:HIS227 4.2 24.9 1.0 O B:ASP250 4.2 29.3 1.0 N B:ASN126 4.2 27.8 1.0 CB B:ASP94 4.2 28.7 1.0 CB B:ASN126 4.4 27.4 1.0 OD2 B:ASP250 4.4 33.1 1.0 C B:ASP250 4.4 26.8 1.0 N B:ASP250 4.4 25.4 1.0 CG B:ASP44 4.7 26.5 1.0 CA B:ASN126 4.8 26.5 1.0 NE2 B:HIS127 4.8 28.9 1.0 NE2 B:HIS46 4.8 27.2 1.0 NE2 B:HIS252 4.9 25.4 1.0 N B:HIS127 4.9 30.8 1.0

Zinc binding site 4 out of 4 in the Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Haemophilus Influenzae Nad Nucleotidase (Nadn) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1589 b:27.7 occ:1.00 OD2 B:ASP44 2.0 26.0 1.0 O B:HOH2007 2.1 27.6 1.0 NE2 B:HIS252 2.1 25.4 1.0 NE2 B:HIS46 2.1 27.2 1.0 OD2 B:ASP94 2.3 27.0 1.0 CE1 B:HIS252 3.0 28.0 1.0 CG B:ASP44 3.0 26.5 1.0 CD2 B:HIS46 3.1 27.6 1.0 CE1 B:HIS46 3.2 29.9 1.0 CD2 B:HIS252 3.2 23.5 1.0 ZN B:ZN1588 3.2 27.7 1.0 CG B:ASP94 3.3 27.8 1.0 CB B:ASP44 3.5 22.3 1.0 CB B:ASP94 3.6 28.7 1.0 O B:HOH2058 4.1 27.1 1.0 OD1 B:ASP44 4.1 27.1 1.0 ND1 B:HIS252 4.2 26.9 1.0 ND1 B:HIS46 4.2 26.3 1.0 CG B:HIS46 4.2 27.2 1.0 CG B:HIS252 4.3 28.3 1.0 CE1 B:HIS227 4.3 26.4 1.0 CA B:ASP44 4.3 24.1 1.0 NE2 B:HIS227 4.3 24.1 1.0 O B:ASP250 4.4 29.3 1.0 OD1 B:ASP94 4.5 26.8 1.0 CD2 B:HIS127 4.5 24.9 1.0 CA B:ASP250 4.5 27.3 1.0 CD2 B:TYR566 4.5 28.9 1.0 C B:ASP250 4.8 26.8 1.0 OD1 B:ASP250 4.8 25.5 1.0 OD1 B:ASN126 4.9 27.2 1.0 N B:ASP250 4.9 25.4 1.0 NE2 B:HIS127 5.0 28.9 1.0

S.Garavaglia, S.Bruzzone, C.Cassani, L.Canella, G.Allegrone, L.Sturla, E.Mannino, E.Millo, A.De Flora, M.Rizzi. The High-Resolution Crystal Structure of Periplasmic Haemophilus Influenzae Nad Nucleotidase Reveals A Novel Enzymatic Function of Human CD73 Related to Nad Metabolism. Biochem.J. V. 441 131 2012.
ISSN: ISSN 0264-6021
PubMed: 21933152
DOI: 10.1042/BJ20111263