Zinc in PDB 2h0r: Structure of the Yeast Nicotinamidase PNC1P

All present enzymatic activity of Structure of the Yeast Nicotinamidase PNC1P:
3.5.1.19;

The structure of Structure of the Yeast Nicotinamidase PNC1P, PDB code: 2h0r was solved by A.B.Taylor, G.Hu, P.J.Hart, L.Mcalister-Henn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	302.040, 302.040, 112.120, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 22

The binding sites of Zinc atom in the Structure of the Yeast Nicotinamidase PNC1P (pdb code 2h0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structure of the Yeast Nicotinamidase PNC1P, PDB code: 2h0r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structure of the Yeast Nicotinamidase PNC1P


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Yeast Nicotinamidase PNC1P within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:84.9 occ:1.00 OD2 A:ASP51 2.0 77.0 1.0 NE2 A:HIS53 2.0 71.3 1.0 NE2 A:HIS94 2.2 72.4 1.0 CE1 A:HIS53 3.0 71.4 1.0 CD2 A:HIS53 3.1 72.1 1.0 CG A:ASP51 3.1 77.8 1.0 CD2 A:HIS94 3.2 70.9 1.0 CE1 A:HIS94 3.2 71.5 1.0 OD1 A:ASP51 3.5 84.2 1.0 OE1 A:GLU129 3.9 82.8 1.0 ND1 A:HIS53 4.1 72.2 1.0 OG A:SER59 4.1 72.4 1.0 CG A:HIS53 4.2 74.1 1.0 ND1 A:HIS94 4.3 69.6 1.0 CG A:HIS94 4.3 69.7 1.0 OE2 A:GLU129 4.3 83.8 1.0 CB A:ASP51 4.4 75.9 1.0 CD A:GLU129 4.6 82.3 1.0

Zinc binding site 2 out of 7 in the Structure of the Yeast Nicotinamidase PNC1P


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Yeast Nicotinamidase PNC1P within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:87.9 occ:1.00 OD2 B:ASP51 1.9 78.4 1.0 NE2 B:HIS53 2.0 73.4 1.0 NE2 B:HIS94 2.1 76.7 1.0 CE1 B:HIS53 2.9 73.0 1.0 CG B:ASP51 3.0 77.2 1.0 CD2 B:HIS53 3.0 73.5 1.0 CE1 B:HIS94 3.0 76.6 1.0 CD2 B:HIS94 3.2 75.0 1.0 OD1 B:ASP51 3.4 81.5 1.0 ND1 B:HIS53 4.0 72.6 1.0 OE1 B:GLU129 4.1 82.7 1.0 CG B:HIS53 4.1 73.2 1.0 ND1 B:HIS94 4.2 74.8 1.0 OG B:SER59 4.3 74.3 1.0 CG B:HIS94 4.3 73.7 1.0 CB B:ASP51 4.3 74.7 1.0 OE2 B:GLU129 4.6 84.5 1.0 CD B:GLU129 4.8 82.8 1.0

Zinc binding site 3 out of 7 in the Structure of the Yeast Nicotinamidase PNC1P


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Yeast Nicotinamidase PNC1P within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:90.6 occ:1.00 NE2 C:HIS53 2.0 70.0 1.0 OD2 C:ASP51 2.1 77.5 1.0 NE2 C:HIS94 2.2 76.0 1.0 CE1 C:HIS53 2.9 70.2 1.0 CG C:ASP51 3.1 76.6 1.0 CE1 C:HIS94 3.1 75.9 1.0 CD2 C:HIS53 3.1 69.9 1.0 CD2 C:HIS94 3.2 76.1 1.0 OD1 C:ASP51 3.4 80.0 1.0 OE1 C:GLU129 3.9 84.9 1.0 ND1 C:HIS53 4.1 69.9 1.0 CG C:HIS53 4.2 70.3 1.0 ND1 C:HIS94 4.2 75.0 1.0 OG C:SER59 4.3 73.7 1.0 CG C:HIS94 4.3 75.4 1.0 OE2 C:GLU129 4.3 84.1 1.0 CB C:ASP51 4.4 74.8 1.0 CD C:GLU129 4.5 83.7 1.0 CE1 C:PHE60 4.9 68.8 1.0

Zinc binding site 4 out of 7 in the Structure of the Yeast Nicotinamidase PNC1P


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Yeast Nicotinamidase PNC1P within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:87.2 occ:1.00 NE2 D:HIS53 1.9 76.8 1.0 OD2 D:ASP51 2.1 77.4 1.0 NE2 D:HIS94 2.4 75.5 1.0 CE1 D:HIS53 2.8 77.3 1.0 CG D:ASP51 3.0 76.8 1.0 CD2 D:HIS53 3.1 76.0 1.0 CE1 D:HIS94 3.1 75.8 1.0 OD1 D:ASP51 3.3 79.9 1.0 CD2 D:HIS94 3.5 74.0 1.0 OE1 D:GLU129 3.8 83.8 1.0 OE2 D:GLU129 3.9 83.4 1.0 ND1 D:HIS53 3.9 76.6 1.0 CG D:HIS53 4.1 75.2 1.0 CD D:GLU129 4.3 83.0 1.0 ND1 D:HIS94 4.3 73.7 1.0 OG D:SER59 4.3 75.9 1.0 CB D:ASP51 4.4 74.9 1.0 CG D:HIS94 4.5 73.1 1.0 O D:TYR130 5.0 81.3 1.0

Zinc binding site 5 out of 7 in the Structure of the Yeast Nicotinamidase PNC1P


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Yeast Nicotinamidase PNC1P within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:97.4 occ:1.00 NE2 E:HIS53 1.7 76.2 1.0 OD2 E:ASP51 2.0 74.2 1.0 NE2 E:HIS94 2.1 75.6 1.0 CE1 E:HIS53 2.7 77.3 1.0 CD2 E:HIS53 2.8 75.9 1.0 CG E:ASP51 3.0 73.5 1.0 CE1 E:HIS94 3.1 75.7 1.0 CD2 E:HIS94 3.1 75.2 1.0 OD1 E:ASP51 3.2 72.9 1.0 OE1 E:GLU129 3.6 80.2 1.0 ND1 E:HIS53 3.8 76.8 1.0 CG E:HIS53 3.9 75.4 1.0 ND1 E:HIS94 4.2 75.7 1.0 CG E:HIS94 4.2 75.2 1.0 OG E:SER59 4.3 77.3 1.0 CB E:ASP51 4.3 73.2 1.0 CD E:GLU129 4.7 80.3 1.0 CE1 E:PHE60 4.9 73.1 1.0

Zinc binding site 6 out of 7 in the Structure of the Yeast Nicotinamidase PNC1P


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the Yeast Nicotinamidase PNC1P within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:92.1 occ:1.00 NE2 F:HIS53 1.9 76.4 1.0 OD2 F:ASP51 2.2 75.4 1.0 NE2 F:HIS94 2.3 75.5 1.0 CE1 F:HIS53 2.8 76.3 1.0 CD2 F:HIS53 3.0 76.4 1.0 CG F:ASP51 3.1 75.3 1.0 CD2 F:HIS94 3.3 74.8 1.0 CE1 F:HIS94 3.3 75.3 1.0 OD1 F:ASP51 3.3 75.1 1.0 ND1 F:HIS53 3.9 76.0 1.0 CG F:HIS53 4.0 75.9 1.0 OE1 F:GLU129 4.1 81.6 1.0 ND1 F:HIS94 4.4 74.8 1.0 CG F:HIS94 4.4 74.1 1.0 OG F:SER59 4.5 77.4 1.0 CB F:ASP51 4.5 74.8 1.0 CD1 F:TRP91 4.7 81.3 1.0

Zinc binding site 7 out of 7 in the Structure of the Yeast Nicotinamidase PNC1P


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the Yeast Nicotinamidase PNC1P within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn301 b:89.0 occ:1.00 NE2 G:HIS53 2.0 74.1 1.0 OD2 G:ASP51 2.1 75.4 1.0 NE2 G:HIS94 2.4 72.1 1.0 CE1 G:HIS53 2.9 74.7 1.0 CG G:ASP51 3.0 74.7 1.0 CD2 G:HIS53 3.1 74.1 1.0 CE1 G:HIS94 3.1 72.2 1.0 OD1 G:ASP51 3.4 75.7 1.0 CD2 G:HIS94 3.5 72.6 1.0 OE1 G:GLU129 3.7 78.3 1.0 ND1 G:HIS53 4.1 73.9 1.0 CG G:HIS53 4.2 74.3 1.0 CB G:ASP51 4.2 74.0 1.0 ND1 G:HIS94 4.3 72.7 1.0 OG G:SER59 4.4 76.1 1.0 CG G:HIS94 4.5 72.7 1.0 CD G:GLU129 4.6 79.5 1.0 OE2 G:GLU129 4.6 80.1 1.0 CD1 G:TRP91 4.8 81.5 1.0

G.Hu, A.B.Taylor, L.Mcalister-Henn, P.J.Hart. Crystal Structure of the Yeast Nicotinamidase PNC1P. Arch.Biochem.Biophys. V. 461 66 2007.
ISSN: ISSN 0003-9861
PubMed: 17382284
DOI: 10.1016/J.ABB.2007.01.037