Zinc in PDB 3r2j: Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate

All present enzymatic activity of Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate:
3.5.1.19;

The structure of Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate, PDB code: 3r2j was solved by E.Gazanion, D.Garcia, J.-F.Guichou, G.Labesse, D.Sereno, B.Vergnes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.25 / 2.68
Space group	P 4 21 2
Cell size a, b, c (Å), α, β, γ (°)	123.386, 123.386, 114.993, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 29.8

The structure of Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate (pdb code 3r2j). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate, PDB code: 3r2j:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate


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 PNC1 From L. Infantum in Complex with Nicotinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.1 occ:1.00 N A:NIO311 2.0 25.2 1.0 OD2 A:ASP73 2.0 15.9 1.0 NE2 A:HIS75 2.2 13.8 1.0 NE2 A:HIS92 2.2 17.1 1.0 C1 A:NIO311 2.9 24.5 1.0 C5 A:NIO311 2.9 26.8 1.0 CE1 A:HIS92 3.0 17.4 1.0 CG A:ASP73 3.0 15.5 1.0 CE1 A:HIS75 3.1 13.4 1.0 CD2 A:HIS75 3.2 13.7 1.0 OD1 A:ASP73 3.3 16.4 1.0 CD2 A:HIS92 3.4 16.0 1.0 ND1 A:HIS92 4.2 15.7 1.0 C2 A:NIO311 4.2 26.4 1.0 OD2 A:ASP124 4.2 28.4 1.0 C4 A:NIO311 4.2 27.6 1.0 ND1 A:HIS75 4.2 13.7 1.0 OG A:SER81 4.3 19.8 1.0 CG A:HIS75 4.3 14.4 1.0 CG A:HIS92 4.4 14.9 1.0 CB A:ASP73 4.5 14.1 1.0 OD1 A:ASP124 4.6 30.3 1.0 C3 A:NIO311 4.8 26.9 1.0 CG A:ASP124 4.9 28.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate


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 PNC1 From L. Infantum in Complex with Nicotinate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.2 occ:1.00 N B:NIO311 2.0 25.7 1.0 NE2 B:HIS75 2.1 25.7 1.0 OD2 B:ASP73 2.1 23.7 1.0 NE2 B:HIS92 2.2 24.9 1.0 C5 B:NIO311 2.9 26.9 1.0 C1 B:NIO311 3.0 23.9 1.0 CE1 B:HIS92 3.0 25.6 1.0 CG B:ASP73 3.0 23.6 1.0 CE1 B:HIS75 3.1 25.0 1.0 CD2 B:HIS75 3.1 26.3 1.0 OD1 B:ASP73 3.2 24.0 1.0 CD2 B:HIS92 3.4 24.4 1.0 OD2 B:ASP124 4.0 31.3 1.0 OD1 B:ASP124 4.1 33.8 1.0 ND1 B:HIS75 4.2 25.8 1.0 C4 B:NIO311 4.2 26.4 1.0 ND1 B:HIS92 4.2 25.5 1.0 CG B:HIS75 4.2 26.3 1.0 C2 B:NIO311 4.3 23.6 1.0 OG B:SER81 4.4 26.2 1.0 CG B:HIS92 4.4 26.4 1.0 CG B:ASP124 4.4 32.9 1.0 CB B:ASP73 4.5 22.5 1.0 C3 B:NIO311 4.8 24.6 1.0 CE1 B:TYR126 5.0 31.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:23.4 occ:1.00 OD2 C:ASP73 2.0 18.3 1.0 NE2 C:HIS75 2.0 17.6 1.0 N C:NIO311 2.0 14.8 1.0 NE2 C:HIS92 2.3 13.6 1.0 CE1 C:HIS75 2.9 18.0 1.0 C1 C:NIO311 2.9 13.4 1.0 C5 C:NIO311 2.9 16.2 1.0 CG C:ASP73 3.0 17.3 1.0 CE1 C:HIS92 3.1 14.9 1.0 CD2 C:HIS75 3.1 17.9 1.0 OD1 C:ASP73 3.4 18.0 1.0 CD2 C:HIS92 3.4 14.1 1.0 OD1 C:ASP124 3.7 33.2 1.0 OD2 C:ASP124 3.7 29.5 1.0 ND1 C:HIS75 4.1 18.1 1.0 CG C:ASP124 4.2 30.3 1.0 CG C:HIS75 4.2 18.3 1.0 C2 C:NIO311 4.2 15.7 1.0 C4 C:NIO311 4.2 17.3 1.0 OG C:SER81 4.3 16.9 1.0 ND1 C:HIS92 4.3 14.3 1.0 CB C:ASP73 4.4 15.5 1.0 CG C:HIS92 4.5 15.8 1.0 C3 C:NIO311 4.8 17.0 1.0 CD1 C:TRP89 5.0 21.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of PNC1 From L. Infantum in Complex with Nicotinate within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:27.8 occ:1.00 NE2 D:HIS75 1.9 19.6 1.0 OD2 D:ASP73 2.1 22.6 1.0 NE2 D:HIS92 2.1 26.5 1.0 N D:NIO311 2.3 29.5 1.0 CE1 D:HIS75 2.9 19.4 1.0 CD2 D:HIS75 2.9 20.1 1.0 CG D:ASP73 3.0 21.6 1.0 CE1 D:HIS92 3.1 28.3 1.0 CD2 D:HIS92 3.1 25.9 1.0 C1 D:NIO311 3.1 27.8 1.0 C5 D:NIO311 3.1 31.2 1.0 OD1 D:ASP73 3.2 21.3 1.0 OD2 D:ASP124 3.9 30.7 1.0 ND1 D:HIS75 4.0 20.4 1.0 CG D:HIS75 4.1 20.7 1.0 ND1 D:HIS92 4.2 28.6 1.0 CG D:HIS92 4.2 26.6 1.0 CB D:ASP73 4.4 19.5 1.0 C4 D:NIO311 4.4 31.7 1.0 C2 D:NIO311 4.4 28.6 1.0 OG D:SER81 4.4 24.1 1.0 OD1 D:ASP124 4.6 31.8 1.0 CG D:ASP124 4.7 30.6 1.0 C3 D:NIO311 5.0 30.4 1.0

E.Gazanion, D.Garcia, R.Silvestre, C.Gerard, J.F.Guichou, G.Labesse, M.Seveno, A.Cordeiro-Da-Silva, A.Ouaissi, D.Sereno, B.Vergnes. The Leishmania Nicotinamidase Is Essential For Nad(+) Production and Parasite Proliferation. Mol.Microbiol. V. 82 21 2011.
ISSN: ISSN 0950-382X
PubMed: 21819459
DOI: 10.1111/J.1365-2958.2011.07799.X