Zinc in PDB 4qn9: Structure of Human Nape-Pld

All present enzymatic activity of Structure of Human Nape-Pld:
3.1.4.54;

The structure of Structure of Human Nape-Pld, PDB code: 4qn9 was solved by G.Garau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.36 / 2.65
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.099, 95.099, 444.170, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 25.3

The binding sites of Zinc atom in the Structure of Human Nape-Pld (pdb code 4qn9). 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 Human Nape-Pld, PDB code: 4qn9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Human Nape-Pld


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Nape-Pld within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:64.4 occ:1.00 O12 A:3PE503 2.2 61.3 1.0 OD2 A:ASP284 2.3 65.3 1.0 NE2 A:HIS253 2.4 59.2 1.0 NE2 A:HIS185 2.4 54.9 1.0 ND1 A:HIS187 2.4 61.6 1.0 P A:3PE503 3.0 65.3 1.0 CE1 A:HIS187 3.2 63.1 1.0 ZN A:ZN502 3.2 66.3 1.0 CD2 A:HIS185 3.2 53.7 1.0 CE1 A:HIS253 3.3 60.7 1.0 O14 A:3PE503 3.3 65.6 1.0 CD2 A:HIS253 3.4 61.7 1.0 CG A:ASP284 3.4 59.4 1.0 CE1 A:HIS185 3.4 54.4 1.0 CG A:HIS187 3.5 59.8 1.0 O11 A:3PE503 3.6 64.5 1.0 C1 A:3PE503 3.7 74.1 1.0 CB A:ASP284 3.8 60.0 1.0 CB A:HIS187 3.9 55.5 1.0 CD2 A:HIS190 4.2 57.8 1.0 NE2 A:HIS190 4.2 57.2 1.0 OD2 A:ASP189 4.3 59.2 1.0 NE2 A:HIS187 4.4 66.9 1.0 ND1 A:HIS253 4.4 61.1 1.0 CG A:HIS185 4.4 58.2 1.0 OD1 A:ASP284 4.5 64.0 1.0 O13 A:3PE503 4.5 73.5 1.0 CG A:HIS253 4.5 59.7 1.0 ND1 A:HIS185 4.5 56.4 1.0 CD2 A:HIS187 4.5 66.0 1.0 CE1 A:HIS321 4.6 66.5 1.0

Zinc binding site 2 out of 4 in the Structure of Human Nape-Pld


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Nape-Pld within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:66.3 occ:1.00 O14 A:3PE503 2.0 65.6 1.0 OD2 A:ASP284 2.2 65.3 1.0 OD1 A:ASP189 2.4 65.7 1.0 NE2 A:HIS190 2.4 57.2 1.0 NE2 A:HIS343 2.4 60.2 1.0 CD2 A:HIS190 3.0 57.8 1.0 CG A:ASP284 3.1 59.4 1.0 CG A:ASP189 3.1 59.8 1.0 CE1 A:HIS343 3.1 60.5 1.0 OD2 A:ASP189 3.1 59.2 1.0 ZN A:ZN501 3.2 64.4 1.0 P A:3PE503 3.2 65.3 1.0 OD1 A:ASP284 3.3 64.0 1.0 CE1 A:HIS190 3.6 56.8 1.0 CD2 A:HIS343 3.6 60.2 1.0 O12 A:3PE503 3.8 61.3 1.0 O11 A:3PE503 3.9 64.5 1.0 NE2 A:HIS132 4.1 55.3 1.0 CG A:HIS190 4.3 57.9 1.0 NE2 A:HIS185 4.3 54.9 1.0 ND1 A:HIS343 4.3 59.0 1.0 CD1 A:LEU349 4.4 62.3 1.0 CE1 A:HIS185 4.4 54.4 1.0 O13 A:3PE503 4.5 73.5 1.0 CE1 A:HIS321 4.5 66.5 1.0 CB A:ASP284 4.5 60.0 1.0 ND1 A:HIS190 4.5 57.2 1.0 CB A:ASP189 4.5 57.8 1.0 CG A:HIS343 4.6 58.6 1.0 O A:HOH630 4.9 58.3 1.0 CE1 A:HIS132 5.0 54.8 1.0 C1 A:3PE503 5.0 74.1 1.0 CD2 A:HIS132 5.0 54.1 1.0

Zinc binding site 3 out of 4 in the Structure of Human Nape-Pld


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Nape-Pld within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn604 b:60.0 occ:1.00 O12 B:3PE606 2.2 54.0 1.0 NE2 B:HIS253 2.3 52.8 1.0 NE2 B:HIS185 2.4 46.2 1.0 ND1 B:HIS187 2.4 50.6 1.0 OD2 B:ASP284 2.5 60.4 1.0 P B:3PE606 2.9 59.8 1.0 CE1 B:HIS187 3.1 52.2 1.0 CE1 B:HIS253 3.2 56.1 1.0 ZN B:ZN605 3.2 58.6 1.0 CD2 B:HIS185 3.3 46.3 1.0 O14 B:3PE606 3.3 64.9 1.0 CD2 B:HIS253 3.3 54.7 1.0 CE1 B:HIS185 3.4 54.2 1.0 CG B:ASP284 3.5 50.1 1.0 CG B:HIS187 3.6 53.1 1.0 O11 B:3PE606 3.6 60.7 1.0 C1 B:3PE606 3.7 65.5 1.0 CB B:ASP284 3.8 51.6 1.0 CB B:HIS187 4.0 47.3 1.0 NE2 B:HIS190 4.3 48.0 1.0 CD2 B:HIS190 4.3 48.9 1.0 NE2 B:HIS187 4.3 59.4 1.0 ND1 B:HIS253 4.4 54.7 1.0 OD2 B:ASP189 4.4 45.3 1.0 O13 B:3PE606 4.4 68.0 1.0 CG B:HIS253 4.4 53.6 1.0 CG B:HIS185 4.5 47.3 1.0 ND1 B:HIS185 4.5 53.1 1.0 OD1 B:ASP284 4.5 56.8 1.0 CD2 B:HIS187 4.6 58.0 1.0 CE1 B:HIS321 4.6 56.5 1.0 NE2 B:HIS321 5.0 54.8 1.0

Zinc binding site 4 out of 4 in the Structure of Human Nape-Pld


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Nape-Pld within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn605 b:58.6 occ:1.00 O14 B:3PE606 2.0 64.9 1.0 OD2 B:ASP284 2.1 60.4 1.0 OD1 B:ASP189 2.3 52.0 1.0 NE2 B:HIS190 2.4 48.0 1.0 NE2 B:HIS343 2.5 56.6 1.0 CD2 B:HIS190 3.0 48.9 1.0 CG B:ASP189 3.1 46.6 1.0 CG B:ASP284 3.1 50.1 1.0 CE1 B:HIS343 3.1 60.9 1.0 P B:3PE606 3.1 59.8 1.0 OD2 B:ASP189 3.2 45.3 1.0 ZN B:ZN604 3.2 60.0 1.0 OD1 B:ASP284 3.4 56.8 1.0 CE1 B:HIS190 3.6 48.5 1.0 CD2 B:HIS343 3.6 56.8 1.0 O12 B:3PE606 3.8 54.0 1.0 O11 B:3PE606 3.9 60.7 1.0 NE2 B:HIS132 4.2 46.6 1.0 CG B:HIS190 4.3 46.5 1.0 NE2 B:HIS185 4.3 46.2 1.0 ND1 B:HIS343 4.3 53.8 1.0 O13 B:3PE606 4.4 68.0 1.0 CE1 B:HIS321 4.4 56.5 1.0 CB B:ASP284 4.4 51.6 1.0 CD2 B:LEU349 4.5 54.2 1.0 CE1 B:HIS185 4.5 54.2 1.0 CB B:ASP189 4.5 50.4 1.0 ND1 B:HIS190 4.5 48.1 1.0 CG B:HIS343 4.6 56.0 1.0 CE1 B:HIS132 5.0 49.2 1.0 C1 B:3PE606 5.0 65.5 1.0

P.Magotti, I.Bauer, M.Igarashi, M.Babagoli, R.Marotta, D.Piomelli, G.Garau. Structure of Human N-Acylphosphatidylethanolamine-Hydrolyzing Phospholipase D: Regulation of Fatty Acid Ethanolamide Biosynthesis By Bile Acids. Structure V. 23 598 2015.
ISSN: ISSN 0969-2126
PubMed: 25684574
DOI: 10.1016/J.STR.2014.12.018