Zinc in PDB 1lam: Leucine Aminopeptidase (Unligated)

All present enzymatic activity of Leucine Aminopeptidase (Unligated):
3.4.11.1;

The structure of Leucine Aminopeptidase (Unligated), PDB code: 1lam was solved by N.Straeter, W.N.Lipscomb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	7.00 / 1.60
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.500, 131.500, 121.300, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 20.4

The binding sites of Zinc atom in the Leucine Aminopeptidase (Unligated) (pdb code 1lam). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Leucine Aminopeptidase (Unligated), PDB code: 1lam:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Leucine Aminopeptidase (Unligated)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Leucine Aminopeptidase (Unligated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn488 b:9.7 occ:1.00 OD1 A:ASP332 2.0 7.7 1.0 O A:HOH739 2.0 6.1 1.0 OE1 A:GLU334 2.0 7.2 1.0 O A:ASP332 2.1 6.2 1.0 OD2 A:ASP255 2.1 7.2 1.0 CD A:GLU334 2.9 6.6 1.0 ZN A:ZN489 3.0 9.3 1.0 CG A:ASP255 3.0 7.8 1.0 C A:ASP332 3.0 7.0 1.0 CG A:ASP332 3.1 8.3 1.0 OE2 A:GLU334 3.2 6.6 1.0 OD1 A:ASP255 3.3 5.5 1.0 CA A:ASP332 3.4 7.7 1.0 O A:HOH764 3.7 13.0 1.0 CB A:ASP332 3.8 6.8 1.0 OD2 A:ASP332 4.0 7.8 1.0 O2 A:CO3500 4.1 8.6 1.0 NZ A:LYS262 4.2 6.4 1.0 N A:ALA333 4.2 5.4 1.0 N A:GLU334 4.3 7.0 1.0 CE A:LYS262 4.3 5.7 1.0 CG A:GLU334 4.4 6.4 1.0 ND2 A:ASN305 4.4 6.4 1.0 CB A:ASP255 4.4 6.6 1.0 OD2 A:ASP273 4.5 9.1 1.0 CA A:ALA333 4.7 6.1 1.0 CA A:GLY257 4.8 7.3 1.0 N A:ASP332 4.8 7.7 1.0 NZ A:LYS250 4.8 6.6 1.0 CB A:GLU334 4.8 5.8 1.0 O A:THR331 4.9 9.9 1.0 C A:CO3500 4.9 10.4 1.0

Zinc binding site 2 out of 3 in the Leucine Aminopeptidase (Unligated)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Leucine Aminopeptidase (Unligated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn489 b:9.3 occ:1.00 O A:HOH739 2.0 6.1 1.0 OD2 A:ASP273 2.0 9.1 1.0 OE2 A:GLU334 2.0 6.6 1.0 NZ A:LYS250 2.2 6.6 1.0 OD2 A:ASP255 2.6 7.2 1.0 CG A:ASP273 2.9 8.8 1.0 CE A:LYS250 3.0 6.4 1.0 ZN A:ZN488 3.0 9.7 1.0 CD A:GLU334 3.0 6.6 1.0 OD1 A:ASP273 3.1 7.2 1.0 OE1 A:GLU334 3.4 7.2 1.0 CG A:ASP255 3.5 7.8 1.0 O2 A:CO3500 3.6 8.6 1.0 O A:HOH764 3.9 13.0 1.0 CB A:ASP255 4.0 6.6 1.0 CB A:ASP273 4.3 6.1 1.0 OD1 A:ASP255 4.4 5.5 1.0 CG A:GLU334 4.4 6.4 1.0 O A:THR359 4.4 7.9 1.0 CD A:LYS250 4.5 7.0 1.0 N A:GLY335 4.5 7.0 1.0 CG1 A:ILE252 4.6 6.8 1.0 O A:ASP332 4.6 6.2 1.0 O A:HOH827 4.6 36.0 1.0 CB A:ILE252 4.6 7.9 1.0 CG2 A:ILE252 4.7 7.3 1.0 OD1 A:ASP332 4.8 7.7 1.0 C A:CO3500 4.8 10.4 1.0 CA A:GLY335 4.9 6.6 1.0

Zinc binding site 3 out of 3 in the Leucine Aminopeptidase (Unligated)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Leucine Aminopeptidase (Unligated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn490 b:21.8 occ:1.00 O A:THR173 2.6 8.6 1.0 O A:HOH570 2.7 7.5 1.0 O A:ARG271 2.7 7.8 1.0 O A:LEU170 2.8 7.1 1.0 O A:MET171 2.9 7.9 1.0 C A:MET171 3.4 7.8 1.0 SD A:MET274 3.6 7.2 1.0 C A:ARG271 3.6 7.0 1.0 C A:THR173 3.7 8.3 1.0 CA A:MET171 3.8 7.0 1.0 C A:LEU170 3.9 7.0 1.0 CG A:MET178 4.0 7.8 1.0 CB A:MET178 4.0 8.4 1.0 N A:THR173 4.0 7.2 1.0 CB A:ARG271 4.1 8.1 1.0 CG A:ARG271 4.2 7.3 1.0 CG A:MET274 4.3 7.7 1.0 CA A:THR173 4.3 7.8 1.0 N A:MET171 4.3 6.5 1.0 CE A:MET274 4.3 6.9 1.0 N A:GLU172 4.4 7.0 1.0 CA A:ARG271 4.4 8.1 1.0 C A:GLU172 4.4 7.4 1.0 N A:ALA272 4.5 6.4 1.0 CB A:THR173 4.6 7.7 1.0 CA A:ALA272 4.6 7.4 1.0 CD A:ARG271 4.7 7.3 1.0 O A:THR253 4.8 7.3 1.0 C A:PRO174 4.8 8.2 1.0 N A:PRO174 4.8 8.1 1.0 N A:ALA175 4.8 8.1 1.0 O A:GLU172 4.8 8.0 1.0 CA A:GLU172 4.9 7.2 1.0

N.Strater, W.N.Lipscomb. Two-Metal Ion Mechanism of Bovine Lens Leucine Aminopeptidase: Active Site Solvent Structure and Binding Mode of L-Leucinal, A Gem-Diolate Transition State Analogue, By X-Ray Crystallography. Biochemistry V. 34 14792 1995.
ISSN: ISSN 0006-2960
PubMed: 7578088
DOI: 10.1021/BI00045A021