Zinc in PDB 4nfr: Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate)

All present enzymatic activity of Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate):
3.5.1.15;

The structure of Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate), PDB code: 4nfr was solved by Y.S.Wijayasinghe, A.G.Pavlovsky, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.76 / 3.00
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	147.736, 147.736, 102.738, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.1

The binding sites of Zinc atom in the Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate) (pdb code 4nfr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate), PDB code: 4nfr:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:67.3 occ:1.00 OAD A:AS9501 1.6 83.1 1.0 OE1 A:GLU24 2.1 50.6 1.0 ND1 A:HIS116 2.2 56.0 1.0 ND1 A:HIS21 2.5 50.9 1.0 CD A:GLU24 2.7 52.1 1.0 PAM A:AS9501 2.7 82.6 1.0 OE2 A:GLU24 2.7 50.7 1.0 OAG A:AS9501 2.8 86.6 1.0 CE1 A:HIS116 3.0 56.4 1.0 CG A:HIS116 3.0 58.4 1.0 CE1 A:HIS21 3.1 53.6 1.0 CB A:HIS116 3.4 60.0 1.0 CG A:HIS21 3.7 52.1 1.0 CAA A:AS9501 3.8 81.2 1.0 NE2 A:HIS116 3.9 59.6 1.0 CD2 A:HIS116 3.9 60.0 1.0 O A:HOH608 4.0 30.3 1.0 OD2 A:AS9501 4.1 0.3 1.0 N A:AS9501 4.1 88.5 1.0 CA A:HIS116 4.1 59.3 1.0 CG A:GLU24 4.2 51.9 1.0 CB A:HIS21 4.2 53.3 1.0 O A:ASN117 4.3 61.5 1.0 NE2 A:HIS21 4.3 52.9 1.0 N A:ASN117 4.5 53.0 1.0 NH1 A:ARG63 4.5 88.5 1.0 OE2 A:GLU178 4.5 73.3 1.0 CD2 A:HIS21 4.6 54.0 1.0 C A:HIS116 4.8 55.5 1.0 CB A:GLU24 4.9 52.7 1.0 NH2 A:ARG63 4.9 83.2 1.0 OE1 A:GLU178 5.0 76.9 1.0 CA A:AS9501 5.0 92.7 1.0

Zinc binding site 2 out of 2 in the Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Brain Aspartoacylase Mutant E285A Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:68.2 occ:1.00 OAD B:AS9501 2.0 0.4 1.0 OE1 B:GLU24 2.4 46.3 1.0 ND1 B:HIS116 2.5 54.3 1.0 ND1 B:HIS21 2.5 55.4 1.0 OAG B:AS9501 2.5 0.1 1.0 OE2 B:GLU24 2.8 45.5 1.0 PAM B:AS9501 2.8 0.1 1.0 CD B:GLU24 2.9 48.1 1.0 CE1 B:HIS21 3.0 57.9 1.0 CE1 B:HIS116 3.2 54.7 1.0 CG B:HIS116 3.2 53.1 1.0 CB B:HIS116 3.7 54.0 1.0 CG B:HIS21 3.7 53.0 1.0 OD2 B:AS9501 4.0 97.1 1.0 N B:AS9501 4.1 0.1 1.0 NE2 B:HIS116 4.1 54.5 1.0 CD2 B:HIS116 4.1 53.9 1.0 CAA B:AS9501 4.1 0.2 1.0 NE2 B:HIS21 4.2 55.4 1.0 NH1 B:ARG63 4.2 83.2 1.0 CA B:AS9501 4.2 97.7 1.0 O B:ASN117 4.3 52.0 1.0 CB B:HIS21 4.4 53.2 1.0 CG B:GLU24 4.4 47.1 1.0 CA B:HIS116 4.5 55.6 1.0 OE2 B:GLU178 4.5 78.6 1.0 CD2 B:HIS21 4.6 53.4 1.0 NH2 B:ARG63 4.6 81.1 1.0 N B:ASN117 4.7 56.3 1.0 CZ B:ARG63 4.9 80.2 1.0 OE1 B:GLU178 4.9 78.5 1.0 CG B:AS9501 5.0 92.9 1.0

Y.S.Wijayasinghe, A.G.Pavlovsky, R.E.Viola. Aspartoacylase Catalytic Deficiency As the Cause of Canavan Disease: A Structural Perspective. Biochemistry V. 53 4970 2014.
ISSN: ISSN 0006-2960
PubMed: 25003821
DOI: 10.1021/BI500719K