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Zinc in PDB 4mri: Human Brain Aspartoacylase Mutant F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate)

Enzymatic activity of Human Brain Aspartoacylase Mutant F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate)

All present enzymatic activity of Human Brain Aspartoacylase Mutant F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate):
3.5.1.15;

Protein crystallography data

The structure of Human Brain Aspartoacylase Mutant F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate), PDB code: 4mri 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) 46.27 / 2.80
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 146.170, 146.170, 103.134, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Brain Aspartoacylase Mutant F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate) (pdb code 4mri). 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 F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate), PDB code: 4mri:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4mri

Go back to Zinc Binding Sites List in 4mri
Zinc binding site 1 out of 2 in the Human Brain Aspartoacylase Mutant F295S 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 F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:38.6
occ:1.00
OE1 A:GLU24 2.0 30.9 1.0
ND1 A:HIS21 2.1 27.2 1.0
OAD A:AS9402 2.4 32.8 1.0
OAG A:AS9402 2.5 29.9 1.0
OE2 A:GLU24 2.5 32.8 1.0
ND1 A:HIS116 2.5 38.9 1.0
CD A:GLU24 2.6 32.4 1.0
CE1 A:HIS21 2.8 28.0 1.0
PAM A:AS9402 2.9 32.6 1.0
CG A:HIS116 3.2 37.8 1.0
CG A:HIS21 3.3 27.8 1.0
CE1 A:HIS116 3.3 39.3 1.0
CB A:HIS116 3.5 35.2 1.0
O A:HOH512 3.6 28.9 1.0
CB A:HIS21 3.8 28.7 1.0
NE2 A:HIS21 4.0 27.5 1.0
N A:AS9402 4.0 33.9 1.0
CG A:GLU24 4.1 32.0 1.0
NH1 A:ARG63 4.1 27.8 1.0
CA A:AS9402 4.1 35.1 1.0
CD2 A:HIS116 4.2 39.2 1.0
CA A:HIS116 4.2 34.9 1.0
O A:ASN117 4.2 28.0 1.0
NE2 A:HIS116 4.2 39.7 1.0
CD2 A:HIS21 4.2 27.8 1.0
CAA A:AS9402 4.4 31.8 1.0
N A:ASN117 4.4 35.3 1.0
C A:AS9402 4.5 35.1 1.0
CB A:GLU24 4.8 31.9 1.0
C A:HIS116 4.9 34.6 1.0
OXT A:AS9402 4.9 33.6 1.0
OE1 A:GLU178 4.9 39.2 1.0
NH2 A:ARG63 4.9 27.9 1.0
CZ A:ARG63 4.9 28.4 1.0
O A:AS9402 5.0 37.9 1.0

Zinc binding site 2 out of 2 in 4mri

Go back to Zinc Binding Sites List in 4mri
Zinc binding site 2 out of 2 in the Human Brain Aspartoacylase Mutant F295S 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 F295S Complex with Intermediate Analog (N-Phosphonomethyl-L-Aspartate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:38.2
occ:1.00
OE1 B:GLU24 1.8 27.6 1.0
ND1 B:HIS21 2.1 32.0 1.0
OAD B:AS9402 2.1 37.5 1.0
ND1 B:HIS116 2.4 35.7 1.0
CD B:GLU24 2.6 30.3 1.0
OAG B:AS9402 2.6 37.7 1.0
OE2 B:GLU24 2.7 33.2 1.0
PAM B:AS9402 2.9 40.1 1.0
CE1 B:HIS21 2.9 32.7 1.0
CE1 B:HIS116 3.0 35.6 1.0
CG B:HIS116 3.3 33.4 1.0
CG B:HIS21 3.3 30.2 1.0
CB B:HIS21 3.8 28.0 1.0
CB B:HIS116 3.8 32.1 1.0
NE2 B:HIS116 3.9 35.8 1.0
N B:AS9402 4.0 40.0 1.0
CG B:GLU24 4.0 30.5 1.0
CD2 B:HIS116 4.1 35.5 1.0
NE2 B:HIS21 4.1 32.8 1.0
CA B:AS9402 4.1 40.6 1.0
NH1 B:ARG63 4.1 29.4 1.0
CAA B:AS9402 4.3 37.4 1.0
CD2 B:HIS21 4.3 31.5 1.0
CA B:HIS116 4.4 32.2 1.0
O B:ASN117 4.4 27.2 1.0
C B:AS9402 4.6 40.9 1.0
CB B:GLU24 4.6 30.7 1.0
O B:HOH510 4.6 28.1 1.0
N B:ASN117 4.8 30.0 1.0
N B:HIS21 4.8 29.4 1.0
OXT B:AS9402 4.8 41.5 1.0
CA B:HIS21 5.0 28.6 1.0
CZ B:ARG63 5.0 28.6 1.0

Reference:

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
Page generated: Wed Dec 16 05:35:42 2020

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