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Zinc in PDB 2o4h: Human Brain Aspartoacylase Complex with Intermediate Analog (N- Phosphonomethyl-L-Aspartate)

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

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

Protein crystallography data

The structure of Human Brain Aspartoacylase Complex with Intermediate Analog (N- Phosphonomethyl-L-Aspartate), PDB code: 2o4h was solved by J.Le Coq, A.Pavlovsky, R.Sanishvili, R.E.Viola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.47 / 2.70
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 143.081, 143.081, 104.604, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 27.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Brain Aspartoacylase Complex with Intermediate Analog (N- Phosphonomethyl-L-Aspartate) (pdb code 2o4h). 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 Complex with Intermediate Analog (N- Phosphonomethyl-L-Aspartate), PDB code: 2o4h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 2o4h

Go back to Zinc Binding Sites List in 2o4h
Zinc binding site 1 out of 2 in the Human Brain Aspartoacylase 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 Complex with Intermediate Analog (N- Phosphonomethyl-L-Aspartate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:87.0
occ:1.00
OE1 A:GLU24 2.1 56.3 1.0
ND1 A:HIS21 2.2 48.0 1.0
ND1 A:HIS116 2.3 55.2 1.0
OAD A:AS9501 2.4 68.0 1.0
OAG A:AS9501 2.5 67.7 1.0
OE2 A:GLU24 2.6 54.9 1.0
CD A:GLU24 2.7 54.7 1.0
PAM A:AS9501 3.0 68.3 1.0
CE1 A:HIS21 3.0 47.2 1.0
CE1 A:HIS116 3.2 56.2 1.0
CG A:HIS116 3.2 52.5 1.0
CG A:HIS21 3.3 48.6 1.0
CB A:HIS116 3.5 50.1 1.0
O A:HOH515 3.6 45.6 1.0
CB A:HIS21 3.8 49.0 1.0
NH1 A:ARG63 4.1 48.4 1.0
CA A:HIS116 4.2 50.1 1.0
CG A:GLU24 4.2 53.6 1.0
N A:AS9501 4.2 68.9 1.0
NE2 A:HIS21 4.2 46.3 1.0
CA A:AS9501 4.2 69.6 1.0
NE2 A:HIS116 4.3 57.0 1.0
O A:ASN117 4.3 48.9 1.0
CAA A:AS9501 4.3 68.0 1.0
CD2 A:HIS116 4.4 55.9 1.0
CD2 A:HIS21 4.4 48.1 1.0
N A:ASN117 4.5 49.3 1.0
OXT A:AS9501 4.8 70.6 1.0
C A:AS9501 4.8 70.1 1.0
CB A:GLU24 4.9 52.2 1.0
C A:HIS116 4.9 50.0 1.0
N A:HIS21 4.9 49.2 1.0
CZ A:ARG63 5.0 48.4 1.0
NH2 A:ARG63 5.0 47.4 1.0

Zinc binding site 2 out of 2 in 2o4h

Go back to Zinc Binding Sites List in 2o4h
Zinc binding site 2 out of 2 in the Human Brain Aspartoacylase 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 Complex with Intermediate Analog (N- Phosphonomethyl-L-Aspartate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:78.1
occ:1.00
OE1 B:GLU24 2.0 53.5 1.0
ND1 B:HIS21 2.0 48.8 1.0
OAG B:AS9501 2.2 70.6 1.0
ND1 B:HIS116 2.4 50.0 1.0
CD B:GLU24 2.8 51.0 1.0
CE1 B:HIS21 2.9 46.9 1.0
OE2 B:GLU24 3.0 51.9 1.0
OAD B:AS9501 3.0 71.5 1.0
CG B:HIS21 3.1 48.0 1.0
PAM B:AS9501 3.1 70.7 1.0
CG B:HIS116 3.2 48.9 1.0
O B:HOH516 3.3 52.9 1.0
CE1 B:HIS116 3.3 50.3 1.0
CB B:HIS116 3.5 48.2 1.0
CB B:HIS21 3.6 47.8 1.0
NE2 B:HIS21 4.1 47.0 1.0
NH1 B:ARG63 4.2 52.0 1.0
CG B:GLU24 4.2 50.3 1.0
CD2 B:HIS21 4.2 48.2 1.0
CA B:HIS116 4.2 48.3 1.0
N B:AS9501 4.2 71.5 1.0
CA B:AS9501 4.3 72.1 1.0
O B:ASN117 4.3 48.1 1.0
CD2 B:HIS116 4.3 50.6 1.0
CAA B:AS9501 4.4 71.3 1.0
NE2 B:HIS116 4.4 51.6 1.0
N B:ASN117 4.6 48.2 1.0
CB B:GLU24 4.7 50.2 1.0
N B:HIS21 4.8 47.6 1.0
CA B:HIS21 4.8 48.5 1.0
C B:HIS116 4.9 48.4 1.0
NH2 B:ARG63 5.0 53.1 1.0
CZ B:ARG63 5.0 52.6 1.0

Reference:

J.Le Coq, A.Pavlovsky, R.Malik, R.Sanishvili, C.Xu, R.E.Viola. Examination of the Mechanism of Human Brain Aspartoacylase Through the Binding of An Intermediate Analogue. Biochemistry V. 47 3484 2008.
ISSN: ISSN 0006-2960
PubMed: 18293939
DOI: 10.1021/BI702400X
Page generated: Wed Dec 16 03:45:16 2020

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