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Chlorine in PDB 5nn6: Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin

Enzymatic activity of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin

All present enzymatic activity of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin:
3.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin, PDB code: 5nn6 was solved by V.Roig-Zamboni, B.Cobucci-Ponzano, R.Iacono, M.C.Ferrara, S.Germany, G.Parenti, Y.Bourne, M.Moracci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.52 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.633, 102.191, 128.348, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin (pdb code 5nn6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin, PDB code: 5nn6:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5nn6

Go back to Chlorine Binding Sites List in 5nn6
Chlorine binding site 1 out of 3 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1019

b:59.0
occ:1.00
 N A:GLN100 3.8 32.6 1.0
CB A:THR99 4.1 36.9 1.0
CA A:THR99 4.1 34.5 1.0
OH A:TYR110 4.2 39.6 1.0
O A:HOH1435 4.3 39.0 1.0
C A:THR99 4.5 33.1 1.0
CB A:GLN100 4.5 34.6 1.0
CG2 A:THR99 4.7 37.8 1.0
CZ A:TYR110 4.8 30.5 1.0
CA A:GLN100 4.8 34.7 1.0

Chlorine binding site 2 out of 3 in 5nn6

Go back to Chlorine Binding Sites List in 5nn6
Chlorine binding site 2 out of 3 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1020

b:51.1
occ:1.00
 O A:HOH1661 2.8 39.9 1.0
OG A:SER566 3.0 15.1 1.0
O A:HOH1675 3.3 37.8 1.0
CB A:SER566 3.7 14.8 1.0
CB A:TYR191 4.2 15.3 1.0
ND2 A:ASN570 4.3 12.6 1.0
CA A:SER566 4.3 14.6 1.0
O A:LEU565 4.4 14.9 1.0
CA A:TYR191 4.5 15.6 1.0
CD1 A:TYR191 4.6 13.9 1.0
O A:HOH1219 4.7 34.7 1.0
N A:TYR191 4.8 16.3 1.0
O A:HOH1648 4.8 34.0 1.0
CG A:TYR191 4.9 14.6 1.0

Chlorine binding site 3 out of 3 in 5nn6

Go back to Chlorine Binding Sites List in 5nn6
Chlorine binding site 3 out of 3 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Hydroxyethyl-1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1021

b:41.6
occ:1.00
 O A:HOH1426 2.8 19.2 1.0
O A:HOH1727 2.8 26.2 1.0
O A:HOH1505 2.9 24.4 1.0
NH1 A:ARG224 3.0 16.2 1.0
CD A:ARG224 3.6 18.1 1.0
CG A:ARG224 3.6 17.7 1.0
CB A:PRO345 3.8 18.5 1.0
CB A:LEU226 3.9 23.5 1.0
CZ A:ARG224 4.0 16.3 1.0
NE A:ARG224 4.2 17.3 1.0
CG A:PRO345 4.2 18.4 1.0
CD1 A:LEU208 4.2 23.6 1.0
CD2 A:LEU226 4.3 25.1 1.0
O A:HOH1728 4.3 36.5 1.0
O A:HOH1732 4.4 29.2 1.0
CB A:LEU208 4.5 20.8 1.0
O A:HOH1672 4.6 38.6 1.0
CD A:PRO345 4.6 17.9 1.0
CD2 A:LEU208 4.7 25.1 1.0
CG A:LEU226 4.7 24.1 1.0
CG A:LEU208 4.7 22.9 1.0
O A:HOH1256 4.8 37.0 1.0
CA A:PRO345 4.8 17.4 1.0
N A:LEU226 4.8 22.7 1.0
O A:LEU208 4.9 18.2 1.0
O A:LEU343 4.9 17.5 1.0

Reference:

V.Roig-Zamboni, B.Cobucci-Ponzano, R.Iacono, M.C.Ferrara, S.Germany, Y.Bourne, G.Parenti, M.Moracci, G.Sulzenbacher. Structure of Human Lysosomal Acid Alpha-Glucosidase-A Guide For the Treatment of Pompe Disease. Nat Commun V. 8 1111 2017.
ISSN: ESSN 2041-1723
PubMed: 29061980
DOI: 10.1038/S41467-017-01263-3
Page generated: Sat Dec 12 12:10:12 2020

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