Chlorine in PDB 8cb1: Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15

Enzymatic activity of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15

All present enzymatic activity of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15:
3.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15, PDB code: 8cb1 was solved by G.Sulzenbacher, V.Roig-Zamboni, H.Overkleeft, M.Artola, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.73 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 96.75, 102.604, 129.179, 90, 90, 90
R / Rfree (%) 14.2 / 17.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 (pdb code 8cb1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15, PDB code: 8cb1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 8cb1

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Chlorine binding site 1 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


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-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl301

b:78.6
occ:1.00
 NH2 G:ARG106 3.4 47.5 1.0
NE G:ARG106 3.5 44.6 1.0
O G:HOH428 3.5 61.1 1.0
CZ G:ARG106 3.9 45.4 1.0
CB G:PHE159 4.4 42.8 1.0
CG G:ARG106 4.5 48.3 1.0
CD G:ARG106 4.6 45.9 1.0
NZ G:LYS96 4.6 106.4 1.0
CE G:LYS96 4.6 86.2 1.0

Chlorine binding site 2 out of 10 in 8cb1

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Chlorine binding site 2 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


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-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:76.4
occ:1.00
 N G:GLN100 3.8 46.4 1.0
CA G:THR99 4.1 53.5 1.0
CB G:THR99 4.1 62.3 1.0
OH G:TYR110 4.1 66.9 1.0
O G:HOH475 4.1 56.6 1.0
C G:THR99 4.4 53.9 1.0
CB G:GLN100 4.6 49.0 1.0
CG2 G:THR99 4.6 57.5 1.0
CZ G:TYR110 4.7 61.9 1.0
CA G:GLN100 4.8 55.5 1.0

Chlorine binding site 3 out of 10 in 8cb1

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Chlorine binding site 3 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


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-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1006

b:76.1
occ:1.00
 O A:HOH1683 2.5 71.0 1.0
OG A:SER566 3.1 34.6 1.0
O A:HOH1653 3.3 61.3 1.0
O A:HOH1217 3.5 56.7 1.0
CB A:SER566 3.8 34.3 1.0
NH1 G:ARG189 4.0 84.5 1.0
CB G:TYR191 4.2 36.1 1.0
NH2 G:ARG189 4.3 93.1 1.0
O A:LEU565 4.3 35.3 1.0
ND2 A:ASN570 4.4 34.9 1.0
CA A:SER566 4.4 35.4 1.0
CA G:TYR191 4.4 36.2 1.0
N G:TYR191 4.7 34.7 1.0
CZ G:ARG189 4.7 103.2 1.0
CD1 G:TYR191 4.7 34.7 1.0
O A:HOH1651 4.9 54.1 1.0
CG G:TYR191 4.9 32.4 1.0
O G:HOH484 4.9 49.1 1.0

Chlorine binding site 4 out of 10 in 8cb1

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Chlorine binding site 4 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1007

b:79.1
occ:1.00
 O A:HOH1601 2.8 68.7 1.0
O A:PHE564 3.8 33.0 1.0
O A:HOH1253 4.2 44.5 1.0
CE2 A:PHE564 4.6 42.0 1.0
CZ A:PHE564 4.8 39.9 1.0
CD2 A:LEU565 4.8 46.6 1.0
C A:PHE564 4.9 33.9 1.0
CA A:LEU565 4.9 32.5 1.0
CD2 A:PHE564 4.9 40.5 1.0

Chlorine binding site 5 out of 10 in 8cb1

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Chlorine binding site 5 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1008

b:80.4
occ:1.00
 OG A:SER736 3.5 45.8 1.0
NE1 A:TRP804 3.5 47.8 1.0
O A:HOH1252 3.6 64.0 1.0
CB A:SER736 3.9 47.3 1.0
CD1 A:TRP804 4.1 48.4 1.0
CA A:SER736 4.6 37.6 1.0
CE2 A:TRP804 4.7 46.0 1.0
O A:HOH1387 4.7 62.3 1.0

Chlorine binding site 6 out of 10 in 8cb1

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Chlorine binding site 6 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1009

b:61.1
occ:1.00
 OG A:SER918 2.9 49.6 1.0
N A:SER940 3.2 42.0 1.0
O A:HOH1639 3.3 55.6 1.0
CB A:SER918 3.4 50.6 1.0
O A:HOH1470 3.5 54.8 1.0
CA A:VAL939 3.8 43.5 1.0
CB A:VAL939 3.9 46.7 1.0
C A:VAL939 4.0 37.8 1.0
O A:SER940 4.0 41.8 1.0
CA A:SER940 4.0 48.2 0.5
CA A:SER940 4.1 46.7 0.5
CB A:SER940 4.2 45.9 0.5
C A:SER940 4.2 43.0 1.0
CG1 A:VAL939 4.3 47.7 1.0
CB A:SER940 4.3 46.7 0.5
CD2 A:LEU941 4.3 39.2 1.0
CG A:LEU941 4.4 41.6 1.0
OG A:SER940 4.7 50.9 0.5
O A:HOH1509 4.7 42.3 1.0
CA A:SER918 4.8 45.5 1.0
O A:SER918 4.9 46.3 1.0
CD1 A:LEU941 4.9 44.2 1.0

Chlorine binding site 7 out of 10 in 8cb1

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Chlorine binding site 7 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1010

b:84.8
occ:1.00
 O A:HOH1736 3.2 69.0 1.0
O A:HOH1545 3.3 57.7 1.0
O A:HOH1187 3.5 37.1 1.0
O A:HOH1212 3.5 60.4 1.0
O A:GLN255 4.0 37.2 1.0
CE1 A:TYR256 4.2 46.4 1.0
CB A:MET268 4.2 38.6 1.0
O A:LEU269 4.3 38.0 1.0
CD1 A:TYR256 4.3 42.4 1.0
O A:HOH1669 4.8 54.0 1.0
O A:MET268 4.9 41.5 1.0
CZ A:TYR256 4.9 50.9 1.0
C A:MET268 5.0 36.2 1.0
C A:GLN255 5.0 35.2 1.0

Chlorine binding site 8 out of 10 in 8cb1

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Chlorine binding site 8 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1011

b:90.6
occ:1.00
 CE2 A:TRP804 3.9 46.0 1.0
CD2 A:TRP804 3.9 43.0 1.0
NE1 A:TRP804 4.2 47.8 1.0
CG A:TRP804 4.2 43.4 1.0
CZ2 A:TRP804 4.3 46.6 1.0
CE3 A:TRP804 4.3 41.8 1.0
CD1 A:TRP804 4.4 48.4 1.0
CZ3 A:TRP804 4.6 46.4 1.0
CH2 A:TRP804 4.6 45.0 1.0
CB A:TRP804 5.0 43.5 1.0

Chlorine binding site 9 out of 10 in 8cb1

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Chlorine binding site 9 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1012

b:80.5
occ:1.00
 O A:HOH1277 3.1 35.2 1.0
O A:HOH1679 3.2 59.2 1.0
O A:HOH1713 3.2 60.9 1.0
O A:HOH1147 3.6 57.5 1.0
CE1 A:HIS432 4.0 44.4 1.0
CB A:PRO511 4.1 38.3 1.0
ND1 A:HIS432 4.3 38.0 1.0
O A:HOH1381 4.4 42.4 1.0
CE1 A:HIS507 4.5 42.6 1.0
O A:PRO511 4.6 34.0 1.0
NE2 A:HIS507 4.6 36.1 1.0
OD1 A:ASP513 4.7 37.4 1.0
O A:HOH1328 4.8 75.7 1.0
NE2 A:HIS432 4.9 36.2 1.0
CG A:PRO511 5.0 37.7 1.0

Chlorine binding site 10 out of 10 in 8cb1

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Chlorine binding site 10 out of 10 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with N-Pnt-Dnm 15 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1013

b:71.5
occ:1.00
 N A:ILE814 3.2 42.1 1.0
O A:HOH1619 3.4 66.0 1.0
O A:ILE814 3.4 42.6 1.0
O A:HOH1631 3.5 48.2 1.0
CA A:THR813 3.7 41.0 1.0
CE A:LYS697 3.8 100.6 1.0
NZ A:LYS697 3.9 114.4 1.0
C A:THR813 3.9 43.3 1.0
CG2 A:ILE814 4.0 41.8 1.0
O A:ASP812 4.0 48.0 1.0
C A:ILE814 4.2 38.7 1.0
CD A:LYS697 4.2 88.2 1.0
CA A:ILE814 4.2 39.1 1.0
CG2 A:THR813 4.3 49.4 1.0
O A:HOH1260 4.4 41.1 1.0
CB A:THR813 4.5 48.8 1.0
OG1 A:THR813 4.7 51.2 1.0
N A:THR813 4.7 42.8 1.0
CG A:LYS697 4.7 67.7 1.0
CB A:ILE814 4.7 43.0 1.0
C A:ASP812 4.8 47.8 1.0
OE1 A:GLN776 4.8 80.8 1.0
CD A:GLN776 5.0 97.7 1.0

Reference:

D.Van Der Gracht, R.J.Rowland, V.Roig-Zamboni, M.J.Ferraz, M.Louwerse, P.P.Geurink, J.M.F.G.Aerts, G.Sulzenbacher, G.J.Davies, H.S.Overkleeft, M.Artola. Fluorescence Polarisation Activity-Based Protein Profiling For the Identification of Deoxynojirimycin-Type Inhibitors Selective For Lysosomal Retaining Alpha- and Beta-Glucosidases. Chem Sci V. 14 9136 2023.
ISSN: ISSN 2041-6520
PubMed: 37655021
DOI: 10.1039/D3SC01021J
Page generated: Tue Jul 30 07:48:41 2024

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