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Chlorine in PDB 5nn5: Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 1-Deoxynojirimycin

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

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

Protein crystallography data

The structure of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 1-Deoxynojirimycin, PDB code: 5nn5 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) 53.86 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.486, 102.972, 129.028, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 1-Deoxynojirimycin (pdb code 5nn5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 1-Deoxynojirimycin, PDB code: 5nn5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5nn5

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Chlorine binding site 1 out of 6 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 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 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1021

b:50.6
occ:1.00
 O A:HOH1110 3.2 30.8 1.0
N A:GLN100 3.8 28.4 1.0
CA A:THR99 4.0 28.2 1.0
OH A:TYR110 4.0 26.7 1.0
CB A:THR99 4.1 30.6 1.0
C A:THR99 4.4 27.1 1.0
CG2 A:THR99 4.6 30.6 1.0
CZ A:TYR110 4.7 24.9 1.0
CB A:GLN100 4.7 30.2 1.0
CA A:GLN100 4.9 29.5 1.0
CE1 A:TYR110 5.0 24.2 1.0

Chlorine binding site 2 out of 6 in 5nn5

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Chlorine binding site 2 out of 6 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 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 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1022

b:42.2
occ:1.00
 OG A:SER566 3.3 11.1 1.0
O A:HOH1802 3.5 28.1 1.0
CB A:SER566 4.0 12.0 1.0
CB A:TYR191 4.2 13.3 1.0
NH1 A:ARG189 4.2 47.4 1.0
O A:HOH1585 4.2 31.8 1.0
NH2 A:ARG189 4.3 61.6 1.0
CA A:TYR191 4.5 13.5 1.0
O A:LEU565 4.5 12.7 1.0
ND2 A:ASN570 4.5 9.5 1.0
N A:TYR191 4.6 14.1 1.0
CA A:SER566 4.6 11.8 1.0
CZ A:ARG189 4.8 53.0 1.0
CD1 A:TYR191 4.8 12.0 1.0
O A:HOH1208 5.0 16.7 1.0
O A:HOH1603 5.0 14.0 1.0

Chlorine binding site 3 out of 6 in 5nn5

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Chlorine binding site 3 out of 6 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 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 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1023

b:23.7
occ:1.00
 O A:HOH1398 2.9 13.8 1.0
O A:HOH1869 2.9 23.1 1.0
O A:HOH1570 3.0 14.5 1.0
NH1 A:ARG224 3.0 13.6 1.0
CD A:ARG224 3.7 13.9 1.0
CG A:ARG224 3.7 14.0 1.0
CB A:PRO345 3.8 13.6 1.0
CB A:LEU226 3.9 15.7 1.0
CZ A:ARG224 4.1 14.2 1.0
CG A:PRO345 4.2 13.6 1.0
CD2 A:LEU226 4.2 15.7 1.0
O A:HOH1706 4.3 30.1 1.0
NE A:ARG224 4.3 14.5 1.0
O A:HOH1858 4.4 41.3 1.0
CD1 A:LEU208 4.4 17.7 1.0
CD A:PRO345 4.6 13.3 1.0
CD2 A:LEU208 4.7 18.3 1.0
O A:HOH1610 4.7 22.2 1.0
CB A:LEU208 4.7 16.0 1.0
CG A:LEU226 4.7 16.1 1.0
CG A:LEU208 4.8 17.6 1.0
CA A:PRO345 4.8 12.6 1.0
N A:LEU226 4.9 15.9 1.0
O A:LEU208 5.0 13.8 1.0

Chlorine binding site 4 out of 6 in 5nn5

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Chlorine binding site 4 out of 6 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 1-Deoxynojirimycin


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 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1024

b:28.8
occ:1.00
 O A:HOH1754 3.0 27.3 1.0
OG A:SER918 3.1 22.4 1.0
O A:HOH1588 3.1 34.0 1.0
N A:SER940 3.2 18.2 1.0
O A:HOH1708 3.2 27.1 1.0
CB A:SER918 3.5 23.1 1.0
CA A:VAL939 3.9 19.7 1.0
C A:VAL939 4.0 19.4 1.0
CA A:SER940 4.0 18.7 0.5
CB A:VAL939 4.1 19.0 1.0
O A:SER940 4.1 19.8 1.0
CA A:SER940 4.1 18.7 0.5
CB A:SER940 4.2 19.5 0.5
C A:SER940 4.2 17.8 1.0
CB A:SER940 4.4 19.6 0.5
CD2 A:LEU941 4.5 16.7 1.0
CG A:LEU941 4.6 16.4 1.0
CG1 A:VAL939 4.6 19.9 1.0
O A:HOH1385 4.6 34.6 1.0
OG A:SER940 4.8 20.3 0.5
CA A:SER918 4.9 21.8 1.0
O A:SER918 4.9 20.0 1.0

Chlorine binding site 5 out of 6 in 5nn5

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Chlorine binding site 5 out of 6 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 1-Deoxynojirimycin


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 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1025

b:50.7
occ:1.00
 NE1 A:TRP804 3.4 20.6 1.0
OG A:SER736 3.7 17.3 1.0
O A:HOH1810 3.8 32.0 1.0
CB A:SER736 3.9 16.7 1.0
CD1 A:TRP804 4.1 19.0 1.0
CE2 A:TRP804 4.4 19.7 1.0
C2 A:EDO1031 4.5 43.1 1.0
CA A:SER736 4.7 16.6 1.0
CZ2 A:TRP804 4.8 19.4 1.0
O A:HOH1220 5.0 33.5 1.0

Chlorine binding site 6 out of 6 in 5nn5

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Chlorine binding site 6 out of 6 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, in Complex with 1-Deoxynojirimycin


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 1-Deoxynojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1026

b:59.4
occ:1.00
 O A:HOH1828 3.6 20.0 1.0
N A:GLY123 3.8 29.3 1.0
O A:GLY123 3.9 23.7 1.0
O A:TRP273 4.0 24.1 1.0
O A:HOH1401 4.0 34.3 1.0
C A:TRP273 4.2 19.6 1.0
CG1 A:VAL321 4.2 16.6 1.0
CB A:TRP273 4.2 18.5 1.0
O A:HOH1170 4.4 24.9 1.0
CA A:TRP273 4.5 18.8 1.0
CA A:GLY123 4.5 27.9 1.0
C A:GLY123 4.6 25.1 1.0
CB A:ARG275 4.7 22.4 1.0
O A:HOH1825 4.7 39.2 1.0
O A:HOH1627 4.8 37.7 1.0
N A:THR274 4.8 18.6 1.0
C A:THR274 4.9 17.2 1.0
N A:ARG275 4.9 16.5 1.0
CE3 A:TRP273 4.9 16.9 1.0
O A:HOH1793 5.0 40.7 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: Fri Jul 26 13:44:30 2024

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