Atomistry » Chlorine » PDB 5nke-5nry » 5nn5
Atomistry »
  Chlorine »
    PDB 5nke-5nry »
      5nn5 »

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

Go back to Chlorine Binding Sites List in 5nn5
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

Go back to Chlorine Binding Sites List in 5nn5
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

Go back to Chlorine Binding Sites List in 5nn5
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

Go back to Chlorine Binding Sites List in 5nn5
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

Go back to Chlorine Binding Sites List in 5nn5
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

Go back to Chlorine Binding Sites List in 5nn5
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy