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Chlorine in PDB 5nn3: Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa

Enzymatic activity of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa

All present enzymatic activity of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa:
3.2.1.20;

Protein crystallography data

The structure of Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, PDB code: 5nn3 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) 48.88 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.660, 102.401, 128.751, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 18.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa (pdb code 5nn3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa, PDB code: 5nn3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5nn3

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Chlorine binding site 1 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1018

b:41.5
occ:1.00
 OG A:SER918 3.0 33.8 1.0
O A:HOH1658 3.2 41.0 1.0
N A:SER940 3.2 35.8 1.0
O A:HOH1629 3.4 40.5 1.0
CB A:SER918 3.5 35.5 1.0
CA A:VAL939 3.8 34.3 1.0
CB A:VAL939 4.0 33.3 1.0
C A:VAL939 4.0 34.2 1.0
O A:SER940 4.1 34.6 1.0
CA A:SER940 4.1 37.8 1.0
C A:SER940 4.3 34.7 1.0
CB A:SER940 4.4 43.7 1.0
CD2 A:LEU941 4.4 33.8 1.0
CG A:LEU941 4.5 33.1 1.0
O A:HOH1541 4.5 33.2 1.0
CG1 A:VAL939 4.5 33.7 1.0
CA A:SER918 4.9 33.4 1.0
O A:SER918 4.9 33.5 1.0
OG A:SER940 4.9 51.8 1.0

Chlorine binding site 2 out of 8 in 5nn3

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Chlorine binding site 2 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1019

b:57.9
occ:1.00
 N A:GLN100 3.8 43.5 1.0
OH A:TYR110 3.9 49.0 1.0
CA A:THR99 4.0 44.1 1.0
CB A:THR99 4.1 46.9 1.0
C A:THR99 4.4 42.0 1.0
CZ A:TYR110 4.6 42.5 1.0
CB A:GLN100 4.6 48.2 1.0
CG2 A:THR99 4.6 49.2 1.0
CA A:GLN100 4.8 45.9 1.0
CE1 A:TYR110 5.0 40.3 1.0

Chlorine binding site 3 out of 8 in 5nn3

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Chlorine binding site 3 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1020

b:31.1
occ:1.00
 O A:HOH1465 3.0 25.2 1.0
O A:HOH1750 3.0 34.8 1.0
O A:HOH1357 3.1 28.1 1.0
NH1 A:ARG224 3.1 24.3 1.0
CD A:ARG224 3.6 24.9 1.0
CB A:PRO345 3.7 24.4 1.0
CG A:ARG224 3.8 25.1 1.0
CB A:LEU226 3.9 31.0 1.0
CD2 A:LEU226 4.1 31.7 1.0
CZ A:ARG224 4.1 25.0 1.0
CG A:PRO345 4.1 25.5 1.0
CD1 A:LEU208 4.3 29.8 1.0
NE A:ARG224 4.3 26.0 1.0
O A:HOH1577 4.5 39.3 1.0
CD2 A:LEU208 4.6 32.0 1.0
O A:HOH1734 4.6 34.4 1.0
CD A:PRO345 4.6 24.9 1.0
CG A:LEU226 4.7 31.9 1.0
CB A:LEU208 4.7 27.0 1.0
O A:HOH1768 4.7 43.2 1.0
O A:HOH1402 4.7 33.1 1.0
CG A:LEU208 4.8 29.2 1.0
CA A:PRO345 4.8 23.4 1.0
N A:LEU226 5.0 29.4 1.0

Chlorine binding site 4 out of 8 in 5nn3

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Chlorine binding site 4 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1021

b:46.4
occ:1.00
 O A:HOH1293 3.0 34.9 1.0
N A:ASP741 3.2 28.1 1.0
N A:HIS742 3.2 28.8 1.0
CA A:VAL740 3.6 29.4 1.0
CB A:HIS742 3.7 31.8 1.0
OD1 A:ASP741 3.8 30.0 1.0
CG1 A:VAL740 3.8 29.9 1.0
C A:VAL740 3.8 29.6 1.0
ND1 A:HIS742 3.8 41.4 1.0
CA A:HIS742 4.0 28.8 1.0
C A:ASP741 4.1 29.2 1.0
O A:THR739 4.1 32.5 1.0
CG A:HIS742 4.1 35.0 1.0
CA A:ASP741 4.2 28.7 1.0
CB A:VAL740 4.2 28.6 1.0
C A:HIS742 4.6 29.0 1.0
CG2 A:VAL740 4.6 31.0 1.0
N A:VAL740 4.6 30.0 1.0
N A:GLN743 4.6 27.5 1.0
C A:THR739 4.8 31.1 1.0
CG A:ASP741 4.8 31.8 1.0
CH2 A:TRP804 4.8 35.3 1.0
CE1 A:HIS742 4.9 40.9 1.0

Chlorine binding site 5 out of 8 in 5nn3

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Chlorine binding site 5 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1022

b:49.7
occ:1.00
 O A:HOH1757 2.6 39.6 1.0
O A:HOH1620 3.3 38.5 1.0
N A:LEU677 3.3 27.8 1.0
CE3 A:TRP376 3.4 35.6 1.0
CB A:SER676 3.6 27.0 1.0
CB A:LEU677 3.8 29.1 1.0
CZ3 A:TRP376 3.8 38.7 1.0
CZ A:PHE649 3.9 25.2 1.0
CA A:SER676 4.0 27.1 1.0
CD2 A:TRP376 4.1 33.0 1.0
C A:SER676 4.2 28.1 1.0
CA A:LEU677 4.2 29.5 1.0
O A:HOH1762 4.3 44.1 1.0
CE2 A:PHE649 4.5 25.5 1.0
OG A:SER676 4.5 32.9 1.0
CG A:TRP376 4.7 30.3 1.0
CB A:TRP376 4.7 28.3 1.0
CH2 A:TRP376 4.8 37.7 1.0
O A:HOH1650 4.8 45.4 1.0
CE1 A:PHE649 4.8 25.1 1.0
CE2 A:TRP376 5.0 33.6 1.0

Chlorine binding site 6 out of 8 in 5nn3

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Chlorine binding site 6 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1023

b:44.2
occ:1.00
 O A:HOH1416 2.8 39.0 1.0
O A:HOH1690 3.0 41.1 1.0
N A:LEU756 3.0 28.8 1.0
OE1 A:GLN757 3.3 42.0 1.0
CG A:GLN757 3.7 37.5 1.0
N A:GLN757 3.8 32.4 1.0
CA A:VAL755 3.8 29.9 1.0
C A:VAL755 3.9 29.6 1.0
CA A:LEU756 3.9 31.0 1.0
CD A:GLN757 3.9 40.4 1.0
C A:LEU756 4.1 32.5 1.0
CB A:LEU756 4.1 29.7 1.0
CG1 A:VAL755 4.2 30.7 1.0
CB A:GLN757 4.2 36.2 1.0
O A:PRO754 4.3 28.7 1.0
CG2 A:VAL763 4.3 34.1 1.0
O A:HOH1625 4.4 46.4 1.0
CB A:VAL755 4.4 30.9 1.0
CA A:GLN757 4.6 35.1 1.0
CG A:LYS760 4.7 43.4 1.0
CG A:LEU756 4.8 28.7 1.0
CG2 A:VAL755 4.8 31.3 1.0
N A:VAL755 4.9 29.8 1.0
CB A:VAL763 4.9 33.8 1.0
O A:HOH1733 5.0 52.3 1.0

Chlorine binding site 7 out of 8 in 5nn3

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Chlorine binding site 7 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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

b:67.6
occ:1.00
 NE A:ARG106 3.5 41.1 1.0
NH2 A:ARG106 3.5 40.7 1.0
O A:HOH1526 3.6 50.3 1.0
CZ A:ARG106 4.0 40.2 1.0
NZ A:LYS96 4.3 65.5 1.0
CG A:ARG106 4.5 40.7 1.0
CB A:PHE159 4.6 36.3 1.0
CD A:ARG106 4.6 39.6 1.0

Chlorine binding site 8 out of 8 in 5nn3

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Chlorine binding site 8 out of 8 in the Crystal Structure of Human Lysosomal Acid-Alpha-Glucosidase, Gaa


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

b:53.8
occ:1.00
 O A:HOH1702 2.6 46.4 1.0
OG A:SER566 3.2 22.8 1.0
O A:HOH1558 3.4 47.1 1.0
O A:HOH1700 3.7 36.9 1.0
CB A:SER566 3.9 23.4 1.0
CB A:TYR191 4.0 25.5 1.0
NH1 A:ARG189 4.1 68.5 1.0
CA A:TYR191 4.2 25.5 1.0
ND2 A:ASN570 4.4 23.1 1.0
O A:HOH1552 4.4 37.9 1.0
O A:LEU565 4.4 24.9 1.0
N A:TYR191 4.4 26.3 1.0
CD1 A:TYR191 4.5 24.1 1.0
CA A:SER566 4.6 23.7 1.0
NH2 A:ARG189 4.6 75.9 1.0
CG A:TYR191 4.8 24.2 1.0
CZ A:ARG189 4.8 71.3 1.0
O A:HOH1544 4.9 33.6 1.0
O A:HOH1566 5.0 26.8 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 13:43:38 2024

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