Atomistry » Chlorine » PDB 3th3-3tnm » 3thd
Atomistry »
  Chlorine »
    PDB 3th3-3tnm »
      3thd »

Chlorine in PDB 3thd: Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin

Enzymatic activity of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin

All present enzymatic activity of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin:
3.2.1.23;

Protein crystallography data

The structure of Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin, PDB code: 3thd was solved by U.Ohto, T.Shimizu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.29 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.792, 115.996, 140.327, 90.00, 92.22, 90.00
R / Rfree (%) 19.8 / 22.8

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin (pdb code 3thd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin, PDB code: 3thd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3thd

Go back to Chlorine Binding Sites List in 3thd
Chlorine binding site 1 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


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 Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:7.5
occ:1.00
 OG A:SER54 3.1 10.1 1.0
NE2 A:HIS56 3.2 7.9 1.0
NH2 A:ARG121 3.2 8.1 1.0
NE A:ARG121 3.4 8.8 1.0
CB A:SER54 3.6 9.3 1.0
CG A:GLN81 3.7 10.1 1.0
O A:GLN81 3.7 9.4 1.0
CZ A:ARG121 3.8 8.7 1.0
CD2 A:HIS56 3.8 7.6 1.0
CA A:THR82 3.8 8.7 1.0
C A:GLN81 3.8 9.5 1.0
OE1 A:GLN81 3.9 11.4 1.0
N A:THR82 3.9 9.0 1.0
C A:THR82 3.9 8.9 1.0
CD2 A:TYR83 4.1 7.5 1.0
N A:TYR83 4.1 8.7 1.0
CE1 A:TYR306 4.1 8.5 1.0
CB A:GLN81 4.2 10.0 1.0
CE2 A:TYR83 4.2 7.2 1.0
CD1 A:TYR306 4.2 8.9 1.0
CD A:GLN81 4.2 11.0 1.0
CG A:TYR83 4.3 7.6 1.0
O A:THR82 4.4 9.5 1.0
CA A:SER54 4.4 9.3 1.0
CE1 A:HIS56 4.4 8.3 1.0
CZ A:TYR83 4.6 7.7 1.0
CD A:ARG121 4.6 9.1 1.0
CA A:GLN81 4.7 9.9 1.0
CD1 A:TYR83 4.7 7.6 1.0
CE1 A:TYR83 4.8 8.0 1.0
CG A:ARG121 4.8 8.8 1.0
CB A:TYR83 4.9 7.7 1.0
CA A:TYR83 4.9 8.1 1.0

Chlorine binding site 2 out of 4 in 3thd

Go back to Chlorine Binding Sites List in 3thd
Chlorine binding site 2 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


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 Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl801

b:5.6
occ:1.00
 OG B:SER54 3.0 8.2 1.0
NE2 B:HIS56 3.2 7.3 1.0
NH2 B:ARG121 3.2 8.5 1.0
NE B:ARG121 3.4 10.3 1.0
CB B:SER54 3.7 8.0 1.0
CG B:GLN81 3.7 8.8 1.0
O B:GLN81 3.7 8.2 1.0
NE2 B:GLN81 3.7 9.0 1.0
CZ B:ARG121 3.7 10.0 1.0
CD2 B:HIS56 3.8 6.8 1.0
C B:GLN81 3.8 7.9 1.0
N B:THR82 3.8 7.9 1.0
CA B:THR82 3.8 7.1 1.0
C B:THR82 3.9 7.5 1.0
CE1 B:TYR306 4.0 8.1 1.0
N B:TYR83 4.1 7.4 1.0
CD2 B:TYR83 4.1 8.0 1.0
CD1 B:TYR306 4.1 8.3 1.0
CD B:GLN81 4.2 9.5 1.0
CB B:GLN81 4.3 8.4 1.0
CE2 B:TYR83 4.3 8.2 1.0
O B:THR82 4.4 7.8 1.0
CG B:TYR83 4.4 7.8 1.0
CA B:SER54 4.4 8.5 1.0
CE1 B:HIS56 4.4 7.2 1.0
CD B:ARG121 4.6 9.8 1.0
CZ B:TYR83 4.6 8.6 1.0
CA B:GLN81 4.7 8.4 1.0
CD1 B:TYR83 4.8 7.6 1.0
CG B:ARG121 4.8 9.6 1.0
CE1 B:TYR83 4.9 8.5 1.0
ND2 B:ASN304 5.0 8.6 1.0
CA B:TYR83 5.0 7.1 1.0
CB B:TYR83 5.0 7.3 1.0

Chlorine binding site 3 out of 4 in 3thd

Go back to Chlorine Binding Sites List in 3thd
Chlorine binding site 3 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


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 Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl801

b:6.2
occ:1.00
 OG C:SER54 3.1 10.3 1.0
NE2 C:HIS56 3.2 8.6 1.0
NH2 C:ARG121 3.3 9.6 1.0
NE C:ARG121 3.5 9.8 1.0
CB C:SER54 3.6 9.4 1.0
CG C:GLN81 3.7 9.6 1.0
O C:GLN81 3.7 10.0 1.0
NE2 C:GLN81 3.7 9.1 1.0
CD2 C:HIS56 3.7 8.0 1.0
C C:GLN81 3.8 9.9 1.0
N C:THR82 3.8 9.9 1.0
CZ C:ARG121 3.8 9.9 1.0
CA C:THR82 3.8 9.8 1.0
C C:THR82 4.0 10.4 1.0
CE1 C:TYR306 4.0 9.2 1.0
CD2 C:TYR83 4.1 9.8 1.0
CB C:GLN81 4.2 9.5 1.0
CD1 C:TYR306 4.2 9.9 1.0
N C:TYR83 4.2 10.4 1.0
CD C:GLN81 4.2 9.5 1.0
CE2 C:TYR83 4.2 9.4 1.0
CE1 C:HIS56 4.4 8.3 1.0
CG C:TYR83 4.4 9.9 1.0
CA C:SER54 4.4 9.3 1.0
O C:THR82 4.5 11.3 1.0
CA C:GLN81 4.6 10.0 1.0
CZ C:TYR83 4.7 9.7 1.0
CD C:ARG121 4.7 10.2 1.0
CD1 C:TYR83 4.8 9.6 1.0
CG C:ARG121 4.9 10.1 1.0
CE1 C:TYR83 4.9 9.8 1.0
ND2 C:ASN304 4.9 9.2 1.0

Chlorine binding site 4 out of 4 in 3thd

Go back to Chlorine Binding Sites List in 3thd
Chlorine binding site 4 out of 4 in the Crystal Structure of Human Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin


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 Beta-Galactosidase in Complex with 1- Deoxygalactonojirimycin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl801

b:6.0
occ:1.00
 OG D:SER54 3.0 10.6 1.0
NH2 D:ARG121 3.2 10.0 1.0
NE2 D:HIS56 3.2 10.6 1.0
NE D:ARG121 3.5 10.4 1.0
O D:GLN81 3.6 9.0 1.0
CB D:SER54 3.7 9.7 1.0
CZ D:ARG121 3.8 10.6 1.0
NE2 D:GLN81 3.8 9.8 1.0
CG D:GLN81 3.8 9.4 1.0
CD2 D:HIS56 3.8 10.2 1.0
C D:GLN81 3.8 8.9 1.0
N D:THR82 3.9 8.8 1.0
CA D:THR82 3.9 9.2 1.0
CE1 D:TYR306 3.9 9.9 1.0
C D:THR82 4.1 9.5 1.0
CD2 D:TYR83 4.1 9.9 1.0
CD1 D:TYR306 4.1 10.4 1.0
CE2 D:TYR83 4.2 10.1 1.0
N D:TYR83 4.2 9.7 1.0
CB D:GLN81 4.2 9.5 1.0
CD D:GLN81 4.3 9.8 1.0
CG D:TYR83 4.4 10.2 1.0
CE1 D:HIS56 4.4 10.8 1.0
CA D:SER54 4.4 9.7 1.0
CZ D:TYR83 4.6 10.0 1.0
O D:THR82 4.6 10.1 1.0
CD D:ARG121 4.7 11.8 1.0
CA D:GLN81 4.7 9.2 1.0
CD1 D:TYR83 4.8 10.0 1.0
CE1 D:TYR83 4.9 10.1 1.0
ND2 D:ASN304 4.9 12.0 1.0

Reference:

U.Ohto, K.Usui, T.Ochi, K.Yuki, Y.Satow, T.Shimizu. Crystal Structure of Human Beta-Galactosidase: Structural Basis of GM1 Gangliosidosis and Morquio B Diseases J.Biol.Chem. V. 287 1801 2012.
ISSN: ISSN 0021-9258
PubMed: 22128166
DOI: 10.1074/JBC.M111.293795
Page generated: Sun Jul 21 05:13:23 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy