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Chlorine in PDB 1dyp: 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase

Enzymatic activity of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase

All present enzymatic activity of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase:
3.2.1.83;

Protein crystallography data

The structure of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase, PDB code: 1dyp was solved by G.Michel, L.Chantalat, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.25 / 1.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.408, 61.120, 75.523, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.3

Other elements in 1dyp:

The structure of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase also contains other interesting chemical elements:

Cadmium (Cd) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase (pdb code 1dyp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase, PDB code: 1dyp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 1dyp

Go back to Chlorine Binding Sites List in 1dyp
Chlorine binding site 1 out of 7 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1305

b:8.3
occ:1.00
 CD A:CD1298 2.5 8.7 1.0
O A:HOH2344 3.7 10.5 1.0
OE1 A:GLU241 3.7 7.7 1.0
CL A:CL1306 4.0 11.8 1.0
CD A:GLU241 4.6 7.8 1.0
OE2 A:GLU241 4.7 8.2 1.0

Chlorine binding site 2 out of 7 in 1dyp

Go back to Chlorine Binding Sites List in 1dyp
Chlorine binding site 2 out of 7 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1306

b:11.8
occ:1.00
 CD A:CD1298 2.4 8.7 1.0
O A:HOH2344 3.6 10.5 1.0
OE2 A:GLU241 3.7 8.2 1.0
CE A:LYS229 3.7 9.1 1.0
NZ A:LYS229 3.9 9.1 1.0
O A:HOH2343 4.0 19.7 1.0
CL A:CL1305 4.0 8.3 1.0
CD A:LYS229 4.3 9.0 1.0
CD A:GLU241 4.6 7.8 1.0
OE1 A:GLU241 4.7 7.7 1.0
CG A:LYS229 4.8 9.1 1.0
O A:HOH2328 4.9 19.3 1.0

Chlorine binding site 3 out of 7 in 1dyp

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Chlorine binding site 3 out of 7 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1307

b:22.1
occ:0.45
 CD A:CD1300 2.2 12.6 0.5
O A:HOH2256 2.5 13.8 1.0
O A:HOH2141 2.9 31.2 1.0
CL A:CL1308 3.1 20.4 0.5
NE2 A:HIS183 3.2 8.8 1.0
O A:HOH2253 3.2 17.0 1.0
O A:HOH2259 3.3 24.5 1.0
O A:HOH2131 3.5 27.0 1.0
CE1 A:HIS183 3.7 8.6 1.0
CG A:PRO197 3.7 12.9 1.0
O A:HOH2289 3.8 14.6 1.0
CD A:PRO197 4.3 12.9 1.0
CD2 A:HIS183 4.5 8.4 1.0
NE2 A:GLN171 4.5 7.6 1.0
OE2 A:GLU168 4.5 10.1 1.0
OE1 A:GLU168 4.5 10.2 1.0
O A:HOH2276 4.5 25.7 1.0
O A:HOH2275 4.6 9.3 1.0
OD2 A:ASP181 4.6 6.4 1.0
O A:HOH2133 4.8 34.4 1.0
CD A:GLU168 4.9 9.3 1.0
ND1 A:HIS183 5.0 8.4 1.0
OE1 A:GLN171 5.0 8.1 1.0

Chlorine binding site 4 out of 7 in 1dyp

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Chlorine binding site 4 out of 7 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1308

b:20.4
occ:0.45
 CD A:CD1300 2.4 12.6 0.5
O A:HOH2289 2.9 14.6 1.0
CL A:CL1307 3.1 22.1 0.5
CD A:ARG196 3.4 14.8 1.0
NE2 A:HIS183 3.4 8.8 1.0
O A:HOH2286 3.6 30.6 1.0
O A:HOH2276 3.6 25.7 1.0
CD2 A:HIS183 3.8 8.4 1.0
CB A:ARG196 3.8 14.7 1.0
CH2 A:TRP266 3.8 14.4 1.0
CZ2 A:TRP266 3.8 14.5 1.0
O A:HOH2131 3.9 27.0 1.0
CG A:ARG196 3.9 15.1 1.0
NE A:ARG196 4.3 11.3 1.0
CD A:PRO197 4.4 12.9 1.0
CE1 A:HIS183 4.6 8.6 1.0
O A:HOH2141 4.6 31.2 1.0
CG A:PRO197 4.6 12.9 1.0
CZ3 A:TRP266 4.7 14.3 1.0
CE2 A:TRP266 4.7 13.8 1.0
O A:HOH2290 4.8 31.5 1.0
O A:HOH2253 4.8 17.0 1.0
CA A:ARG196 5.0 14.1 1.0

Chlorine binding site 5 out of 7 in 1dyp

Go back to Chlorine Binding Sites List in 1dyp
Chlorine binding site 5 out of 7 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1309

b:16.9
occ:0.45
 CD A:CD1301 2.4 17.4 0.5
OE1 A:GLU287 3.4 9.8 0.5
NZ A:LYS131 3.7 13.8 1.0
CE1 A:PHE218 3.7 8.6 1.0
CL A:CL1310 4.0 26.2 0.5
CZ A:PHE218 4.1 8.6 1.0
O A:HOH2398 4.2 39.8 1.0
CD A:GLU287 4.4 9.6 0.5
OE2 A:GLU287 4.7 9.8 0.5
CD A:LYS131 4.7 12.0 1.0
CE A:LYS80 4.9 12.6 1.0
CE A:LYS131 4.9 13.3 1.0
CD1 A:PHE218 4.9 8.8 1.0

Chlorine binding site 6 out of 7 in 1dyp

Go back to Chlorine Binding Sites List in 1dyp
Chlorine binding site 6 out of 7 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1310

b:26.2
occ:0.45
 CD A:CD1301 2.6 17.4 0.5
O A:HOH2398 3.8 39.8 1.0
CL A:CL1309 4.0 16.9 0.5
OE2 A:GLU287 4.1 9.8 0.5
O A:HOH2120 4.3 26.4 1.0
OE1 A:GLU287 4.6 9.8 0.5
O A:SER77 4.6 13.3 1.0
CB A:LYS78 4.6 15.2 1.0
CD A:GLU287 4.7 9.6 0.5
CD A:LYS80 4.8 12.8 1.0

Chlorine binding site 7 out of 7 in 1dyp

Go back to Chlorine Binding Sites List in 1dyp
Chlorine binding site 7 out of 7 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1311

b:8.7
occ:0.40
 CD A:CD1302 2.5 14.8 0.4
N A:SER134 3.1 9.3 1.0
N A:SER285 3.2 9.2 1.0
OG1 A:THR284 3.3 9.2 1.0
OG A:SER134 3.3 11.5 0.8
O A:SER285 3.3 9.5 1.0
CB A:SER134 3.7 10.4 1.0
O A:HOH2223 3.7 44.6 1.0
CA A:THR284 3.9 9.1 1.0
CA A:ALA133 3.9 9.1 1.0
C A:ALA133 4.0 9.2 1.0
CA A:SER134 4.0 9.8 1.0
C A:THR284 4.0 9.2 1.0
OG A:SER285 4.1 10.1 0.5
C A:SER285 4.1 9.4 1.0
CA A:SER285 4.1 9.4 1.0
CB A:THR284 4.2 9.2 1.0
CB A:ALA133 4.3 9.2 1.0
O A:HOH2399 4.4 23.5 1.0
O A:HOH2397 4.5 17.8 1.0
O A:HOH2312 4.5 17.0 1.0
CB A:SER285 4.8 9.6 1.0
N A:THR135 4.9 9.2 1.0
OE2 A:GLU287 4.9 9.9 0.5

Reference:

G.Michel, L.Chantalat, E.Duee, T.Barbeyron, B.Henrissat, B.Kloareg, O.Dideberg. The Kappa-Carrageenase of P. Carrageenovora Features A Tunnel-Shaped Active Site: A Novel Insight in the Evolution of Clan-B Glycoside Hydrolases Structure V. 9 513 2001.
ISSN: ISSN 0969-2126
PubMed: 11435116
DOI: 10.1016/S0969-2126(01)00612-8
Page generated: Fri Jul 19 21:42:40 2024

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