Atomistry » Chlorine » PDB 1dhj-1e2y » 1dyp
Atomistry »
  Chlorine »
    PDB 1dhj-1e2y »
      1dyp »

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

Go back to Chlorine Binding Sites List in 1dyp
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

Go back to Chlorine Binding Sites List in 1dyp
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: Sat Dec 12 08:34:19 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy