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Cadmium 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:

Chlorine (Cl) 7 atoms

Cadmium Binding Sites:

The binding sites of Cadmium 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 Cadmium atom.
In total 7 binding sites of Cadmium 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 Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 1dyp

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1298

b:8.7
occ:1.00
 OE2 A:GLU241 2.4 8.2 1.0
O A:HOH2344 2.4 10.5 1.0
OE1 A:GLU241 2.4 7.7 1.0
CL A:CL1306 2.4 11.8 1.0
CL A:CL1305 2.5 8.3 1.0
CD A:GLU241 2.7 7.8 1.0
O A:HOH2343 4.1 19.7 1.0
CG A:GLU241 4.2 7.5 1.0
NZ A:LYS229 4.5 9.1 1.0
CE A:LYS229 4.8 9.1 1.0
O A:HOH2329 4.8 22.5 1.0
CD A:LYS229 4.9 9.0 1.0

Cadmium binding site 2 out of 7 in 1dyp

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1299

b:13.7
occ:0.50
 O A:GLY79 2.3 11.2 1.0
O A:HOH2064 2.3 8.1 1.0
O A:ASP289 2.3 7.1 1.0
O A:GLU48 2.3 7.7 1.0
O A:HOH2052 2.4 8.8 1.0
OD1 A:ASP289 2.5 9.2 1.0
O A:HOH2401 2.6 15.7 1.0
C A:GLY79 3.3 11.7 1.0
C A:ASP289 3.4 7.8 1.0
C A:GLU48 3.5 7.8 1.0
CG A:ASP289 3.6 9.2 1.0
CA A:GLY79 3.8 12.2 1.0
CA A:ASP289 3.9 8.0 1.0
CA A:GLU48 4.2 7.8 1.0
CB A:ASP289 4.4 8.5 1.0
CB A:GLU48 4.4 8.2 1.0
OD2 A:ASP289 4.5 10.0 1.0
N A:LYS80 4.5 11.1 1.0
N A:TYR290 4.5 7.8 1.0
N A:PHE49 4.6 7.8 1.0
O A:PHE49 4.6 7.9 1.0
CB A:TYR290 4.6 8.5 1.0
CB A:PHE49 4.7 7.9 1.0
OE1 A:GLU48 4.7 9.1 1.0
C A:PHE49 4.7 8.2 1.0
OD1 A:ASN50 4.8 9.1 1.0
O A:HOH2041 4.8 23.1 1.0
CA A:PHE49 4.8 7.9 1.0
CA A:TYR290 4.9 7.9 1.0
CA A:LYS80 4.9 10.7 1.0
CD A:CD1303 4.9 22.9 0.4

Cadmium binding site 3 out of 7 in 1dyp

Go back to Cadmium Binding Sites List in 1dyp
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1300

b:12.6
occ:0.45
 CL A:CL1307 2.2 22.1 0.5
O A:HOH2276 2.3 25.7 1.0
CL A:CL1308 2.4 20.4 0.5
NE2 A:HIS183 2.4 8.8 1.0
O A:HOH2131 2.4 27.0 1.0
O A:HOH2253 2.5 17.0 1.0
CE1 A:HIS183 3.3 8.6 1.0
CD2 A:HIS183 3.3 8.4 1.0
O A:HOH2259 3.9 24.5 1.0
O A:HOH2251 4.0 26.5 1.0
O A:HOH2286 4.1 30.6 1.0
O A:HOH2256 4.1 13.8 1.0
ND1 A:HIS183 4.4 8.4 1.0
CG A:HIS183 4.4 8.3 1.0
O A:HOH2252 4.7 29.5 1.0
O A:HOH2289 4.7 14.6 1.0
CH2 A:TRP266 4.8 14.4 1.0
OE2 A:GLU168 4.8 10.1 1.0
CD A:PRO197 4.9 12.9 1.0
O A:HOH2141 4.9 31.2 1.0

Cadmium binding site 4 out of 7 in 1dyp

Go back to Cadmium Binding Sites List in 1dyp
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1301

b:17.4
occ:0.45
 OE1 A:GLU287 2.3 9.8 0.5
CL A:CL1309 2.4 16.9 0.5
O A:HOH2398 2.5 39.8 1.0
OE2 A:GLU287 2.5 9.8 0.5
CL A:CL1310 2.6 26.2 0.5
CD A:GLU287 2.7 9.6 0.5
OE1 A:GLU287 3.9 10.5 0.5
CG A:GLU287 4.2 9.6 0.5
CG A:GLU287 4.2 9.4 0.5
CD A:GLU287 4.2 10.0 0.5
NZ A:LYS131 4.6 13.8 1.0
CZ A:PHE218 4.8 8.6 1.0
CB A:GLU287 4.9 9.2 0.5
CB A:GLU287 4.9 9.1 0.5

Cadmium binding site 5 out of 7 in 1dyp

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1302

b:14.8
occ:0.40
 O A:SER285 2.3 9.5 1.0
OE2 A:GLU287 2.4 9.9 0.5
CL A:CL1311 2.5 8.7 0.4
OG A:SER285 2.8 10.1 0.5
O A:HOH2399 2.8 23.5 1.0
C A:SER285 3.2 9.4 1.0
CD A:GLU287 3.3 10.0 0.5
OE1 A:GLU287 3.4 10.5 0.5
N A:SER285 3.6 9.2 1.0
CA A:SER285 3.6 9.4 1.0
CB A:SER285 3.7 9.6 1.0
N A:MSE286 4.3 9.3 1.0
CG A:GLU287 4.3 9.4 0.5
OG A:SER285 4.5 9.4 0.5
CA A:ALA133 4.6 9.1 1.0
CD A:GLU287 4.7 9.6 0.5
O A:HOH2397 4.7 17.8 1.0
O A:GLY132 4.7 8.9 1.0
CG A:GLU287 4.7 9.6 0.5
OE2 A:GLU287 4.7 9.8 0.5
CA A:MSE286 4.8 9.3 1.0
O A:HOH2312 4.8 17.0 1.0
N A:SER134 4.8 9.3 1.0
C A:THR284 4.9 9.2 1.0
C A:MSE286 5.0 9.0 1.0

Cadmium binding site 6 out of 7 in 1dyp

Go back to Cadmium Binding Sites List in 1dyp
Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1303

b:22.9
occ:0.40
 OD2 A:ASP289 2.1 10.0 1.0
O A:HOH2400 2.3 29.0 1.0
O A:HOH2041 2.5 23.1 1.0
CG A:ASP289 3.0 9.2 1.0
OD1 A:ASP289 3.2 9.2 1.0
O A:HOH2221 3.4 28.9 1.0
O A:HOH2401 3.7 15.7 1.0
NH1 A:ARG129 3.7 11.6 1.0
O A:HOH2052 4.1 8.8 1.0
CB A:ASP289 4.4 8.5 1.0
CZ A:ARG129 4.6 11.5 1.0
O A:HOH2219 4.6 33.6 1.0
CD2 A:TYR290 4.9 9.3 1.0
CD A:CD1299 4.9 13.7 0.5
CD A:ARG129 5.0 10.6 1.0

Cadmium binding site 7 out of 7 in 1dyp

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Cadmium 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 Cadmium with other atoms in the Cd 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:Cd1304

b:23.7
occ:0.40
 OE2 A:GLU72 2.2 12.9 0.5
OE1 A:GLU72 2.4 12.7 0.5
CD A:GLU72 2.6 12.8 1.0
O A:HOH2115 3.6 23.2 1.0
O A:HOH2139 4.0 13.9 1.0
CG A:GLU72 4.1 11.9 1.0
O A:HOH2112 4.4 27.4 1.0
NZ A:LYS86 4.8 13.3 1.0
CB A:GLU72 4.8 11.2 1.0

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 13:14:01 2024

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