Atomistry » Cadmium » PDB 1dpe-1gwg » 1dyp
Atomistry »
  Cadmium »
    PDB 1dpe-1gwg »
      1dyp »

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

Go back to Cadmium Binding Sites List in 1dyp
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

Go back to Cadmium Binding Sites List in 1dyp
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

Go back to Cadmium Binding Sites List in 1dyp
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

Go back to Cadmium Binding Sites List in 1dyp
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

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