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Sodium in PDB 1h80: 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase

Enzymatic activity of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase

All present enzymatic activity of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase:
3.2.1.157;

Protein crystallography data

The structure of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase, PDB code: 1h80 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) 20.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.870, 90.070, 124.120, 90.00, 93.53, 90.00
R / Rfree (%) 20.7 / 22.3

Other elements in 1h80:

The structure of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase (pdb code 1h80). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase, PDB code: 1h80:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 1h80

Go back to Sodium Binding Sites List in 1h80
Sodium binding site 1 out of 6 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1496

b:15.8
occ:1.00
 O A:HOH2159 2.3 22.9 1.0
O B:HOH2072 2.3 24.9 1.0
OE2 A:GLU108 2.3 17.4 1.0
O A:HOH2157 2.4 28.5 1.0
OE1 A:GLU108 2.4 17.1 1.0
O B:HOH2096 2.6 28.4 1.0
O A:HOH2160 2.6 25.5 1.0
CD A:GLU108 2.7 16.4 1.0
NA B:NA1498 3.0 25.3 1.0
CG A:GLU108 4.2 15.1 1.0
O B:HOH2071 4.3 32.1 1.0
OD1 B:ASP54 4.6 20.5 1.0
CB A:PRO88 4.6 13.9 1.0
ND2 A:ASN89 4.6 18.6 1.0
O B:ASN48 4.6 16.2 1.0
O B:HOH2056 4.7 28.4 1.0
O A:HOH2158 4.7 16.2 1.0
O A:HOH2134 4.7 20.4 1.0
OD2 B:ASP54 4.8 17.1 1.0
O B:HOH2094 4.8 48.9 1.0
N A:ASN89 4.8 14.0 1.0
CA A:PRO88 5.0 13.5 1.0

Sodium binding site 2 out of 6 in 1h80

Go back to Sodium Binding Sites List in 1h80
Sodium binding site 2 out of 6 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1497

b:16.6
occ:1.00
 O A:LEU159 2.3 16.8 1.0
O A:PHE184 2.3 13.6 1.0
O A:ILE183 2.4 16.1 1.0
OG1 A:THR182 2.4 15.6 1.0
O A:HOH2259 2.4 16.5 1.0
C A:ILE183 3.3 16.0 1.0
C A:PHE184 3.3 13.6 1.0
CB A:THR182 3.5 16.9 1.0
C A:LEU159 3.5 16.8 1.0
O A:THR182 3.7 15.8 1.0
C A:THR182 3.7 16.5 1.0
CB A:PHE184 3.8 16.6 1.0
CA A:PHE184 3.8 14.8 1.0
N A:PHE184 3.8 15.7 1.0
O A:HOH2258 3.9 16.0 1.0
N A:ILE183 4.0 16.0 1.0
CA A:THR182 4.2 16.6 1.0
CA A:ILE183 4.3 16.7 1.0
O A:ALA185 4.3 14.1 1.0
O A:HOH2251 4.3 17.3 1.0
OD2 A:ASP179 4.4 20.1 1.0
CA A:LEU159 4.4 18.3 1.0
C A:ALA185 4.4 13.5 1.0
N A:ALA160 4.4 16.0 1.0
N A:ALA185 4.4 13.6 1.0
N A:LEU159 4.4 19.4 1.0
CA A:ALA160 4.5 15.1 1.0
CG2 A:THR182 4.7 17.0 1.0
CE2 A:PHE151 4.7 19.5 1.0
OD1 A:ASP179 4.7 18.6 1.0
N A:SER186 4.7 13.1 1.0
CB A:LEU159 4.8 19.4 1.0
CA A:ALA185 4.8 13.8 1.0
N A:THR182 4.9 17.1 1.0
CG A:ASP179 5.0 18.6 1.0
OG A:SER186 5.0 15.9 1.0

Sodium binding site 3 out of 6 in 1h80

Go back to Sodium Binding Sites List in 1h80
Sodium binding site 3 out of 6 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1498

b:27.4
occ:1.00
 O A:HOH2045 2.3 23.4 1.0
OD2 A:ASP54 2.4 18.4 1.0
O B:HOH2196 2.4 24.9 1.0
O A:HOH2074 2.4 25.1 1.0
OD1 A:ASP54 2.6 20.4 1.0
CG A:ASP54 2.8 19.3 1.0
O A:HOH2073 2.8 45.0 1.0
O A:HOH2046 2.9 38.0 1.0
NA B:NA1496 3.0 15.3 1.0
CB A:ASP54 4.3 18.4 1.0
O B:HOH2193 4.4 23.6 1.0
O B:HOH2082 4.4 34.7 1.0
O B:HOH2083 4.5 31.0 1.0
O A:HOH2069 4.5 38.1 1.0
OE2 B:GLU108 4.6 17.4 1.0
O A:ASN48 4.6 16.9 1.0
N A:ASP50 4.6 14.3 1.0
CB A:ASP53 4.8 18.9 1.0
CB A:ASP50 4.8 14.9 1.0
O B:HOH2194 4.9 30.0 1.0
CA A:TYR49 4.9 14.2 1.0

Sodium binding site 4 out of 6 in 1h80

Go back to Sodium Binding Sites List in 1h80
Sodium binding site 4 out of 6 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1496

b:15.3
occ:1.00
 O B:HOH2193 2.2 23.6 1.0
O A:HOH2045 2.3 23.4 1.0
OE2 B:GLU108 2.4 17.4 1.0
O A:HOH2074 2.4 25.1 1.0
OE1 B:GLU108 2.5 17.3 1.0
O B:HOH2194 2.5 30.0 1.0
O B:HOH2196 2.5 24.9 1.0
CD B:GLU108 2.7 16.3 1.0
NA A:NA1498 3.0 27.4 1.0
CG B:GLU108 4.3 14.5 1.0
OD1 A:ASP54 4.5 20.4 1.0
O A:HOH2046 4.5 38.0 1.0
ND2 B:ASN89 4.6 18.2 1.0
CB B:PRO88 4.6 12.7 1.0
O A:ASN48 4.6 16.9 1.0
O B:HOH2195 4.6 18.2 1.0
O B:HOH2102 4.7 29.1 1.0
OD2 A:ASP54 4.8 18.4 1.0
O B:HOH2170 4.8 22.6 1.0
N B:ASN89 4.9 13.2 1.0

Sodium binding site 5 out of 6 in 1h80

Go back to Sodium Binding Sites List in 1h80
Sodium binding site 5 out of 6 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1497

b:13.0
occ:1.00
 O B:LEU159 2.3 13.7 1.0
O B:PHE184 2.3 11.7 1.0
O B:ILE183 2.4 15.1 1.0
OG1 B:THR182 2.4 14.6 1.0
O B:HOH2307 2.4 14.3 1.0
C B:ILE183 3.3 14.5 1.0
C B:PHE184 3.3 12.0 1.0
CB B:THR182 3.4 13.7 1.0
C B:LEU159 3.5 13.8 1.0
O B:THR182 3.7 13.9 1.0
C B:THR182 3.7 13.8 1.0
CA B:PHE184 3.8 13.3 1.0
CB B:PHE184 3.8 14.9 1.0
N B:PHE184 3.8 13.9 1.0
O B:HOH2348 3.9 14.2 1.0
N B:ILE183 4.0 13.8 1.0
CA B:THR182 4.2 13.7 1.0
O B:ALA185 4.3 12.2 1.0
CA B:ILE183 4.3 14.9 1.0
OD2 B:ASP179 4.4 17.3 1.0
CA B:LEU159 4.4 15.6 1.0
O B:HOH2296 4.4 13.8 1.0
C B:ALA185 4.4 11.4 1.0
N B:LEU159 4.4 16.5 1.0
N B:ALA185 4.4 11.6 1.0
N B:ALA160 4.4 14.0 1.0
CA B:ALA160 4.5 13.4 1.0
CG2 B:THR182 4.6 15.0 1.0
OD1 B:ASP179 4.7 15.0 1.0
CE2 B:PHE151 4.7 16.4 1.0
CB B:LEU159 4.7 16.6 1.0
N B:SER186 4.7 10.4 1.0
CA B:ALA185 4.8 11.5 1.0
N B:THR182 4.9 13.7 1.0
CG B:ASP179 4.9 15.4 1.0
OG B:SER186 5.0 13.5 1.0

Sodium binding site 6 out of 6 in 1h80

Go back to Sodium Binding Sites List in 1h80
Sodium binding site 6 out of 6 in the 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate- 3,6-Anhydro-D-Galactose-2- Sulfate 4 Galactohydrolase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1498

b:25.3
occ:1.00
 O B:HOH2072 2.3 24.9 1.0
O B:HOH2096 2.4 28.4 1.0
OD2 B:ASP54 2.4 17.1 1.0
O A:HOH2157 2.4 28.5 1.0
OD1 B:ASP54 2.6 20.5 1.0
O B:HOH2071 2.7 32.1 1.0
CG B:ASP54 2.8 18.2 1.0
NA A:NA1496 3.0 15.8 1.0
O B:HOH2094 3.1 48.9 1.0
CB B:ASP54 4.3 16.9 1.0
O A:HOH2159 4.4 22.9 1.0
O A:HOH2058 4.5 30.1 1.0
O A:HOH2059 4.5 40.8 1.0
OE2 A:GLU108 4.5 17.4 1.0
O B:ASN48 4.6 16.2 1.0
N B:ASP50 4.6 13.1 1.0
O A:HOH2064 4.7 48.9 1.0
O A:HOH2160 4.8 25.5 1.0
CB B:ASP50 4.9 14.1 1.0
CA B:TYR49 4.9 13.6 1.0

Reference:

G.Michel, L.Chantalat, E.Fanchon, B.Henrissat, B.Kloareg, O.Dideberg. The Iota-Carrageenase of Alteromonas Fortis. A Beta-Helix Fold-Containing Enzyme For the Degradation of A Highly Polyanionic Polysaccharide J.Biol.Chem. V. 276 40202 2001.
ISSN: ISSN 0021-9258
PubMed: 11493601
DOI: 10.1074/JBC.M100670200
Page generated: Sun Oct 6 18:40:50 2024

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