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Calcium 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
Sodium (Na) 6 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 6 in 1h80

Go back to Calcium Binding Sites List in 1h80
Calcium 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 Calcium with other atoms in the Ca 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:Ca1492

b:16.0
occ:1.00
 OD1 A:ASN145 2.3 18.3 1.0
O A:GLY146 2.3 12.6 1.0
O A:SER109 2.3 16.1 1.0
O A:HOH2164 2.3 25.1 1.0
O A:HOH2161 2.4 22.7 1.0
OG A:SER109 2.5 19.2 1.0
O A:HOH2214 2.5 23.4 1.0
O A:HOH2213 2.6 32.6 1.0
C A:SER109 3.4 14.8 1.0
CG A:ASN145 3.4 17.1 1.0
C A:GLY146 3.5 11.6 1.0
CB A:SER109 3.7 15.3 1.0
CA A:SER109 3.8 14.6 1.0
ND2 A:ASN145 4.0 20.8 1.0
N A:GLY146 4.2 12.3 1.0
C A:ASN145 4.3 14.4 1.0
O A:HOH2211 4.3 45.1 1.0
O A:ASN145 4.4 15.3 1.0
CA A:GLY146 4.4 12.8 1.0
N A:PHE147 4.4 12.2 1.0
CA A:PHE147 4.5 12.3 1.0
N A:ASP110 4.5 15.6 1.0
CB A:ASN145 4.6 16.5 1.0
O A:HOH2168 4.6 19.6 1.0
OD1 A:ASP110 4.7 24.6 0.8
O A:HOH2525 4.7 24.2 1.0
CA A:ASP110 4.8 17.1 1.0
CA A:ASN145 4.8 14.7 1.0
O A:HOH2165 4.8 46.2 1.0
O A:HOH2163 4.9 15.7 1.0

Calcium binding site 2 out of 6 in 1h80

Go back to Calcium Binding Sites List in 1h80
Calcium 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 Calcium with other atoms in the Ca 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:Ca1493

b:16.6
occ:1.00
 O A:HOH2086 2.3 22.6 1.0
O A:ASN58 2.3 20.4 1.0
OD1 A:ASP61 2.4 23.6 1.0
OD1 A:ASP65 2.4 17.4 1.0
O A:SER63 2.4 20.3 1.0
OD2 A:ASP65 2.4 15.3 1.0
O A:HOH2087 2.4 18.4 1.0
CG A:ASP65 2.7 17.3 1.0
CG A:ASP61 3.4 25.6 1.0
C A:SER63 3.4 20.9 1.0
C A:ASN58 3.5 19.9 1.0
OD2 A:ASP61 3.8 23.8 0.5
N A:SER63 3.9 23.5 1.0
CB A:ASN58 4.0 22.2 1.0
CA A:SER63 4.1 22.2 1.0
CA A:ASN58 4.1 20.8 1.0
CB A:ASP65 4.1 16.1 1.0
N A:ASN58 4.2 19.5 1.0
O A:ASP61 4.3 24.4 1.0
CB A:SER63 4.3 23.6 1.0
O A:THR91 4.4 15.5 1.0
C A:ASP64 4.4 17.7 1.0
C A:ASP61 4.5 24.6 1.0
N A:ASP65 4.5 16.5 1.0
N A:ASP64 4.5 19.6 1.0
O A:ASP64 4.5 17.9 1.0
N A:GLY59 4.6 20.3 1.0
CB A:ASP61 4.7 24.5 1.0
CA A:ASP65 4.7 16.1 1.0
C A:THR62 4.7 24.5 1.0
O A:HOH2100 4.7 25.6 1.0
ND1 A:HIS93 4.8 18.8 1.0
N A:ASP61 4.8 24.6 1.0
N A:HIS93 4.8 14.5 1.0
CA A:GLY59 4.8 20.8 1.0
CG A:ASN58 4.9 24.1 1.0
N A:THR62 4.9 24.7 1.0
CA A:ASP64 4.9 18.5 1.0
CA A:ASP61 4.9 24.7 1.0
CA A:TYR92 5.0 14.5 1.0

Calcium binding site 3 out of 6 in 1h80

Go back to Calcium Binding Sites List in 1h80
Calcium 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 Calcium with other atoms in the Ca 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:Ca1494

b:27.4
occ:1.00
 O A:TYR446 2.4 21.1 1.0
OD1 A:ASP447 2.5 28.2 1.0
OG1 A:THR438 2.5 24.1 1.0
O A:HOH2449 2.5 33.2 1.0
OD2 A:ASP445 2.6 27.2 1.0
OD1 A:ASP445 2.8 27.4 1.0
CG A:ASP445 3.0 27.6 1.0
CB A:THR438 3.4 25.3 1.0
C A:TYR446 3.4 22.2 1.0
CG A:ASP447 3.6 26.7 1.0
CA A:ASP447 3.9 23.5 1.0
O A:HOH2457 4.0 20.6 1.0
N A:ASP447 4.1 22.3 1.0
N A:TYR446 4.2 24.1 1.0
CB A:ASP447 4.2 25.2 1.0
CG2 A:THR438 4.3 24.5 1.0
O A:THR438 4.4 28.0 1.0
C A:THR438 4.5 27.6 1.0
CB A:ASP445 4.5 27.3 1.0
CA A:TYR446 4.5 22.1 1.0
OD1 A:ASP436 4.5 18.2 0.5
OD2 A:ASP436 4.6 20.0 0.5
CA A:THR438 4.6 26.0 1.0
OD2 A:ASP447 4.6 28.9 1.0
CA A:GLU440 4.6 33.9 1.0
N A:GLU440 4.7 32.8 1.0
O A:HOH2461 4.8 34.9 1.0
O A:HOH2459 4.9 36.4 1.0
C A:PRO439 4.9 31.7 1.0
O A:PRO439 4.9 32.5 1.0
C A:ASP445 4.9 26.0 1.0
CG A:ASP436 5.0 19.4 0.5

Calcium binding site 4 out of 6 in 1h80

Go back to Calcium Binding Sites List in 1h80
Calcium 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 Calcium with other atoms in the Ca 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:Ca1492

b:15.4
occ:1.00
 OD1 B:ASN145 2.2 16.8 1.0
O B:HOH2202 2.3 23.5 1.0
O B:GLY146 2.3 11.9 1.0
O B:SER109 2.4 14.9 1.0
O B:HOH2197 2.4 25.6 1.0
O B:HOH2254 2.5 20.2 1.0
O B:HOH2253 2.6 32.7 1.0
OG B:SER109 2.6 18.5 1.0
CG B:ASN145 3.4 17.3 1.0
C B:SER109 3.4 13.1 1.0
C B:GLY146 3.5 10.9 1.0
CB B:SER109 3.8 15.1 1.0
CA B:SER109 3.9 13.8 1.0
ND2 B:ASN145 3.9 20.1 1.0
C B:ASN145 4.2 13.4 1.0
N B:GLY146 4.2 11.6 1.0
O B:ASN145 4.3 14.6 1.0
CA B:GLY146 4.4 11.0 1.0
N B:PHE147 4.4 10.9 1.0
CA B:PHE147 4.5 10.3 1.0
N B:ASP110 4.5 13.8 1.0
CB B:ASN145 4.6 15.2 1.0
OD1 B:ASP110 4.6 21.8 0.8
O B:HOH2204 4.6 17.3 1.0
CA B:ASN145 4.8 13.4 1.0
O B:HOH2576 4.8 21.0 1.0
CA B:ASP110 4.8 14.7 1.0
O B:HOH2252 4.9 48.7 1.0
O B:HOH2198 4.9 15.6 1.0

Calcium binding site 5 out of 6 in 1h80

Go back to Calcium Binding Sites List in 1h80
Calcium 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 Calcium with other atoms in the Ca 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:Ca1493

b:15.3
occ:1.00
 O B:HOH2110 2.3 19.3 1.0
O B:ASN58 2.3 18.6 1.0
OD2 B:ASP65 2.3 12.3 1.0
OD1 B:ASP61 2.3 26.7 1.0
O B:HOH2111 2.4 15.5 1.0
O B:SER63 2.4 21.2 1.0
OD1 B:ASP65 2.5 17.5 1.0
CG B:ASP65 2.7 14.5 1.0
CG B:ASP61 3.4 28.7 1.0
C B:ASN58 3.5 18.9 1.0
C B:SER63 3.5 21.3 1.0
OD2 B:ASP61 3.8 28.2 1.0
N B:SER63 3.9 25.0 1.0
CB B:ASN58 4.1 21.0 1.0
CA B:SER63 4.2 23.4 1.0
CA B:ASN58 4.2 19.6 1.0
CB B:ASP65 4.2 13.7 1.0
N B:ASN58 4.2 18.5 1.0
O B:ASP61 4.3 26.7 1.0
O B:THR91 4.4 14.9 1.0
C B:ASP64 4.4 17.2 1.0
O B:ASP64 4.5 17.7 1.0
CB B:SER63 4.5 24.9 1.0
C B:ASP61 4.5 27.1 1.0
N B:ASP65 4.5 14.8 1.0
N B:GLY59 4.6 18.9 1.0
N B:ASP64 4.6 19.8 1.0
CB B:ASP61 4.7 27.4 1.0
CA B:ASP65 4.8 13.9 1.0
N B:ASP61 4.8 26.9 1.0
N B:HIS93 4.8 12.3 1.0
O B:HOH2126 4.8 29.6 1.0
CA B:GLY59 4.8 19.6 1.0
C B:THR62 4.8 26.4 1.0
ND1 B:HIS93 4.8 15.9 1.0
CA B:ASP61 4.9 27.0 1.0
N B:THR62 4.9 26.9 1.0
CA B:TYR92 4.9 12.6 1.0
CA B:ASP64 4.9 17.6 1.0
CG B:ASN58 5.0 22.9 1.0

Calcium binding site 6 out of 6 in 1h80

Go back to Calcium Binding Sites List in 1h80
Calcium 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 Calcium with other atoms in the Ca 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:Ca1494

b:26.2
occ:1.00
 OG1 B:THR438 2.4 25.0 1.0
O B:TYR446 2.5 23.6 1.0
OD1 B:ASP447 2.5 30.4 1.0
O B:HOH2501 2.5 49.8 1.0
O B:HOH2497 2.6 34.6 1.0
OD2 B:ASP445 2.7 32.3 1.0
OD1 B:ASP445 2.7 32.4 1.0
CG B:ASP445 3.1 32.7 1.0
CB B:THR438 3.4 25.8 1.0
C B:TYR446 3.5 24.8 1.0
CG B:ASP447 3.6 29.5 1.0
CA B:ASP447 3.9 26.0 1.0
O B:HOH2507 4.0 19.7 1.0
N B:ASP447 4.1 24.9 1.0
CB B:ASP447 4.2 27.8 1.0
CG2 B:THR438 4.2 25.4 1.0
N B:TYR446 4.3 27.5 1.0
O B:THR438 4.4 29.3 1.0
OD1 B:ASP436 4.4 24.1 0.8
C B:THR438 4.5 29.2 1.0
CA B:THR438 4.5 26.9 1.0
CA B:TYR446 4.5 25.1 1.0
OD2 B:ASP436 4.6 25.0 0.8
CB B:ASP445 4.6 32.2 1.0
OD2 B:ASP447 4.6 30.0 1.0
CA B:GLU440 4.9 37.0 1.0
CG B:ASP436 4.9 23.7 1.0
C B:ASP445 5.0 30.1 1.0
N B:GLU440 5.0 35.8 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: Thu Jul 11 10:00:00 2024

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