Calcium in PDB 9hh4: Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose

The structure of Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose, PDB code: 9hh4 was solved by A.Chevenier, M.Czjzek, G.Michel, E.Ficko-Blean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.57 / 1.92
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.23, 197.6, 75.02, 90, 99.79, 90
R / Rfree (%)	16.7 / 20.7

The structure of Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose also contains other interesting chemical elements:

Chlorine	(Cl)	21 atoms
Bromine	(Br)	12 atoms

The binding sites of Calcium atom in the Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose (pdb code 9hh4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose, PDB code: 9hh4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:34.1 occ:1.00 OD1 A:ASP56 2.2 27.7 1.0 OD1 A:ASP57 2.2 24.2 1.0 OD2 A:ASP314 2.4 25.6 1.0 O3S A:OSE96 2.4 35.8 1.0 OD1 A:ASN315 2.5 26.6 1.0 OD1 A:ASP314 2.6 27.2 1.0 CG A:ASP314 2.8 27.4 1.0 CG A:ASN315 3.3 27.2 1.0 CG A:ASP57 3.4 25.7 1.0 CG A:ASP56 3.4 26.8 1.0 ND2 A:ASN315 3.4 22.9 1.0 N A:ASP57 3.4 23.2 1.0 CB A:OSE96 3.6 35.7 1.0 S A:OSE96 3.8 40.7 1.0 N A:OSE96 4.0 30.0 1.0 CA A:OSE96 4.0 30.8 1.0 C A:ASP56 4.0 24.5 1.0 CA A:ASP56 4.1 19.4 1.0 CA A:ASP57 4.1 25.1 1.0 OD2 A:ASP57 4.2 23.1 1.0 OD2 A:ASP56 4.2 29.7 1.0 CB A:ASP57 4.3 23.5 1.0 CB A:ASP314 4.3 25.7 1.0 OG A:OSE96 4.3 40.6 1.0 CB A:ASP56 4.3 22.6 1.0 O2S A:OSE96 4.3 42.5 1.0 NH2 A:ARG100 4.5 24.4 1.0 CE A:LYS332 4.5 23.8 1.0 CD2 A:HIS256 4.6 24.5 1.0 NZ A:LYS155 4.6 20.8 1.0 CB A:ASN315 4.7 21.1 1.0 N A:ASN315 4.7 23.9 1.0 NZ A:LYS332 4.7 26.1 1.0 O1S A:OSE96 4.8 38.2 1.0 C A:ASP314 4.9 22.7 1.0 NE A:ARG100 4.9 23.7 1.0 C A:PHE95 4.9 28.4 1.0 O A:ASP56 5.0 22.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:35.3 occ:1.00 OD1 B:ASP56 2.2 26.7 1.0 OD1 B:ASP57 2.2 22.7 1.0 O3S B:OSE96 2.4 38.6 1.0 OD2 B:ASP314 2.5 28.2 1.0 OD1 B:ASN315 2.7 27.7 1.0 OD1 B:ASP314 2.7 26.1 1.0 CG B:ASP314 2.9 27.9 1.0 CG B:ASP57 3.2 26.5 1.0 ND2 B:ASN315 3.3 23.9 1.0 CG B:ASN315 3.3 25.0 1.0 CG B:ASP56 3.4 27.6 1.0 N B:ASP57 3.5 21.5 1.0 S B:OSE96 3.5 38.4 1.0 CB B:OSE96 3.6 36.7 1.0 O2S B:OSE96 3.8 44.8 1.0 OD2 B:ASP57 4.0 25.9 1.0 N B:OSE96 4.0 31.2 1.0 CA B:OSE96 4.0 33.1 1.0 C B:ASP56 4.1 22.7 1.0 CA B:ASP57 4.1 24.1 1.0 OG B:OSE96 4.1 39.5 1.0 CB B:ASP57 4.2 22.4 1.0 OD2 B:ASP56 4.2 25.4 1.0 CA B:ASP56 4.2 24.6 1.0 CE B:LYS332 4.3 22.9 1.0 CB B:ASP56 4.4 24.6 1.0 CD2 B:HIS256 4.4 24.8 1.0 CB B:ASP314 4.4 25.2 1.0 NZ B:LYS332 4.4 23.9 1.0 NH2 B:ARG100 4.5 21.4 1.0 NZ B:LYS155 4.6 27.5 1.0 O1S B:OSE96 4.7 40.4 1.0 CB B:ASN315 4.8 21.6 1.0 N B:ASN315 4.9 21.9 1.0 C B:PHE95 5.0 29.1 1.0 CD B:LYS332 5.0 28.0 1.0 O B:ASP56 5.0 25.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:43.3 occ:1.00 OD1 C:ASP57 2.2 30.9 1.0 OD1 C:ASP56 2.3 29.4 1.0 O1S C:OSE96 2.3 45.1 1.0 OD1 C:ASN315 2.5 29.6 1.0 OD2 C:ASP314 2.6 29.8 1.0 OD1 C:ASP314 2.6 31.8 1.0 CG C:ASP314 2.9 30.1 1.0 CG C:ASN315 3.2 32.4 1.0 ND2 C:ASN315 3.2 25.8 1.0 CG C:ASP57 3.3 33.2 1.0 N C:ASP57 3.4 27.6 1.0 CG C:ASP56 3.5 32.9 1.0 S C:OSE96 3.5 43.3 1.0 CB C:OSE96 3.7 41.9 1.0 O3S C:OSE96 3.8 46.7 1.0 N C:OSE96 4.0 33.3 1.0 OD2 C:ASP57 4.1 31.0 1.0 CA C:ASP57 4.1 26.9 1.0 C C:ASP56 4.1 25.4 1.0 CA C:OSE96 4.1 38.7 1.0 OG C:OSE96 4.2 46.2 1.0 CB C:ASP57 4.2 29.0 1.0 CA C:ASP56 4.2 29.9 1.0 OD2 C:ASP56 4.3 31.6 1.0 CB C:ASP314 4.4 29.3 1.0 CE C:LYS332 4.4 34.2 1.0 CB C:ASP56 4.4 28.3 1.0 CD2 C:HIS256 4.5 27.8 1.0 CB C:ASN315 4.6 25.1 1.0 NZ C:LYS332 4.6 32.8 1.0 NH2 C:ARG100 4.7 31.8 1.0 O2S C:OSE96 4.7 46.5 1.0 N C:ASN315 4.7 29.2 1.0 NZ C:LYS155 4.9 29.2 1.0 C C:ASP314 5.0 28.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Family S1_19 Carrageenan Sulfatase Zgcgsa From Zobellia Galactanivorans in Complex with Hybrid B-K- Neocarratetraose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:39.5 occ:1.00 OD1 D:ASP56 2.0 34.8 1.0 OD2 D:ASP314 2.2 29.0 1.0 OD1 D:ASP57 2.3 29.6 1.0 OD1 D:ASP314 2.4 29.6 1.0 O1S D:OSE96 2.5 44.2 1.0 CG D:ASP314 2.6 31.2 1.0 OD1 D:ASN315 2.7 27.5 1.0 N D:ASP57 3.3 30.2 1.0 CG D:ASP56 3.3 34.0 1.0 CG D:ASN315 3.3 30.5 1.0 ND2 D:ASN315 3.4 27.8 1.0 CG D:ASP57 3.4 30.2 1.0 S D:OSE96 3.8 43.1 1.0 CB D:OSE96 3.9 41.4 1.0 C D:ASP56 3.9 31.3 1.0 CA D:ASP56 4.0 28.8 1.0 CA D:ASP57 4.0 30.8 1.0 N D:OSE96 4.1 34.9 1.0 CB D:ASP314 4.1 27.1 1.0 CA D:OSE96 4.1 31.1 1.0 OD2 D:ASP56 4.2 32.7 1.0 CB D:ASP56 4.2 29.8 1.0 NH2 D:ARG100 4.2 27.9 1.0 CB D:ASP57 4.2 27.8 1.0 O3S D:OSE96 4.3 45.8 1.0 OD2 D:ASP57 4.3 32.7 1.0 OG D:OSE96 4.4 41.8 1.0 CD2 D:HIS256 4.6 30.4 1.0 NZ D:LYS155 4.6 32.4 1.0 CE D:LYS332 4.7 30.4 1.0 CB D:ASN315 4.8 27.5 1.0 N D:ASN315 4.8 27.8 1.0 NE D:ARG100 4.8 30.4 1.0 NZ D:LYS332 4.8 31.9 1.0 O D:ASP56 4.9 28.2 1.0 O2S D:OSE96 4.9 42.4 1.0 C D:ASP314 4.9 28.2 1.0 CA D:ASP314 5.0 25.4 1.0

A.Chevenier, M.Fanuel, E.Sokolova, D.Mico Latorre, D.Jouanneau, A.Jeudy, A.Prechoux, M.K.Zuhlke, J.Bartel, D.Becher, M.Czjzek, D.Ropartz, G.Michel, E.Ficko-Blean. Structure, Function and Catalytic Mechanism of the Carrageenan-Sulfatases From the Marine Bacterium Zobellia Galactanivorans Dsij T. Carbohydr Polym V. 358 23487 2025.
ISSN: ESSN 1879-1344
PubMed: 40383559
DOI: 10.1016/J.CARBPOL.2025.123487