Calcium in PDB 9hh3: Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans

The structure of Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans, PDB code: 9hh3 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)	49.36 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	73.8, 199.15, 75.35, 90, 99.33, 90
R / Rfree (%)	19.5 / 24.6

The structure of Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans also contains other interesting chemical elements:

Bromine	(Br)	10 atoms
Chlorine	(Cl)	25 atoms

The binding sites of Calcium atom in the Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans (pdb code 9hh3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans, PDB code: 9hh3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca612 b:52.1 occ:1.00 OD1 A:ASP56 2.2 38.0 1.0 OD1 A:ASP57 2.3 39.0 1.0 OD2 A:ASP314 2.4 42.0 1.0 OD1 A:ASN315 2.5 36.5 1.0 OD1 A:ASP314 2.7 43.6 1.0 SG A:DDZ96 2.7 43.8 0.3 CG A:ASP314 2.9 39.6 1.0 OG1 A:DDZ96 2.9 44.4 0.7 CG A:ASN315 3.3 36.4 1.0 CG A:ASP57 3.4 44.3 1.0 ND2 A:ASN315 3.5 35.8 1.0 CG A:ASP56 3.5 45.2 1.0 N A:ASP57 3.6 34.0 1.0 CA A:DDZ96 3.8 40.0 0.7 CB A:DDZ96 3.8 42.4 0.3 CA A:DDZ96 3.8 40.0 0.3 CB A:DDZ96 3.8 42.6 0.7 N A:DDZ96 4.0 41.8 0.7 N A:DDZ96 4.0 41.7 0.3 NZ A:LYS332 4.1 35.9 1.0 OD2 A:ASP57 4.1 45.8 1.0 C A:ASP56 4.2 36.8 1.0 CA A:ASP57 4.2 37.8 1.0 CA A:ASP56 4.2 39.6 1.0 OD2 A:ASP56 4.3 42.1 1.0 CB A:ASP314 4.3 41.0 1.0 CB A:ASP57 4.4 36.5 1.0 CB A:ASP56 4.5 38.4 1.0 NH2 A:ARG100 4.5 39.0 1.0 CE A:LYS332 4.5 38.3 1.0 CD2 A:HIS256 4.5 40.0 1.0 OG2 A:DDZ96 4.6 43.0 0.7 NZ A:LYS155 4.6 35.8 1.0 CB A:ASN315 4.7 35.4 1.0 N A:ASN315 4.8 31.3 1.0 C A:PHE95 4.9 41.8 1.0 C A:ASP314 5.0 36.1 1.0 NE A:ARG100 5.0 40.2 1.0 CD A:LYS332 5.0 43.0 1.0

Calcium binding site 2 out of 4 in the Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca610 b:51.7 occ:1.00 ND2 B:ASN315 2.3 33.3 1.0 OD1 B:ASP57 2.3 42.0 1.0 OD2 B:ASP314 2.4 43.6 1.0 OD1 B:ASP56 2.4 46.0 1.0 OD1 B:ASP314 2.6 41.7 1.0 SG B:DDZ96 2.7 42.4 0.3 CG B:ASP314 2.8 43.1 1.0 OG2 B:DDZ96 3.0 43.7 0.7 CG B:ASN315 3.1 39.6 1.0 OD1 B:ASN315 3.3 40.8 1.0 CG B:ASP57 3.5 44.1 1.0 N B:ASP57 3.6 35.4 1.0 CG B:ASP56 3.6 42.4 1.0 CB B:DDZ96 3.7 42.3 0.3 CA B:DDZ96 3.8 39.8 0.7 CA B:DDZ96 3.8 39.6 0.3 CB B:DDZ96 4.0 42.3 0.7 N B:DDZ96 4.1 41.0 0.7 N B:DDZ96 4.1 40.7 0.3 OD2 B:ASP57 4.2 43.9 1.0 C B:ASP56 4.2 41.8 1.0 CA B:ASP57 4.2 36.5 1.0 CB B:ASP314 4.3 38.8 1.0 CA B:ASP56 4.3 38.1 1.0 NH2 B:ARG100 4.3 38.8 1.0 NZ B:LYS332 4.3 47.3 1.0 OD2 B:ASP56 4.4 38.4 1.0 CB B:ASP57 4.4 36.8 1.0 CB B:ASN315 4.5 39.6 1.0 NZ B:LYS155 4.6 44.0 1.0 CB B:ASP56 4.6 34.9 1.0 CE B:LYS332 4.6 42.1 1.0 N B:ASN315 4.7 35.5 1.0 OG1 B:DDZ96 4.7 45.7 0.7 CD2 B:HIS256 4.7 39.2 1.0 C B:ASP314 4.8 38.1 1.0 C B:PHE95 4.9 40.1 1.0 NE B:ARG100 4.9 42.4 1.0

Calcium binding site 3 out of 4 in the Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca608 b:70.6 occ:1.00 OD1 C:ASP56 2.2 66.9 1.0 OD2 C:ASP314 2.2 63.6 1.0 ND2 C:ASN315 2.3 59.2 1.0 OD1 C:ASP57 2.4 56.5 1.0 OG1 C:DDZ96 2.5 62.7 0.7 OD1 C:ASP314 2.6 55.6 1.0 CG C:ASP314 2.8 57.9 1.0 CG C:ASN315 3.2 54.9 1.0 SG C:DDZ96 3.2 60.5 0.3 OD1 C:ASN315 3.4 56.9 1.0 CG C:ASP56 3.4 64.3 1.0 CG C:ASP57 3.6 59.6 1.0 CB C:DDZ96 3.6 64.8 0.7 CA C:DDZ96 3.7 61.5 0.7 N C:ASP57 3.7 56.7 1.0 CA C:DDZ96 3.7 61.5 0.3 CB C:DDZ96 3.8 64.2 0.3 N C:DDZ96 3.9 62.1 0.3 N C:DDZ96 3.9 62.1 0.7 OD2 C:ASP56 4.1 64.0 1.0 NZ C:LYS332 4.1 66.0 1.0 CB C:ASP314 4.3 52.8 1.0 CA C:ASP56 4.3 60.8 1.0 C C:ASP56 4.3 57.2 1.0 OD2 C:ASP57 4.3 60.5 1.0 CA C:ASP57 4.4 57.3 1.0 NZ C:LYS155 4.5 67.3 1.0 CB C:ASP56 4.5 62.5 1.0 NH2 C:ARG100 4.5 51.8 1.0 CD2 C:HIS256 4.5 66.0 1.0 CB C:ASN315 4.5 58.8 1.0 CB C:ASP57 4.5 51.2 1.0 CE C:LYS332 4.6 62.9 1.0 C C:PHE95 4.7 63.0 1.0 N C:ASN315 4.8 54.2 1.0 OG2 C:DDZ96 4.8 63.7 0.7 NE C:ARG100 4.8 58.1 1.0 C C:ASP314 4.9 50.9 1.0 O C:HOH722 4.9 63.4 1.0

Calcium binding site 4 out of 4 in the Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Apo Zgcgsa Carrageenan-Sulfatase (S1_19) From the Marine Bacterium Zobellia Galactanivorans within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca609 b:67.6 occ:1.00 OD1 D:ASP56 2.2 58.5 1.0 OD1 D:ASP57 2.4 62.1 1.0 OD1 D:ASP314 2.4 59.3 1.0 OD2 D:ASP314 2.4 63.5 1.0 OD1 D:ASN315 2.5 56.0 1.0 CG D:ASP314 2.8 60.7 1.0 SG D:DDZ96 3.1 59.5 0.3 OG2 D:DDZ96 3.2 59.5 0.7 CG D:ASN315 3.3 61.2 1.0 CG D:ASP57 3.4 60.3 1.0 CG D:ASP56 3.4 59.0 1.0 N D:ASP57 3.5 56.0 1.0 ND2 D:ASN315 3.5 53.2 1.0 CA D:DDZ96 3.9 61.3 0.7 CA D:DDZ96 3.9 61.2 0.3 CB D:DDZ96 4.0 59.0 0.3 CB D:DDZ96 4.0 58.9 0.7 C D:ASP56 4.1 59.2 1.0 CA D:ASP56 4.1 56.6 1.0 NZ D:LYS332 4.1 62.2 1.0 OD2 D:ASP57 4.2 60.9 1.0 N D:DDZ96 4.2 62.7 0.3 N D:DDZ96 4.2 62.8 0.7 CA D:ASP57 4.2 59.4 1.0 OD2 D:ASP56 4.2 57.8 1.0 CB D:ASP314 4.3 56.9 1.0 CB D:ASP57 4.3 56.7 1.0 CB D:ASP56 4.4 54.3 1.0 NZ D:LYS155 4.5 55.0 1.0 CE D:LYS332 4.5 52.7 1.0 CD2 D:HIS256 4.6 60.0 1.0 NH2 D:ARG100 4.6 57.5 1.0 OG1 D:DDZ96 4.7 59.8 0.7 N D:ASN315 4.7 61.3 1.0 CB D:ASN315 4.7 56.4 1.0 C D:ASP314 4.9 57.6 1.0 C D:PHE95 5.0 64.6 1.0 O D:ASP56 5.0 58.7 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