Calcium in PDB 6b0j: Crystal Structure of Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose

The structure of Crystal Structure of Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose, PDB code: 6b0j was solved by A.G.Hettle, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	109.75 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	123.390, 123.390, 240.110, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 23.4

The binding sites of Calcium atom in the Crystal Structure of Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose (pdb code 6b0j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose, PDB code: 6b0j:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose


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 Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:45.3 occ:1.00 OD1 A:ASP38 2.3 22.4 1.0 O7 A:G4S504 2.3 28.9 1.0 OD1 A:ASP39 2.4 21.1 1.0 OD1 A:ASN292 2.5 23.6 1.0 OD2 A:ASP291 2.6 21.5 1.0 OD1 A:ASP291 2.8 22.4 1.0 CG A:ASP291 3.1 21.8 1.0 CG A:ASN292 3.3 22.7 1.0 CG A:ASP39 3.4 22.3 1.0 ND2 A:ASN292 3.4 22.1 1.0 CG A:ASP38 3.5 21.9 1.0 N A:ASP39 3.6 20.9 1.0 CB A:SER78 3.8 19.8 1.0 S A:G4S504 3.9 22.6 1.0 OD2 A:ASP39 4.1 23.2 1.0 C A:ASP38 4.1 20.9 1.0 CA A:ASP39 4.2 21.2 1.0 CA A:SER78 4.2 19.7 1.0 CD2 A:HIS233 4.2 24.5 1.0 OD2 A:ASP38 4.2 21.6 1.0 N A:SER78 4.3 20.0 1.0 CA A:ASP38 4.3 20.9 1.0 CB A:ASP39 4.3 21.8 1.0 CE A:LYS309 4.4 23.2 1.0 OG A:SER78 4.4 20.9 1.0 NZ A:LYS132 4.5 21.1 1.0 O8 A:G4S504 4.5 24.5 1.0 CB A:ASP38 4.5 21.7 1.0 O9 A:G4S504 4.5 22.9 1.0 CB A:ASP291 4.5 21.8 1.0 NH2 A:ARG82 4.6 19.5 1.0 NZ A:LYS309 4.6 23.3 1.0 CB A:ASN292 4.7 22.1 1.0 N A:ASN292 4.9 21.6 1.0 O4 A:G4S504 4.9 23.6 1.0 O A:ASP38 5.0 21.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose


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 Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:45.3 occ:1.00 OD1 B:ASP38 2.4 20.9 1.0 O9 B:G4S504 2.4 29.4 1.0 OD1 B:ASP39 2.4 27.5 1.0 OD1 B:ASN292 2.5 24.7 1.0 OD2 B:ASP291 2.7 25.0 1.0 OD1 B:ASP291 3.0 24.1 1.0 CG B:ASP291 3.2 24.5 1.0 CG B:ASN292 3.3 24.4 1.0 CG B:ASP39 3.4 24.8 1.0 ND2 B:ASN292 3.5 23.1 1.0 CG B:ASP38 3.6 21.2 1.0 N B:ASP39 3.7 22.9 1.0 CB B:SER78 3.7 21.5 1.0 S B:G4S504 3.8 27.1 1.0 OD2 B:ASP39 4.0 25.8 1.0 CD2 B:HIS233 4.1 21.3 1.0 CA B:SER78 4.2 21.9 1.0 N B:SER78 4.2 23.4 1.0 CE B:LYS309 4.2 26.2 1.0 C B:ASP38 4.2 22.5 1.0 OD2 B:ASP38 4.3 20.4 1.0 CA B:ASP39 4.3 23.7 1.0 O7 B:G4S504 4.3 26.6 1.0 CB B:ASP39 4.3 24.1 1.0 OG B:SER78 4.4 20.9 1.0 CA B:ASP38 4.4 22.5 1.0 NZ B:LYS132 4.4 22.6 1.0 NZ B:LYS309 4.4 26.1 1.0 O8 B:G4S504 4.5 26.2 1.0 CB B:ASP38 4.6 21.9 1.0 NH2 B:ARG82 4.7 22.1 1.0 CB B:ASP291 4.7 23.6 1.0 CB B:ASN292 4.8 24.6 1.0 O4 B:G4S504 4.8 25.7 1.0 NE2 B:HIS233 4.9 20.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose


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 Ps I-Cgsb in Complex with K-I-K-Neocarrahexaose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:33.3 occ:0.75 OD1 C:ASP39 2.3 15.3 1.0 OD1 C:ASP38 2.4 19.9 1.0 O8 C:G4S504 2.4 24.1 1.0 OD1 C:ASN292 2.6 19.1 1.0 OD2 C:ASP291 2.7 21.5 1.0 OD1 C:ASP291 3.1 20.5 1.0 CG C:ASP291 3.3 21.2 1.0 CG C:ASP39 3.3 15.9 1.0 CG C:ASN292 3.4 19.1 1.0 ND2 C:ASN292 3.5 17.8 1.0 CG C:ASP38 3.5 19.7 1.0 N C:ASP39 3.7 17.8 1.0 S C:G4S504 3.7 21.8 1.0 CB C:SER78 3.7 21.0 1.0 OD2 C:ASP39 4.0 14.9 1.0 CD2 C:HIS233 4.1 21.0 1.0 CE C:LYS309 4.2 17.6 1.0 C C:ASP38 4.2 18.5 1.0 CA C:SER78 4.2 20.7 1.0 N C:SER78 4.2 20.6 1.0 OD2 C:ASP38 4.3 20.2 1.0 CA C:ASP39 4.3 17.2 1.0 CB C:ASP39 4.3 16.3 1.0 O7 C:G4S504 4.3 21.8 1.0 NZ C:LYS309 4.3 17.4 1.0 NZ C:LYS132 4.4 22.6 1.0 CA C:ASP38 4.4 19.2 1.0 OG C:SER78 4.4 22.1 1.0 O9 C:G4S504 4.4 22.5 1.0 CB C:ASP38 4.6 19.6 1.0 NH2 C:ARG82 4.7 20.4 1.0 CB C:ASP291 4.8 21.8 1.0 O4 C:G4S504 4.8 22.4 1.0 CB C:ASN292 4.8 19.7 1.0 NE2 C:HIS233 4.8 21.2 1.0 CD C:LYS309 5.0 17.6 1.0

A.G.Hettle, C.Vickers, C.S.Robb, F.Liu, S.G.Withers, J.H.Hehemann, A.B.Boraston. The Molecular Basis of Polysaccharide Sulfatase Activity and A Nomenclature For Catalytic Subsites in This Class of Enzyme. Structure V. 26 747 2018.
ISSN: ISSN 1878-4186
PubMed: 29681469
DOI: 10.1016/J.STR.2018.03.012