Calcium in PDB 6b1v: Crystal Structure of Ps I-Cgsb C78S in Complex with I-Neocarratetraose

The structure of Crystal Structure of Ps I-Cgsb C78S in Complex with I-Neocarratetraose, PDB code: 6b1v 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)	113.43 / 2.84
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	130.440, 130.440, 229.754, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 26.4

The binding sites of Calcium atom in the Crystal Structure of Ps I-Cgsb C78S in Complex with I-Neocarratetraose (pdb code 6b1v). 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 C78S in Complex with I-Neocarratetraose, PDB code: 6b1v:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Ps I-Cgsb C78S in Complex with I-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 Ps I-Cgsb C78S in Complex with I-Neocarratetraose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:34.9 occ:0.50 OD1 A:ASP38 2.3 47.3 1.0 OD1 A:ASN292 2.3 37.9 1.0 O8 A:G4S503 2.3 42.0 1.0 OD1 A:ASP39 2.4 41.6 1.0 OD2 A:ASP291 2.4 36.7 1.0 OD1 A:ASP291 2.9 38.5 1.0 CG A:ASP291 3.0 38.2 1.0 CG A:ASN292 3.2 36.1 1.0 CG A:ASP39 3.5 43.6 1.0 ND2 A:ASN292 3.5 35.6 1.0 CG A:ASP38 3.5 46.8 1.0 N A:ASP39 3.6 46.4 1.0 CB A:SER78 3.8 37.0 1.0 S A:G4S503 3.9 42.5 1.0 CD2 A:HIS233 4.2 43.5 1.0 CA A:ASP39 4.2 46.1 1.0 N A:SER78 4.2 40.0 1.0 CA A:SER78 4.2 38.4 1.0 C A:ASP38 4.2 46.1 1.0 CE A:LYS309 4.2 40.6 1.0 OD2 A:ASP39 4.3 38.5 1.0 OD2 A:ASP38 4.3 45.3 1.0 CA A:ASP38 4.3 46.5 1.0 CB A:ASP39 4.4 46.6 1.0 O7 A:G4S503 4.4 42.9 1.0 NZ A:LYS132 4.4 38.6 1.0 CB A:ASP38 4.5 48.5 1.0 OG A:SER78 4.5 34.9 1.0 NZ A:LYS309 4.5 42.2 1.0 CB A:ASP291 4.5 38.5 1.0 O9 A:G4S503 4.6 41.8 1.0 CB A:ASN292 4.6 36.8 1.0 NE2 A:HIS233 4.9 44.1 1.0 O4 A:G4S503 4.9 43.2 1.0 N A:ASN292 4.9 37.1 1.0 NH2 A:ARG82 4.9 53.0 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Ps I-Cgsb C78S in Complex with I-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 Ps I-Cgsb C78S in Complex with I-Neocarratetraose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:43.6 occ:0.50 OD1 B:ASP38 2.2 36.9 1.0 OD1 B:ASP39 2.3 48.3 1.0 O9 B:G4S503 2.3 39.1 1.0 OD1 B:ASN292 2.4 36.9 1.0 OD2 B:ASP291 2.6 42.0 1.0 OD1 B:ASP291 3.0 45.1 1.0 CG B:ASP291 3.1 43.0 1.0 CG B:ASN292 3.3 37.5 1.0 CG B:ASP39 3.3 47.3 1.0 CG B:ASP38 3.5 38.9 1.0 ND2 B:ASN292 3.5 35.1 1.0 N B:ASP39 3.5 44.4 1.0 CB B:SER78 3.9 37.7 1.0 S B:G4S503 3.9 34.7 1.0 CD2 B:HIS233 4.0 36.6 1.0 OD2 B:ASP39 4.1 46.9 1.0 CA B:ASP39 4.1 46.3 1.0 C B:ASP38 4.1 40.9 1.0 CE B:LYS309 4.2 49.2 1.0 CB B:ASP39 4.2 46.7 1.0 OD2 B:ASP38 4.2 38.3 1.0 CA B:ASP38 4.3 39.5 1.0 N B:SER78 4.3 38.8 1.0 CA B:SER78 4.4 38.4 1.0 O8 B:G4S503 4.4 35.9 1.0 NZ B:LYS309 4.4 51.0 1.0 CB B:ASP38 4.5 39.0 1.0 NZ B:LYS132 4.5 45.2 1.0 O7 B:G4S503 4.6 34.6 1.0 OG B:SER78 4.6 37.8 1.0 CB B:ASP291 4.7 41.1 1.0 CB B:ASN292 4.7 36.9 1.0 NE2 B:HIS233 4.8 35.7 1.0 O4 B:G4S503 4.9 35.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Ps I-Cgsb C78S in Complex with I-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 Ps I-Cgsb C78S in Complex with I-Neocarratetraose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:45.3 occ:0.50 OD1 C:ASP38 2.2 44.4 1.0 OD1 C:ASP39 2.3 40.3 1.0 O8 C:G4S504 2.3 47.1 1.0 OD1 C:ASN292 2.4 43.6 1.0 OD2 C:ASP291 2.6 47.0 1.0 OD1 C:ASP291 2.9 46.1 1.0 CG C:ASP291 3.1 45.2 1.0 CG C:ASN292 3.3 46.1 1.0 CG C:ASP39 3.3 43.0 1.0 CG C:ASP38 3.5 45.5 1.0 ND2 C:ASN292 3.5 45.4 1.0 N C:ASP39 3.5 43.9 1.0 CB C:SER78 3.9 46.5 1.0 S C:G4S504 3.9 42.5 1.0 CD2 C:HIS233 4.0 54.0 1.0 OD2 C:ASP39 4.1 41.8 1.0 CA C:ASP39 4.1 46.3 1.0 C C:ASP38 4.1 43.8 1.0 CE C:LYS309 4.2 44.2 1.0 CB C:ASP39 4.2 45.5 1.0 OD2 C:ASP38 4.2 45.4 1.0 CA C:ASP38 4.3 45.5 1.0 N C:SER78 4.3 46.4 1.0 CA C:SER78 4.4 45.4 1.0 O7 C:G4S504 4.4 40.7 1.0 O9 C:G4S504 4.5 41.5 1.0 CB C:ASP38 4.5 46.1 1.0 NZ C:LYS309 4.5 43.6 1.0 NZ C:LYS132 4.5 51.1 1.0 OG C:SER78 4.6 48.5 1.0 CB C:ASP291 4.6 45.2 1.0 CB C:ASN292 4.7 45.2 1.0 NE2 C:HIS233 4.8 54.0 1.0 O4 C:G4S504 4.9 43.4 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