Calcium in PDB 6b0k: Crystal Structure of Ps I-Cgsb C78S in Complex with K-Carrapentaose

The structure of Crystal Structure of Ps I-Cgsb C78S in Complex with K-Carrapentaose, PDB code: 6b0k was solved by A.Hettle, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	114.40 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	133.070, 133.070, 223.940, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 27.3

The structure of Crystal Structure of Ps I-Cgsb C78S in Complex with K-Carrapentaose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Ps I-Cgsb C78S in Complex with K-Carrapentaose (pdb code 6b0k). 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 K-Carrapentaose, PDB code: 6b0k:
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 K-Carrapentaose


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 K-Carrapentaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:46.5 occ:1.00 OD1 A:ASP39 2.3 25.0 1.0 O8 A:G4S503 2.4 33.7 1.0 OD1 A:ASP38 2.4 28.7 1.0 OD2 A:ASP291 2.5 26.2 1.0 OD1 A:ASN292 2.6 32.1 1.0 OD1 A:ASP291 2.9 27.2 1.0 CG A:ASP291 3.1 25.3 1.0 CG A:ASN292 3.4 29.8 1.0 CG A:ASP39 3.4 25.1 1.0 ND2 A:ASN292 3.5 26.6 1.0 N A:ASP39 3.6 24.2 1.0 CG A:ASP38 3.6 29.9 1.0 CB A:SER78 3.6 26.3 1.0 S A:G4S503 4.0 28.9 1.0 N A:SER78 4.0 25.5 1.0 CA A:SER78 4.0 24.7 1.0 OD2 A:ASP39 4.1 26.2 1.0 CD2 A:HIS233 4.2 29.2 1.0 C A:ASP38 4.2 25.8 1.0 CA A:ASP39 4.2 24.1 1.0 CE A:LYS309 4.3 28.9 1.0 CB A:ASP39 4.3 24.1 1.0 CA A:ASP38 4.3 27.5 1.0 OD2 A:ASP38 4.4 29.0 1.0 OG A:SER78 4.4 28.6 1.0 NZ A:LYS132 4.5 23.9 1.0 CB A:ASP291 4.6 25.5 1.0 O7 A:G4S503 4.6 28.3 1.0 O9 A:G4S503 4.6 26.9 1.0 CB A:ASP38 4.6 28.9 1.0 NZ A:LYS309 4.6 30.6 1.0 NH2 A:ARG82 4.7 32.6 1.0 CB A:ASN292 4.8 28.8 1.0 C A:PHE77 4.9 25.3 1.0 N A:ASN292 4.9 28.0 1.0 NE2 A:HIS233 5.0 30.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Ps I-Cgsb C78S in Complex with K-Carrapentaose


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 K-Carrapentaose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:51.6 occ:1.00 OD1 B:ASP39 2.3 25.8 1.0 O9 B:G4S504 2.4 38.4 1.0 OD1 B:ASP38 2.4 25.4 1.0 OD2 B:ASP291 2.5 33.0 1.0 OD1 B:ASN292 2.6 15.0 1.0 OD1 B:ASP291 2.9 29.1 1.0 CG B:ASP291 3.1 29.4 1.0 CG B:ASN292 3.4 17.8 1.0 CG B:ASP39 3.4 25.4 1.0 ND2 B:ASN292 3.5 18.0 1.0 N B:ASP39 3.6 26.4 1.0 CG B:ASP38 3.6 24.8 1.0 CB B:SER78 3.6 28.4 1.0 S B:G4S504 4.0 35.7 1.0 N B:SER78 4.0 28.0 1.0 CA B:SER78 4.0 28.0 1.0 OD2 B:ASP39 4.0 25.9 1.0 CD2 B:HIS233 4.2 24.8 1.0 CA B:ASP39 4.2 25.8 1.0 C B:ASP38 4.2 26.6 1.0 CE B:LYS309 4.2 24.2 1.0 CB B:ASP39 4.3 24.8 1.0 OD2 B:ASP38 4.4 24.3 1.0 CA B:ASP38 4.4 25.6 1.0 OG B:SER78 4.4 30.5 1.0 NZ B:LYS132 4.4 27.9 1.0 NZ B:LYS309 4.5 25.9 1.0 O8 B:G4S504 4.5 35.6 1.0 CB B:ASP291 4.6 26.9 1.0 O7 B:G4S504 4.6 31.6 1.0 CB B:ASP38 4.6 25.1 1.0 NH2 B:ARG82 4.8 22.4 1.0 CB B:ASN292 4.8 18.8 1.0 NE2 B:HIS233 4.9 25.6 1.0 C B:PHE77 4.9 25.8 1.0 N B:ASN292 5.0 20.1 1.0 CD B:LYS309 5.0 24.2 1.0 O4 B:G4S504 5.0 34.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Ps I-Cgsb C78S in Complex with K-Carrapentaose


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 K-Carrapentaose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca501 b:49.7 occ:1.00 OD1 C:ASP39 2.3 36.1 1.0 O8 C:G4S505 2.4 35.0 1.0 OD1 C:ASP38 2.4 33.9 1.0 OD1 C:ASN292 2.6 30.0 1.0 OD2 C:ASP291 2.6 35.3 1.0 OD1 C:ASP291 3.0 35.0 1.0 CG C:ASP291 3.2 35.5 1.0 CG C:ASP39 3.4 34.0 1.0 CG C:ASN292 3.4 32.4 1.0 ND2 C:ASN292 3.5 30.4 1.0 CB C:SER78 3.6 29.9 1.0 CG C:ASP38 3.6 32.7 1.0 N C:ASP39 3.7 28.9 1.0 S C:G4S505 3.8 34.1 1.0 N C:SER78 4.0 30.6 1.0 OD2 C:ASP39 4.0 33.4 1.0 CA C:SER78 4.0 30.5 1.0 CD2 C:HIS233 4.1 31.4 1.0 CE C:LYS309 4.2 38.9 1.0 CA C:ASP39 4.3 31.6 1.0 C C:ASP38 4.3 31.1 1.0 O9 C:G4S505 4.3 33.2 1.0 CB C:ASP39 4.4 32.4 1.0 OD2 C:ASP38 4.4 34.0 1.0 OG C:SER78 4.4 30.3 1.0 O7 C:G4S505 4.4 32.4 1.0 NZ C:LYS132 4.4 31.5 1.0 CA C:ASP38 4.5 31.5 1.0 NZ C:LYS309 4.5 39.5 1.0 CB C:ASP38 4.7 31.8 1.0 CB C:ASP291 4.7 36.7 1.0 CB C:ASN292 4.8 33.0 1.0 NH2 C:ARG82 4.8 37.0 1.0 NE2 C:HIS233 4.9 30.8 1.0 O4 C:G4S505 4.9 34.2 1.0 C C:PHE77 4.9 29.6 1.0 CD C:LYS309 4.9 38.2 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