Calcium in PDB 6j66: Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase

All present enzymatic activity of Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase:
3.1.6.12;

The structure of Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase, PDB code: 6j66 was solved by L.Gu, F.Li, T.Su, S.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.92 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.426, 107.732, 87.569, 90.00, 104.04, 90.00
R / Rfree (%)	18.1 / 21.4

The binding sites of Calcium atom in the Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase (pdb code 6j66). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase, PDB code: 6j66:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca600 b:29.8 occ:1.00 OD2 A:ASP343 2.2 26.2 1.0 OG2 A:DDZ96 2.2 33.3 1.0 OD1 A:ASP56 2.2 30.0 1.0 NE2 A:HIS344 2.2 27.5 1.0 O A:HOH727 2.3 35.7 1.0 CG A:ASP56 2.8 32.4 1.0 OD2 A:ASP56 2.8 34.0 1.0 CD2 A:HIS344 3.0 27.9 1.0 CG A:ASP343 3.1 28.0 1.0 CB A:DDZ96 3.1 27.5 1.0 CE1 A:HIS344 3.2 26.1 1.0 OD1 A:ASP343 3.4 25.5 1.0 OG1 A:DDZ96 3.4 31.9 1.0 CA A:DDZ96 3.4 25.1 1.0 N A:DDZ96 3.7 24.5 1.0 CG A:HIS344 4.1 27.0 1.0 CD2 A:HIS263 4.2 31.5 1.0 ND1 A:HIS344 4.2 28.0 1.0 CB A:ASP56 4.2 28.8 1.0 NZ A:LYS158 4.4 33.0 1.0 N A:GLU57 4.4 22.0 1.0 CB A:ASP343 4.4 27.6 1.0 CA A:ASP56 4.7 27.6 1.0 C A:LEU95 4.7 26.1 1.0 NH2 A:ARG100 4.8 29.0 1.0 OE1 A:GLU57 4.8 30.6 1.0 NE2 A:HIS263 4.8 31.6 1.0 C A:ASP56 4.8 28.5 1.0 C A:DDZ96 4.9 23.8 1.0 CB A:GLU57 4.9 24.5 1.0 CA A:GLU57 5.0 21.7 1.0

Calcium binding site 2 out of 2 in the Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chondroitin Sulfate/Dermatan Sulfate Endolytic 4-O-Sulfatase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca600 b:27.1 occ:1.00 OD1 B:ASP56 2.2 30.1 1.0 OD2 B:ASP343 2.2 26.5 1.0 O B:HOH709 2.2 37.7 1.0 NE2 B:HIS344 2.3 30.9 1.0 OG2 B:DDZ96 2.3 33.1 1.0 CG B:ASP56 2.7 30.0 1.0 OD2 B:ASP56 2.8 31.9 1.0 CD2 B:HIS344 3.1 27.4 1.0 CG B:ASP343 3.1 28.7 1.0 CB B:DDZ96 3.2 30.3 1.0 CE1 B:HIS344 3.2 25.8 1.0 OG1 B:DDZ96 3.3 35.4 1.0 CA B:DDZ96 3.5 23.3 1.0 OD1 B:ASP343 3.5 24.2 1.0 N B:DDZ96 3.8 24.5 1.0 CD2 B:HIS263 4.1 34.0 1.0 CB B:ASP56 4.1 30.1 1.0 CG B:HIS344 4.2 24.1 1.0 ND1 B:HIS344 4.2 27.0 1.0 NZ B:LYS158 4.4 36.1 1.0 N B:GLU57 4.4 26.5 1.0 CB B:ASP343 4.4 25.7 1.0 CA B:ASP56 4.6 29.3 1.0 C B:LEU95 4.8 23.3 1.0 NE2 B:HIS263 4.8 34.2 1.0 OE2 B:GLU57 4.8 28.8 1.0 C B:ASP56 4.8 25.2 1.0 C B:DDZ96 4.9 22.1 1.0 CB B:GLU57 4.9 25.7 1.0 NZ B:LYS356 4.9 35.4 1.0 CA B:GLU57 5.0 26.4 1.0 CE B:LYS356 5.0 32.1 1.0 NH1 B:ARG100 5.0 28.7 1.0

S.Wang, T.Su, Q.Zhang, J.Guan, J.He, L.Gu, F.Li. Comparative Study of Two Chondroitin Sulfate/Dermatan Sulfate 4-O-Sulfatases with High Identity. Front Microbiol V. 10 1309 2019.
ISSN: ESSN 1664-302X
PubMed: 31244815
DOI: 10.3389/FMICB.2019.01309