Calcium in PDB 6byp: Structure of PL24 Family Polysaccharide Lyase-LOR107

The structure of Structure of PL24 Family Polysaccharide Lyase-LOR107, PDB code: 6byp was solved by T.S.Ulaganathan, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.07 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.551, 121.263, 123.811, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.2

The binding sites of Calcium atom in the Structure of PL24 Family Polysaccharide Lyase-LOR107 (pdb code 6byp). 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 PL24 Family Polysaccharide Lyase-LOR107, PDB code: 6byp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of PL24 Family Polysaccharide Lyase-LOR107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of PL24 Family Polysaccharide Lyase-LOR107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:34.4 occ:1.00 OD2 A:ASP212 2.4 39.1 1.0 O A:LYS224 2.4 38.2 1.0 O A:HOH743 2.4 33.7 1.0 O A:HOH782 2.4 34.4 1.0 OD2 A:ASP222 2.4 36.8 1.0 O A:HOH888 2.5 30.1 1.0 OD1 A:ASP222 2.6 36.2 1.0 CG A:ASP222 2.9 38.0 1.0 CG A:ASP212 3.4 41.4 1.0 C A:LYS224 3.6 32.7 1.0 CB A:ASP212 3.8 39.5 1.0 O A:HOH795 4.1 31.3 1.0 CB A:LYS224 4.1 35.5 1.0 CA A:LYS224 4.2 30.4 1.0 O A:ASP184 4.4 40.0 1.0 N A:LYS224 4.4 34.5 1.0 CB A:ASP222 4.4 34.9 1.0 OD1 A:ASP212 4.5 44.6 1.0 OE1 A:GLN218 4.6 66.9 1.0 O A:LEU216 4.6 41.4 1.0 N A:GLN218 4.6 40.2 1.0 N A:HIS225 4.6 32.4 1.0 CG A:GLN218 4.7 49.9 1.0 CA A:SER217 4.7 44.9 1.0 OD1 A:ASP185 4.7 35.6 1.0 CA A:HIS225 4.9 35.4 1.0 CD A:GLN218 4.9 61.7 1.0 O A:HOH979 5.0 45.7 1.0

Calcium binding site 2 out of 4 in the Structure of PL24 Family Polysaccharide Lyase-LOR107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of PL24 Family Polysaccharide Lyase-LOR107 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:34.9 occ:1.00 O A:PHE328 2.3 31.5 1.0 O A:ASN323 2.4 35.2 1.0 O A:HOH809 2.4 30.9 1.0 O A:HOH791 2.4 31.4 1.0 O A:HOH893 2.5 33.9 1.0 O A:HOH837 2.5 31.4 1.0 OD1 A:ASP326 2.5 38.5 1.0 C A:PHE328 3.5 33.2 1.0 C A:ASN323 3.6 34.4 1.0 CG A:ASP326 3.6 37.2 1.0 OD2 A:ASP326 4.0 39.9 1.0 CA A:ASN324 4.1 33.3 1.0 CA A:PHE328 4.3 29.0 1.0 N A:ASN324 4.3 28.5 1.0 CB A:PHE328 4.3 28.9 1.0 O A:SER321 4.3 30.2 1.0 N A:PHE328 4.3 30.5 1.0 OD1 A:ASN381 4.4 32.4 1.0 O A:LYS329 4.4 31.8 1.0 OD1 A:ASN324 4.4 33.6 1.0 O A:HOH804 4.4 29.2 1.0 O A:ASP326 4.5 33.5 1.0 C A:LYS329 4.5 30.0 1.0 N A:LYS329 4.5 30.7 1.0 C A:ASN324 4.6 37.4 1.0 N A:ASP326 4.6 36.4 1.0 CA A:LYS329 4.6 30.6 1.0 CA A:ASN323 4.6 34.7 1.0 O A:TYR330 4.7 30.4 1.0 CB A:ASN323 4.8 37.1 1.0 C A:ASP326 4.8 36.4 1.0 CB A:ASP326 4.9 42.7 1.0 N A:ASP325 4.9 36.3 1.0 N A:ASN323 5.0 34.7 1.0 O A:HOH848 5.0 30.2 1.0 CA A:ASP326 5.0 41.3 1.0

Calcium binding site 3 out of 4 in the Structure of PL24 Family Polysaccharide Lyase-LOR107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of PL24 Family Polysaccharide Lyase-LOR107 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:32.1 occ:1.00 O B:PHE328 2.3 27.4 1.0 O B:ASN323 2.3 30.3 1.0 O B:HOH760 2.4 27.8 1.0 O B:HOH731 2.4 31.6 1.0 O B:HOH839 2.5 26.1 1.0 OD1 B:ASP326 2.5 35.6 1.0 O B:HOH828 2.5 29.2 1.0 C B:PHE328 3.5 26.2 1.0 C B:ASN323 3.5 35.9 1.0 CG B:ASP326 3.6 33.8 1.0 OD2 B:ASP326 3.9 40.2 1.0 CA B:ASN324 4.1 31.8 1.0 N B:ASN324 4.3 34.7 1.0 O B:SER321 4.3 29.9 1.0 O B:LYS329 4.3 30.4 1.0 CA B:PHE328 4.3 25.9 1.0 CB B:PHE328 4.4 25.4 1.0 OD1 B:ASN381 4.4 33.0 1.0 O B:HOH807 4.4 25.9 1.0 N B:PHE328 4.4 25.2 1.0 C B:LYS329 4.5 30.7 1.0 OD1 B:ASN324 4.5 37.7 1.0 N B:LYS329 4.5 28.1 1.0 O B:ASP326 4.6 30.4 1.0 CA B:LYS329 4.6 27.5 1.0 CA B:ASN323 4.6 29.7 1.0 O B:TYR330 4.6 27.3 1.0 C B:ASN324 4.7 33.6 1.0 N B:ASP326 4.7 30.8 1.0 CB B:ASN323 4.8 32.5 1.0 CB B:ASP326 4.9 31.3 1.0 C B:ASP326 4.9 31.3 1.0 N B:ASN323 4.9 30.0 1.0 N B:ASP325 5.0 32.9 1.0 O B:HOH832 5.0 33.6 1.0

Calcium binding site 4 out of 4 in the Structure of PL24 Family Polysaccharide Lyase-LOR107


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of PL24 Family Polysaccharide Lyase-LOR107 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:47.1 occ:1.00 OD2 B:ASP222 2.3 64.7 1.0 OD2 B:ASP212 2.4 68.7 1.0 O B:LYS224 2.4 59.8 1.0 O B:HOH812 2.4 42.8 1.0 O B:HOH772 2.5 53.2 1.0 OD1 B:ASP222 2.6 63.5 1.0 O B:HOH941 2.7 43.6 1.0 CG B:ASP222 2.8 63.8 1.0 CG B:ASP212 3.3 66.9 1.0 C B:LYS224 3.5 53.4 1.0 CB B:ASP212 3.5 62.1 1.0 O B:HOH794 4.2 48.4 1.0 CB B:LYS224 4.2 60.9 1.0 CA B:LYS224 4.2 53.5 1.0 OE1 B:GLN218 4.3 81.7 1.0 CB B:ASP222 4.3 66.7 1.0 N B:LYS224 4.3 56.3 1.0 CG B:GLN218 4.5 85.0 1.0 OD1 B:ASP212 4.5 65.6 1.0 O B:LEU216 4.5 73.0 1.0 N B:HIS225 4.5 56.7 1.0 CD B:GLN218 4.6 85.9 1.0 N B:GLN218 4.6 72.3 1.0 CA B:SER217 4.7 70.8 1.0 O B:ASP184 4.7 60.1 1.0 CA B:HIS225 4.8 52.5 1.0 O B:HOH955 5.0 50.7 1.0

T.Ulaganathan, W.Helbert, M.Kopel, E.Banin, M.Cygler. Structure-Function Analyses of A PL24 Family Ulvan Lyase Reveal Key Features and Suggest Its Catalytic Mechanism. J. Biol. Chem. V. 293 4026 2018.
ISSN: ESSN 1083-351X
PubMed: 29382716
DOI: 10.1074/JBC.RA117.001642