Calcium in PDB 6byx: Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate

The structure of Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate, PDB code: 6byx was solved by T.Ulaganathan, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.89 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.050, 120.959, 127.221, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.5

The binding sites of Calcium atom in the Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate (pdb code 6byx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate, PDB code: 6byx:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:43.9 occ:0.92 OD2 A:ASP212 2.4 45.9 1.0 O A:HOH731 2.4 35.6 1.0 O A:LYS224 2.4 49.9 1.0 OD2 A:ASP222 2.5 51.8 1.0 O A:HOH796 2.6 42.3 1.0 OD1 A:ASP222 2.6 46.3 1.0 O A:HOH773 2.8 38.8 1.0 CG A:ASP222 2.9 56.6 1.0 CG A:ASP212 3.4 55.3 1.0 C A:LYS224 3.6 49.0 1.0 CB A:ASP212 3.7 54.7 1.0 O A:HOH726 3.9 42.5 1.0 CB A:LYS224 4.0 44.5 1.0 CA A:LYS224 4.2 46.0 1.0 O A:ASP184 4.3 53.8 1.0 N A:LYS224 4.4 46.8 1.0 OD1 A:ASP185 4.4 51.0 1.0 CB A:ASP222 4.4 60.6 1.0 OD1 A:ASP212 4.5 51.4 1.0 CA A:SER217 4.6 62.0 1.0 N A:GLN218 4.6 57.8 1.0 N A:HIS225 4.6 47.7 1.0 CG A:GLN218 4.6 56.8 1.0 OE1 A:GLN218 4.7 69.9 1.0 CD A:GLN218 4.9 65.7 1.0 CA A:HIS225 4.9 46.7 1.0 O A:LEU216 5.0 50.0 1.0

Calcium binding site 2 out of 4 in the Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:37.2 occ:1.00 O A:PHE328 2.3 37.2 1.0 O A:HOH816 2.3 39.8 1.0 O A:ASN323 2.4 34.6 1.0 O A:HOH719 2.4 37.2 1.0 O A:HOH760 2.5 35.2 1.0 OD1 A:ASP326 2.5 39.0 1.0 O A:HOH850 2.5 45.4 1.0 CG A:ASP326 3.4 39.0 1.0 C A:PHE328 3.4 36.5 1.0 C A:ASN323 3.5 38.8 1.0 OD2 A:ASP326 3.7 40.8 1.0 CA A:ASN324 4.0 34.0 1.0 N A:ASN324 4.2 33.0 1.0 CA A:PHE328 4.2 33.8 1.0 N A:PHE328 4.3 33.0 1.0 O A:LYS329 4.3 43.5 1.0 CB A:PHE328 4.3 24.9 1.0 OD1 A:ASN324 4.4 42.0 1.0 OD1 A:ASN381 4.4 39.9 1.0 O A:ASP326 4.4 38.4 1.0 C A:LYS329 4.5 36.0 1.0 O A:SER321 4.5 44.3 1.0 N A:LYS329 4.5 38.5 1.0 C A:ASN324 4.6 38.1 1.0 CA A:LYS329 4.6 37.1 1.0 O A:HOH737 4.6 33.4 1.0 CA A:ASN323 4.7 42.0 1.0 N A:ASP326 4.7 37.4 1.0 O A:TYR330 4.7 31.6 1.0 CB A:ASP326 4.7 36.5 1.0 C A:ASP326 4.8 35.1 1.0 O A:HOH764 4.8 31.3 1.0 N A:ASP325 4.9 36.5 1.0 CB A:ASN323 4.9 41.1 1.0 CA A:ASP326 5.0 33.6 1.0

Calcium binding site 3 out of 4 in the Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:38.2 occ:1.00 O B:PHE328 2.2 36.0 1.0 O B:HOH723 2.3 27.7 1.0 O B:ASN323 2.3 34.1 1.0 OD1 B:ASP326 2.5 41.5 1.0 O B:HOH814 2.5 31.9 1.0 O B:HOH798 2.5 34.5 1.0 O B:HOH738 2.6 39.2 1.0 CG B:ASP326 3.4 40.4 1.0 C B:PHE328 3.4 32.7 1.0 C B:ASN323 3.5 35.6 1.0 OD2 B:ASP326 3.7 40.0 1.0 CA B:ASN324 4.1 36.9 1.0 CA B:PHE328 4.2 31.4 1.0 N B:ASN324 4.2 32.4 1.0 CB B:PHE328 4.3 34.1 1.0 N B:PHE328 4.3 29.1 1.0 OD1 B:ASN381 4.3 38.8 1.0 O B:SER321 4.4 32.9 1.0 OD1 B:ASN324 4.4 43.7 1.0 N B:LYS329 4.5 31.5 1.0 O B:LYS329 4.5 36.0 1.0 C B:LYS329 4.5 38.2 1.0 O B:ASP326 4.6 39.4 1.0 O B:HOH752 4.6 27.8 1.0 CA B:ASN323 4.6 30.5 1.0 C B:ASN324 4.6 39.5 1.0 CA B:LYS329 4.6 33.9 1.0 N B:ASP326 4.7 36.6 1.0 CB B:ASP326 4.7 35.8 1.0 CB B:ASN323 4.7 28.3 1.0 O B:TYR330 4.8 33.2 1.0 C B:ASP326 4.8 36.5 1.0 N B:ASN323 4.9 34.8 1.0 N B:ASP325 4.9 36.9 1.0 O B:HOH807 5.0 37.6 1.0 CA B:ASP326 5.0 34.9 1.0

Calcium binding site 4 out of 4 in the Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex Structure of LOR107 Mutant (R259N) with Tetrasaccharide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:55.8 occ:1.00 OD2 B:ASP212 2.1 0.3 1.0 O B:LYS224 2.2 0.7 1.0 O B:HOH746 2.3 53.2 1.0 O B:HOH791 2.3 52.6 1.0 OD2 B:ASP222 2.4 0.7 1.0 OD1 B:ASP222 2.5 0.8 1.0 CG B:ASP222 2.7 0.1 1.0 CG B:ASP212 3.0 0.5 1.0 O B:HOH853 3.1 50.0 1.0 CB B:ASP212 3.3 99.4 1.0 C B:LYS224 3.3 90.7 1.0 OD1 B:ASP212 4.1 0.2 1.0 CA B:LYS224 4.2 90.5 1.0 CB B:ASP222 4.2 0.2 1.0 N B:HIS225 4.3 82.6 1.0 CB B:LYS224 4.3 90.7 1.0 N B:LYS224 4.3 90.0 1.0 O B:HOH854 4.3 51.9 1.0 O B:HOH884 4.4 62.6 1.0 CA B:HIS225 4.4 81.5 1.0 CA B:SER217 4.6 0.9 1.0 CA B:ASP212 4.8 0.7 1.0 N B:GLN218 4.9 0.7 1.0 C B:HIS225 5.0 78.0 1.0 O B:ASP184 5.0 87.0 1.0 O B:LEU216 5.0 0.7 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