Calcium in PDB 6d3u: Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48

The structure of Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d3u 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)	46.05 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.464, 102.664, 103.034, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22

The binding sites of Calcium atom in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 (pdb code 6d3u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48, PDB code: 6d3u:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48


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 Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:42.3 occ:1.00 O A:ALA84 2.2 40.8 1.0 OD1 A:ASN61 2.2 40.2 1.0 O A:SER81 2.3 41.5 1.0 OD1 A:ASN85 2.4 41.1 1.0 OD2 A:ASP79 2.4 38.4 1.0 OD1 A:ASP79 2.6 41.2 1.0 O A:GLY59 2.7 47.0 1.0 CG A:ASP79 2.9 42.1 1.0 CG A:ASN61 3.3 40.3 1.0 C A:ALA84 3.3 42.2 1.0 C A:SER81 3.5 46.6 1.0 CG A:ASN85 3.6 43.4 1.0 C A:GLY59 3.6 44.8 1.0 CA A:ASN85 3.8 43.2 1.0 N A:ASN85 3.9 40.7 1.0 CA A:GLY59 4.0 44.8 1.0 CB A:ASN61 4.1 40.0 1.0 ND2 A:ASN61 4.1 39.5 1.0 N A:ASN61 4.2 43.0 1.0 CB A:ASN85 4.3 44.1 1.0 CA A:CYS82 4.3 46.4 1.0 N A:SER81 4.3 39.3 1.0 N A:CYS82 4.4 43.7 1.0 N A:ALA84 4.4 43.4 1.0 CB A:ASP79 4.4 40.9 1.0 CA A:SER81 4.4 38.3 1.0 CA A:ALA84 4.5 41.8 1.0 CE1 A:HIS107 4.6 37.2 1.0 ND2 A:ASN85 4.6 45.8 1.0 CD1 A:ILE118 4.6 36.7 1.0 N A:THR60 4.7 43.7 1.0 C A:CYS82 4.7 49.5 1.0 CA A:ASN61 4.8 43.7 1.0 CB A:SER81 4.8 39.1 1.0 O A:HOH539 4.9 40.6 1.0 N A:TYR83 5.0 44.3 1.0 NE2 A:HIS107 5.0 45.0 1.0

Calcium binding site 2 out of 2 in the Complex Structure of Ulvan Lyase From Nonlaben Ulvanivorans- NLR48


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 Ulvan Lyase From Nonlaben Ulvanivorans- NLR48 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:44.9 occ:1.00 OD1 B:ASN61 2.2 44.4 1.0 O B:ALA84 2.3 40.0 1.0 O B:SER81 2.3 43.6 1.0 OD1 B:ASN85 2.4 47.8 1.0 OD2 B:ASP79 2.5 38.8 1.0 OD1 B:ASP79 2.6 39.2 1.0 O B:GLY59 2.7 45.6 1.0 CG B:ASP79 2.8 42.9 1.0 CG B:ASN61 3.2 47.7 1.0 C B:ALA84 3.3 45.5 1.0 C B:SER81 3.5 51.0 1.0 CG B:ASN85 3.6 47.3 1.0 C B:GLY59 3.6 43.9 1.0 CA B:ASN85 3.8 42.3 1.0 N B:ASN85 3.9 41.7 1.0 CB B:ASN61 4.0 45.6 1.0 CA B:GLY59 4.0 45.7 1.0 N B:ASN61 4.1 45.7 1.0 ND2 B:ASN61 4.2 41.6 1.0 CA B:CYS82 4.2 50.8 1.0 CB B:ASN85 4.3 44.1 1.0 N B:CYS82 4.3 43.7 1.0 CB B:ASP79 4.4 41.0 1.0 N B:SER81 4.4 46.9 1.0 N B:ALA84 4.5 43.5 1.0 CA B:SER81 4.5 42.9 1.0 CA B:ALA84 4.5 46.3 1.0 CE1 B:HIS107 4.5 44.6 1.0 ND2 B:ASN85 4.6 45.1 1.0 N B:THR60 4.7 42.6 1.0 C B:CYS82 4.7 56.0 1.0 CA B:ASN61 4.7 47.5 1.0 CD1 B:ILE118 4.8 35.1 1.0 CB B:SER81 5.0 45.6 1.0 O B:HOH554 5.0 44.9 1.0

T.Ulaganathan, E.Banin, W.Helbert, M.Cygler. Structural and Functional Characterization of PL28 Family Ulvan Lyase NLR48 Fromnonlabens Ulvanivorans. J. Biol. Chem. V. 293 11564 2018.
ISSN: ESSN 1083-351X
PubMed: 29875159
DOI: 10.1074/JBC.RA118.003659