Calcium in PDB 5lxv: Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein

The structure of Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein, PDB code: 5lxv was solved by S.Najmudin, P.Bule, C.M.G.A.Fontes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.590, 66.730, 109.600, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26

The binding sites of Calcium atom in the Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein (pdb code 5lxv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein, PDB code: 5lxv:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein


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 Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:34.1 occ:1.00 O B:HOH1108 2.2 27.9 1.0 O B:GLU898 2.3 45.5 1.0 OD1 B:ASP892 2.4 46.3 1.0 OD1 B:ASP894 2.4 46.4 1.0 OD1 B:ASP896 2.4 46.8 1.0 OD2 B:ASP903 2.6 36.6 1.0 OD1 B:ASP903 2.7 37.8 1.0 CG B:ASP903 3.0 36.3 1.0 CG B:ASP896 3.3 49.0 1.0 C B:GLU898 3.4 46.1 1.0 CG B:ASP894 3.4 45.5 1.0 CG B:ASP892 3.5 47.2 1.0 OD2 B:ASP896 3.7 47.9 1.0 OD2 B:ASP894 3.7 44.1 1.0 N B:GLU898 4.0 51.8 1.0 N B:ASP896 4.1 50.8 1.0 CA B:GLU898 4.1 50.3 1.0 CA B:ASP892 4.2 42.2 1.0 OD2 B:ASP892 4.3 50.7 1.0 CB B:ASP892 4.4 44.7 1.0 N B:GLY895 4.4 47.2 1.0 N B:VAL899 4.4 43.1 1.0 CB B:GLU898 4.4 52.4 1.0 CB B:ASP896 4.4 52.4 1.0 OD1 B:ASP900 4.5 36.8 1.0 CB B:ASP903 4.5 34.3 1.0 N B:ASP894 4.5 43.9 1.0 CA B:VAL899 4.6 39.3 1.0 C B:ASP892 4.6 42.4 1.0 CA B:ASP896 4.6 53.5 1.0 N B:LEU893 4.7 41.0 1.0 N B:GLY897 4.7 53.4 1.0 CB B:ASP894 4.7 46.1 1.0 CG B:ASP900 4.9 37.5 1.0 C B:ASP896 4.9 54.3 1.0 OD2 B:ASP900 4.9 40.1 1.0 N B:ASP900 4.9 35.3 1.0 CA B:ASP894 5.0 45.9 1.0 C B:ASP894 5.0 48.2 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein


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 Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:30.0 occ:1.00 O B:VAL929 2.2 31.8 1.0 OD1 B:ASN925 2.2 33.1 1.0 OD1 B:ASP923 2.3 34.7 1.0 O B:HOH1109 2.3 43.6 1.0 OD2 B:ASP934 2.4 30.7 1.0 OD1 B:ASP927 2.5 33.9 1.0 OD1 B:ASP934 2.8 31.0 1.0 CG B:ASP934 3.0 29.9 1.0 CG B:ASN925 3.3 33.3 1.0 C B:VAL929 3.4 32.9 1.0 CG B:ASP923 3.5 35.4 1.0 CG B:ASP927 3.5 34.5 1.0 ND2 B:ASN925 3.8 33.4 1.0 OD2 B:ASP927 4.0 34.0 1.0 N B:VAL929 4.2 35.3 1.0 CG2 B:VAL929 4.2 34.6 1.0 CA B:ASP923 4.2 33.9 1.0 OD2 B:ASP923 4.3 36.8 1.0 N B:ASP927 4.3 35.7 1.0 CA B:VAL929 4.3 34.8 1.0 N B:ILE930 4.4 32.8 1.0 N B:ASN925 4.4 32.8 1.0 CB B:ASP923 4.4 35.2 1.0 CA B:ILE930 4.4 32.2 1.0 CB B:ASP934 4.5 27.8 1.0 OD1 B:ASP931 4.5 31.2 1.0 N B:CYS926 4.5 35.1 1.0 C B:ASP923 4.6 33.4 1.0 N B:LEU924 4.6 32.3 1.0 CB B:ASN925 4.6 33.5 1.0 CB B:ASP927 4.7 36.2 1.0 N B:ASP931 4.8 30.6 1.0 CA B:ASN925 4.8 34.0 1.0 C B:ASN925 4.8 35.2 1.0 CB B:VAL929 4.8 35.2 1.0 CA B:ASP927 4.9 36.8 1.0 N B:GLY928 4.9 36.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein


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 Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:28.2 occ:1.00 O D:GLU898 2.3 34.4 1.0 OD1 D:ASP892 2.4 35.8 1.0 OD1 D:ASP894 2.4 32.1 1.0 O D:HOH1109 2.4 25.6 1.0 OD2 D:ASP903 2.5 27.2 1.0 OD1 D:ASP896 2.5 35.1 1.0 OD1 D:ASP903 2.6 28.4 1.0 CG D:ASP903 2.9 26.6 1.0 CG D:ASP896 3.4 36.4 1.0 CG D:ASP894 3.4 32.4 1.0 C D:GLU898 3.4 34.3 1.0 CG D:ASP892 3.5 35.8 1.0 OD2 D:ASP894 3.7 32.6 1.0 OD2 D:ASP896 3.8 35.9 1.0 N D:GLU898 4.1 39.0 1.0 N D:ASP896 4.1 37.9 1.0 CA D:ASP892 4.2 31.8 1.0 CA D:GLU898 4.2 37.6 1.0 OD2 D:ASP892 4.3 38.1 1.0 CB D:ASP892 4.4 33.9 1.0 N D:VAL899 4.4 31.3 1.0 N D:GLY895 4.4 34.9 1.0 CB D:ASP903 4.4 24.9 1.0 CB D:GLU898 4.5 39.0 1.0 OD1 D:ASP900 4.5 27.5 1.0 N D:ASP894 4.5 31.6 1.0 CB D:ASP896 4.5 39.3 1.0 CA D:VAL899 4.6 29.0 1.0 C D:ASP892 4.6 32.3 1.0 N D:LEU893 4.6 30.7 1.0 CB D:ASP894 4.7 33.5 1.0 CA D:ASP896 4.7 39.9 1.0 N D:GLY897 4.8 40.7 1.0 N D:ASP900 4.9 26.0 1.0 CG D:ASP900 4.9 27.2 1.0 OD2 D:ASP900 4.9 28.3 1.0 CA D:ASP894 4.9 33.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Ruminococcus Flavefaciens Scaffoldin C Cohesin in Complex with A Dockerin From An Uncharacterized Cbm-Containing Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1002 b:31.8 occ:1.00 O D:HOH1106 2.2 25.3 1.0 OD1 D:ASN925 2.2 37.9 1.0 O D:VAL929 2.3 38.0 1.0 OD1 D:ASP923 2.4 36.4 1.0 OD2 D:ASP934 2.4 33.9 1.0 OD1 D:ASP927 2.5 38.5 1.0 OD1 D:ASP934 2.9 33.7 1.0 CG D:ASP934 3.0 33.7 1.0 CG D:ASN925 3.3 38.6 1.0 CG D:ASP927 3.4 40.7 1.0 C D:VAL929 3.5 38.3 1.0 CG D:ASP923 3.6 37.7 1.0 ND2 D:ASN925 3.8 39.3 1.0 OD2 D:ASP927 3.9 40.2 1.0 CG2 D:VAL929 4.1 42.1 1.0 N D:VAL929 4.2 40.9 1.0 N D:ASP927 4.3 42.0 1.0 CA D:VAL929 4.3 40.3 1.0 CA D:ASP923 4.4 35.6 1.0 OD2 D:ASP923 4.4 39.0 1.0 N D:ILE930 4.4 38.0 1.0 N D:ASN925 4.4 36.6 1.0 OD1 D:ASP931 4.4 35.5 1.0 CA D:ILE930 4.5 35.9 1.0 CB D:ASP934 4.5 31.6 1.0 CB D:ASP923 4.5 37.0 1.0 N D:CYS926 4.6 39.6 1.0 CB D:ASN925 4.6 38.9 1.0 CB D:ASP927 4.6 43.3 1.0 N D:LEU924 4.7 34.5 1.0 C D:ASP923 4.7 35.7 1.0 N D:ASP931 4.8 35.6 1.0 CB D:VAL929 4.8 41.6 1.0 CA D:ASN925 4.8 38.6 1.0 C D:ASN925 4.8 40.2 1.0 CA D:ASP927 4.9 43.7 1.0 N D:GLY928 4.9 42.6 1.0

P.Bule, V.D.Alves, A.Leitao, L.M.Ferreira, E.A.Bayer, S.P.Smith, H.J.Gilbert, S.Najmudin, C.M.Fontes. Single Binding Mode Integration of Hemicellulose-Degrading Enzymes Via Adaptor Scaffoldins in Ruminococcus Flavefaciens Cellulosome. J. Biol. Chem. V. 291 26658 2016.
ISSN: ESSN 1083-351X
PubMed: 27875311
DOI: 10.1074/JBC.M116.761643