Calcium in PDB 5n5p: Crystal Structure of Ruminococcus Flavefaciens' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A

The structure of Crystal Structure of Ruminococcus Flavefaciens' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A, PDB code: 5n5p was solved by P.Bule, A.L.Carvalho, S.Najmudin, C.M.G.A.Fontes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.58 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	30.093, 142.898, 46.588, 90.00, 90.75, 90.00
R / Rfree (%)	18.2 / 21.4

The binding sites of Calcium atom in the Crystal Structure of Ruminococcus Flavefaciens' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A (pdb code 5n5p). 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' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A, PDB code: 5n5p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A


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' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:27.1 occ:1.00 O B:ASP659 2.3 27.7 1.0 OD1 B:ASP653 2.3 29.1 1.0 O B:HOH927 2.3 19.4 1.0 OD1 B:ASN655 2.3 29.6 1.0 OD1 B:ASP657 2.5 32.8 1.0 OD2 B:ASP664 2.5 27.6 1.0 OD1 B:ASP664 2.5 28.7 1.0 CG B:ASP664 2.8 28.1 1.0 CG B:ASP657 3.3 36.9 1.0 CG B:ASN655 3.4 29.9 1.0 C B:ASP659 3.4 27.4 1.0 CG B:ASP653 3.5 29.3 1.0 OD2 B:ASP657 3.7 31.3 1.0 ND2 B:ASN655 3.9 33.0 1.0 CA B:ASP653 4.1 29.0 1.0 N B:ASP657 4.2 32.3 1.0 N B:ASP659 4.3 30.8 1.0 CB B:ASP664 4.3 28.1 1.0 CB B:ASP653 4.3 29.2 1.0 CA B:ASP659 4.3 30.1 1.0 N B:VAL660 4.3 27.0 1.0 OD2 B:ASP653 4.4 29.8 1.0 N B:ASN655 4.4 30.5 1.0 CA B:VAL660 4.4 26.8 1.0 C B:ASP653 4.5 29.7 1.0 CB B:ASP657 4.5 34.0 1.0 CB B:ASN655 4.5 30.7 1.0 N B:VAL654 4.6 29.7 1.0 CB B:ASP659 4.6 35.4 1.0 N B:CYS656 4.6 31.0 1.0 OD1 B:ASN661 4.6 26.9 1.0 CA B:ASP657 4.7 35.5 1.0 N B:ASN661 4.8 26.4 1.0 CA B:ASN655 4.8 31.1 1.0 C B:ASN655 4.8 31.2 1.0 N B:GLY658 4.8 35.9 1.0 N B:ASP664 5.0 28.2 1.0 C B:ASP657 5.0 35.8 1.0 CA B:ASP664 5.0 28.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A


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' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:39.1 occ:1.00 OD1 B:ASP689 2.3 36.7 1.0 O B:PHE691 2.3 35.2 1.0 O B:ASP707 2.4 53.1 1.0 OD1 B:ASP712 2.6 33.4 1.0 OD2 B:ASP712 2.9 34.8 1.0 CG B:ASP712 3.1 33.6 1.0 CG B:ASP689 3.4 35.4 1.0 C B:PHE691 3.4 34.6 1.0 C B:ASP707 3.6 41.4 1.0 N B:PHE691 3.9 32.7 1.0 O B:ASN692 4.0 37.1 1.0 OD2 B:ASP689 4.1 36.5 1.0 CA B:PHE691 4.1 33.3 1.0 CB B:PHE691 4.3 35.0 1.0 O B:HOH909 4.3 32.4 1.0 CA B:ASP689 4.3 33.3 1.0 C B:ASN692 4.3 36.2 1.0 CB B:ASP689 4.4 34.5 1.0 CB B:ASP707 4.4 48.8 1.0 CA B:ASP707 4.5 46.1 1.0 N B:ASN692 4.5 35.1 1.0 N B:LEU708 4.6 38.8 1.0 C B:ASP689 4.6 32.8 1.0 N B:CYS690 4.6 32.1 1.0 CB B:ASP712 4.6 32.7 1.0 CA B:LEU708 4.7 39.0 1.0 OD2 B:ASP707 4.7 55.0 1.0 CA B:ASN692 4.8 36.3 1.0 CD2 B:PHE691 4.8 49.9 1.0 CB B:ASN692 4.8 37.5 1.0 CG B:ASP707 4.8 47.6 1.0 N B:ASP707 4.8 42.7 1.0 N B:PRO693 4.9 35.4 1.0 OG1 B:THR709 4.9 39.0 1.0 N B:THR709 4.9 36.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A


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' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca801 b:29.2 occ:1.00 O D:ASP659 2.2 33.4 1.0 OD1 D:ASP653 2.3 30.9 1.0 OD1 D:ASN655 2.3 32.3 1.0 O D:HOH914 2.3 25.5 1.0 OD1 D:ASP657 2.5 30.2 1.0 OD1 D:ASP664 2.5 29.6 1.0 OD2 D:ASP664 2.5 28.6 1.0 CG D:ASP664 2.8 29.0 1.0 CG D:ASP657 3.3 30.8 1.0 CG D:ASN655 3.4 34.4 1.0 CG D:ASP653 3.4 31.2 1.0 C D:ASP659 3.4 30.5 1.0 OD2 D:ASP657 3.8 30.8 1.0 ND2 D:ASN655 4.0 40.3 1.0 CA D:ASP653 4.1 29.7 1.0 N D:ASP657 4.1 31.6 1.0 N D:ASP659 4.3 34.8 1.0 CB D:ASP653 4.3 31.1 1.0 OD2 D:ASP653 4.3 42.7 1.0 CB D:ASP664 4.3 29.0 1.0 N D:ASN655 4.3 31.2 1.0 N D:VAL660 4.4 28.8 1.0 CA D:ASP659 4.4 34.2 1.0 CA D:VAL660 4.4 28.9 1.0 C D:ASP653 4.4 30.3 1.0 CB D:ASP657 4.5 31.7 1.0 CB D:ASN655 4.5 33.8 1.0 N D:CYS656 4.6 31.7 1.0 N D:VAL654 4.6 30.3 1.0 CB D:ASP659 4.6 34.9 1.0 CA D:ASP657 4.7 31.8 1.0 OD1 D:ASN661 4.7 28.5 1.0 CA D:ASN655 4.8 31.8 1.0 N D:ASN661 4.8 27.7 1.0 C D:ASN655 4.8 32.0 1.0 N D:GLY658 4.8 33.4 1.0 C D:ASP657 4.9 31.6 1.0 O D:ASP653 5.0 31.7 1.0 N D:ASP664 5.0 29.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Ruminococcus Flavefaciens' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A


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' Type III Complex Containing the Fifth Cohesin From Scaffoldin B and the Dockerin From Scaffoldin A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca802 b:47.0 occ:1.00 O D:PHE691 2.1 36.5 1.0 OD1 D:ASP689 2.2 38.2 1.0 OD1 D:ASP712 2.6 34.3 1.0 O D:ASP707 2.6 48.7 1.0 OD2 D:ASP712 3.0 35.8 1.0 CG D:ASP712 3.2 34.5 1.0 C D:PHE691 3.3 35.8 1.0 CG D:ASP689 3.4 36.3 1.0 C D:ASP707 3.8 42.8 1.0 N D:PHE691 3.8 33.6 1.0 O D:ASN692 3.9 38.6 1.0 CA D:PHE691 4.0 34.5 1.0 OD2 D:ASP689 4.1 37.4 1.0 C D:ASN692 4.2 37.7 1.0 CB D:PHE691 4.2 34.5 1.0 CA D:ASP689 4.3 34.0 1.0 N D:ASN692 4.4 37.5 1.0 O D:HOH906 4.4 35.3 1.0 CB D:ASP689 4.4 35.2 1.0 C D:ASP689 4.5 33.5 1.0 N D:CYS690 4.5 32.8 1.0 CB D:ASP707 4.5 46.6 1.0 CA D:ASN692 4.6 37.9 1.0 CB D:ASN692 4.7 40.4 1.0 CB D:ASP712 4.7 33.5 1.0 CA D:ASP707 4.7 46.4 1.0 N D:PRO693 4.7 36.7 1.0 CD2 D:PHE691 4.8 38.1 1.0 N D:LEU708 4.8 40.6 1.0 OD2 D:ASP707 4.8 49.5 1.0 CA D:LEU708 4.9 40.8 1.0 CG D:ASP707 4.9 51.3 1.0 N D:ASP707 4.9 41.5 1.0 CA D:PRO693 5.0 36.7 1.0 C D:CYS690 5.0 32.8 1.0 CG D:PHE691 5.0 35.6 1.0

P.Bule, V.M.R.Pires, V.D.Alves, A.L.Carvalho, J.A.M.Prates, L.M.A.Ferreira, S.P.Smith, H.J.Gilbert, I.Noach, E.A.Bayer, S.Najmudin, C.M.G.A.Fontes. Higher Order Scaffoldin Assembly in Ruminococcus Flavefaciens Cellulosome Is Coordinated By A Discrete Cohesin-Dockerin Interaction. Sci Rep V. 8 6987 2018.
ISSN: ESSN 2045-2322
PubMed: 29725056
DOI: 10.1038/S41598-018-25171-8