Sodium in PDB 5fu2: The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition

The structure of The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition, PDB code: 5fu2 was solved by A.Basle, A.S.Luis, I.Venditto, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.98 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.623, 47.272, 83.958, 90.00, 90.00, 90.00
R / Rfree (%)	15.799 / 19.976

The structure of The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition (pdb code 5fu2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition, PDB code: 5fu2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1516 b:12.9 occ:1.00 O B:HOH2092 3.0 27.8 1.0 O B:HOH2039 3.2 12.2 1.0 O B:HOH2040 3.2 15.8 1.0 NZ B:LYS455 3.3 17.6 1.0 CE B:LYS455 3.7 19.2 1.0 O B:HOH2045 4.1 23.6 1.0 CA B:CA1515 4.6 12.3 1.0 O B:HOH2090 4.7 26.3 1.0 O3 B:BMA1512 4.7 12.8 1.0

Sodium binding site 2 out of 3 in the The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1517 b:14.3 occ:1.00 OD1 B:ASP424 2.2 23.2 1.0 OD1 B:ASN423 2.3 27.1 1.0 O B:HOH2011 2.4 24.8 1.0 O B:HOH2009 2.4 24.9 1.0 CG B:ASP424 3.5 21.5 1.0 CG B:ASN423 3.6 23.9 1.0 O B:HOH2007 4.2 33.0 1.0 OD2 B:ASP424 4.2 21.5 1.0 CA B:ASP424 4.3 18.5 1.0 N B:ASP424 4.4 17.3 1.0 O B:ASN423 4.4 21.4 1.0 C B:ASN423 4.4 19.0 1.0 ND2 B:ASN423 4.4 29.0 1.0 CE1 B:HIS506 4.4 15.4 1.0 CB B:ASP424 4.5 19.6 1.0 OE2 B:GLU504 4.5 22.5 1.0 CB B:ASN423 4.5 21.8 1.0 O B:HOH2010 4.7 22.6 1.0 CD B:GLU504 4.9 18.9 1.0

Sodium binding site 3 out of 3 in the The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1518 b:23.7 occ:1.00 O B:HOH2074 2.2 36.5 1.0 O B:TYR500 2.3 17.2 1.0 O B:HOH2073 2.5 30.0 1.0 C B:TYR500 3.5 16.3 1.0 N B:TYR500 4.1 15.4 1.0 N B:LYS501 4.4 17.4 1.0 CA B:TYR500 4.5 15.2 1.0 CA B:LYS501 4.5 18.1 1.0 CB B:ASP499 4.6 26.2 1.0 CG B:LYS501 4.6 24.4 1.0 O B:HOH2060 4.6 33.1 1.0 O B:HOH2077 4.7 21.8 1.0 CD1 B:TYR500 4.7 16.9 1.0 CG B:TYR500 4.8 15.9 1.0 CE1 B:TYR500 4.9 17.7 1.0

I.Venditto, A.S.Luis, M.Rydahl, J.Schuckel, V.O.Fernandes, S.Vidal-Melgosa, P.Bule, A.Goyal, V.M.R.Pires, C.G.Dourado, L.M.A.Ferreira, P.M.Coutinho, B.Henrissat, J.P.Knox, A.Basle, S.Najmudin, H.J.Gilbert, W.G.T.Willats, C.M.G.A.Fontes. Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects An Expansion in Glycan Recognition. Proc.Natl.Acad.Sci.Usa V. 113 7136 2016.
ISSN: ISSN 0027-8424
PubMed: 27298375
DOI: 10.1073/PNAS.1601558113