Sodium in PDB 5mqr: Sialidase BT_1020

All present enzymatic activity of Sialidase BT_1020:
3.2.1.187;

The structure of Sialidase BT_1020, PDB code: 5mqr was solved by A.Basle, D.Ndeh, A.Rogowski, A.Cartmell, A.S.Luis, I.Venditto, A.Labourel, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	125.720, 316.998, 90.023, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.5

The structure of Sialidase BT_1020 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Sialidase BT_1020 (pdb code 5mqr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Sialidase BT_1020, PDB code: 5mqr:

Sodium binding site 1 out of 1 in the Sialidase BT_1020


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sialidase BT_1020 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1208 b:31.0 occ:1.00 O A:HOH1861 2.1 31.4 1.0 O A:HOH2035 2.3 35.7 1.0 O A:GLU495 2.5 23.5 1.0 O A:HOH1619 2.5 32.1 1.0 O A:GLN45 2.5 21.9 1.0 OD1 A:ASN496 2.5 27.4 1.0 C A:GLU495 3.5 24.9 1.0 CG A:ASN496 3.6 26.4 1.0 O A:HOH2113 3.7 51.6 1.0 C A:GLN45 3.7 21.7 1.0 CA A:ASN496 3.8 25.3 1.0 N A:ASN496 4.0 24.6 1.0 O A:HOH1375 4.0 32.7 1.0 N A:SER47 4.1 20.8 1.0 CA A:LEU46 4.2 21.0 1.0 O A:HOH2087 4.2 25.9 1.0 CB A:ASN496 4.3 26.6 1.0 O A:HOH1381 4.4 18.5 1.0 O A:HOH2156 4.4 45.3 1.0 N A:LEU46 4.4 21.8 1.0 O A:HOH1316 4.4 41.8 1.0 CB A:GLU495 4.5 29.1 1.0 C A:LEU46 4.5 21.2 1.0 CA A:GLU495 4.6 26.2 1.0 ND2 A:ASN496 4.7 27.2 1.0 CB A:GLN45 4.8 22.2 1.0 CG A:GLU495 4.8 32.6 1.0 CA A:GLN45 4.8 21.9 1.0 CB A:SER47 4.9 21.6 1.0

D.Ndeh, A.Rogowski, A.Cartmell, A.S.Luis, A.Basle, J.Gray, I.Venditto, J.Briggs, X.Zhang, A.Labourel, N.Terrapon, F.Buffetto, S.Nepogodiev, Y.Xiao, R.A.Field, Y.Zhu, M.A.O'neill, B.R.Urbanowicz, W.S.York, G.J.Davies, D.W.Abbott, M.C.Ralet, E.C.Martens, B.Henrissat, H.J.Gilbert. Complex Pectin Metabolism By Gut Bacteria Reveals Novel Catalytic Functions. Nature V. 544 65 2017.
ISSN: ISSN 0028-0836
PubMed: 28329766
DOI: 10.1038/NATURE21725