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Sodium in PDB 5mqs: Sialidase BT_1020

Enzymatic activity of Sialidase BT_1020

All present enzymatic activity of Sialidase BT_1020:
3.2.1.187;

Protein crystallography data

The structure of Sialidase BT_1020, PDB code: 5mqs 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) 49.29 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.433, 318.194, 90.579, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26.2

Other elements in 5mqs:

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

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Sialidase BT_1020 (pdb code 5mqs). 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: 5mqs:

Sodium binding site 1 out of 1 in 5mqs

Go back to Sodium Binding Sites List in 5mqs
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:Na1202

b:20.6
occ:1.00
OD1 A:ASN496 2.3 28.2 1.0
O A:GLN45 2.6 23.3 1.0
O A:GLU495 3.0 28.5 1.0
CG A:ASN496 3.6 28.5 1.0
C A:GLN45 3.9 23.7 1.0
OE1 A:GLU495 4.0 28.9 1.0
C A:GLU495 4.0 27.7 1.0
CA A:ASN496 4.3 28.2 1.0
CB A:ASN496 4.5 28.5 1.0
N A:ASN496 4.5 27.9 1.0
CA A:LEU46 4.5 23.2 1.0
ND2 A:ASN496 4.5 28.7 1.0
N A:SER47 4.6 22.4 1.0
N A:LEU46 4.6 23.6 1.0
CB A:GLN45 4.9 23.8 1.0
CB A:GLU495 5.0 27.4 1.0

Reference:

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
Page generated: Tue Dec 15 11:19:06 2020

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