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Sodium in PDB 2ber: Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid).

Enzymatic activity of Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid).

All present enzymatic activity of Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid).:
3.2.1.18;

Protein crystallography data

The structure of Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid)., PDB code: 2ber was solved by S.Newstead, J.N.Watson, A.J.Bennet, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.41 / 1.8
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.440, 49.535, 107.041, 90.00, 101.74, 90.00
R / Rfree (%) 14 / 19.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid). (pdb code 2ber). 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 Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid)., PDB code: 2ber:

Sodium binding site 1 out of 1 in 2ber

Go back to Sodium Binding Sites List in 2ber
Sodium binding site 1 out of 1 in the Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid).


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Y370G Active Site Mutant of the Sialidase From Micromonospora Viridifaciens in Complex with Beta-NEU5AC (Sialic Acid). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1649

b:9.1
occ:1.00
 O A:ASN533 2.3 14.3 1.0
O A:ASN528 2.3 10.3 1.0
O A:ALA639 2.4 10.3 1.0
OD1 A:ASP531 2.4 12.8 1.0
OG1 A:THR536 2.6 14.3 1.0
O A:THR536 2.6 11.4 1.0
CG A:ASP531 3.4 15.2 1.0
C A:ASN533 3.4 15.2 1.0
C A:THR536 3.4 12.8 1.0
C A:ASN528 3.5 9.8 1.0
C A:ALA639 3.5 10.3 1.0
OD2 A:ASP531 3.7 15.3 1.0
CB A:THR536 3.8 13.8 1.0
N A:ASN533 3.9 14.8 1.0
CA A:THR536 4.0 13.2 1.0
CA A:ASN533 4.0 13.7 1.0
N A:THR536 4.1 14.8 1.0
CB A:ASN533 4.1 14.2 1.0
CG A:GLU640 4.1 16.8 1.0
CA A:ALA639 4.3 10.1 1.0
N A:PHE537 4.4 11.3 1.0
N A:VAL529 4.4 9.9 1.0
CA A:VAL529 4.4 9.9 1.0
CA A:ASN528 4.4 9.0 1.0
N A:PRO534 4.5 13.7 1.0
CB A:ASN528 4.5 10.5 1.0
N A:GLU640 4.6 11.3 1.0
C A:VAL529 4.6 9.4 1.0
CB A:ASP531 4.7 12.9 1.0
O A:HOH2824 4.7 14.5 1.0
CA A:PRO534 4.7 14.1 1.0
N A:ASP531 4.7 12.3 1.0
CB A:ALA639 4.7 10.2 1.0
CA A:GLU640 4.8 12.3 1.0
CA A:PHE537 4.8 10.7 1.0
CG2 A:THR536 4.9 12.6 1.0
O A:VAL529 4.9 10.8 1.0
C A:PRO534 4.9 14.3 1.0

Reference:

S.Newstead, J.N.Watson, T.L.Knoll, A.J.Bennet, G.L.Taylor. Structure and Mechanism of Action of An Inverting Mutant Sialidase. Biochemistry V. 44 9117 2005.
ISSN: ISSN 0006-2960
PubMed: 15966735
DOI: 10.1021/BI050517T
Page generated: Sun Aug 17 10:10:30 2025

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