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Calcium in PDB 7wdt: 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S

Enzymatic activity of 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S

All present enzymatic activity of 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S:
3.2.1.52;

Protein crystallography data

The structure of 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S, PDB code: 7wdt was solved by C.Yamada, T.Kashima, S.Fushinobu, T.Katoh, T.Katayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.76 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.131, 57.879, 98.53, 90, 98.59, 90
R / Rfree (%) 17 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S (pdb code 7wdt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S, PDB code: 7wdt:

Calcium binding site 1 out of 1 in 7wdt

Go back to Calcium Binding Sites List in 7wdt
Calcium binding site 1 out of 1 in the 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Glcnac-6S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:17.2
occ:1.00
 O A:LEU71 2.3 15.4 1.0
OE2 A:GLU189 2.4 13.9 1.0
OG A:SER94 2.4 18.5 1.0
O A:TRP188 2.4 14.4 1.0
O A:SER94 2.4 18.3 1.0
O A:HOH1268 2.4 17.4 1.0
OD1 A:ASP74 2.5 19.6 1.0
C A:SER94 3.4 20.4 1.0
CB A:SER94 3.4 20.5 1.0
CG A:ASP74 3.4 18.9 1.0
CD A:GLU189 3.5 15.3 1.0
C A:LEU71 3.5 17.9 1.0
C A:TRP188 3.6 14.1 1.0
OD2 A:ASP74 3.7 22.6 1.0
CA A:SER94 4.0 20.0 1.0
CG A:GLU189 4.0 14.8 1.0
CB A:GLN76 4.3 22.6 1.0
CA A:ALA72 4.3 17.4 1.0
O A:GLN76 4.4 19.3 1.0
N A:ALA72 4.4 16.2 1.0
CA A:TRP188 4.4 15.5 1.0
N A:ARG95 4.4 18.8 1.0
CA A:LEU71 4.5 18.4 1.0
O A:HOH1331 4.5 19.8 1.0
N A:GLU189 4.6 14.6 1.0
C A:ALA72 4.6 16.0 1.0
N A:GLN76 4.6 19.7 1.0
OE1 A:GLU189 4.6 15.8 1.0
CA A:GLU189 4.7 14.0 1.0
CA A:ARG95 4.7 16.9 1.0
N A:ASP74 4.7 17.2 1.0
CB A:ASP74 4.8 18.4 1.0
CB A:LEU71 4.8 18.6 1.0
O A:ALA72 4.8 14.8 1.0
CB A:TRP188 4.9 15.9 1.0
CA A:GLN76 4.9 20.5 1.0
CB A:GLU189 4.9 13.5 1.0

Reference:

T.Katoh, C.Yamada, T.Kashima, K.A.Stubbs, A.Gotoh, S.Fushinobu, T.Katayama. A Unique Mucin O-Glycan Degrading Strategy of Bifidobacterium Bifidum Highlighted By Sulfoglycosidase with A Glcnac-6S-Binding Module To Be Published.
Page generated: Thu Jul 10 02:14:33 2025

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