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

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

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

Protein crystallography data

The structure of 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Pugnac-6S, PDB code: 7wdu was solved by T.Kashima, C.Yamada, 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) 48.36 / 2.23
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.404, 58.947, 84.353, 90, 91.7, 90
R / Rfree (%) 21.8 / 23.8

Calcium Binding Sites:

The binding sites of Calcium atom in the 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Pugnac-6S (pdb code 7wdu). 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 Pugnac-6S, PDB code: 7wdu:

Calcium binding site 1 out of 1 in 7wdu

Go back to Calcium Binding Sites List in 7wdu
Calcium binding site 1 out of 1 in the 6-Sulfo-Beta-D-N-Acetylglucosaminidase From Bifidobacterium Bifidum in Complex with Pugnac-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 Pugnac-6S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:37.3
occ:1.00
 O A:SER94 2.2 36.7 1.0
O A:TRP188 2.4 32.0 1.0
O A:LEU71 2.4 33.8 1.0
OG A:SER94 2.4 36.0 1.0
O A:HOH1009 2.4 43.4 1.0
OE2 A:GLU189 2.6 29.8 1.0
OD1 A:ASP74 2.7 42.2 1.0
C A:SER94 3.2 37.4 1.0
CB A:SER94 3.4 38.8 1.0
CG A:ASP74 3.5 45.2 1.0
C A:TRP188 3.6 34.7 1.0
C A:LEU71 3.6 33.4 1.0
CD A:GLU189 3.6 33.8 1.0
OD2 A:ASP74 3.7 45.6 1.0
CA A:SER94 3.9 40.0 1.0
CG A:GLU189 4.0 36.3 1.0
N A:ARG95 4.2 38.5 1.0
CB A:GLN76 4.2 43.3 1.0
O A:GLN76 4.3 32.5 1.0
CA A:TRP188 4.4 32.5 1.0
N A:ALA72 4.4 35.3 1.0
CA A:ALA72 4.4 35.1 1.0
N A:GLU189 4.6 32.5 1.0
CA A:ARG95 4.6 37.3 1.0
CA A:LEU71 4.6 35.7 1.0
N A:GLN76 4.6 40.7 1.0
C A:ALA72 4.6 33.9 1.0
CA A:GLU189 4.7 33.5 1.0
OE1 A:GLU189 4.8 34.6 1.0
CG A:GLN76 4.8 48.2 1.0
O A:ALA72 4.9 32.5 1.0
N A:ASP74 4.9 34.0 1.0
CA A:GLN76 4.9 39.8 1.0
CB A:TRP188 4.9 34.6 1.0
CB A:LEU71 4.9 35.0 1.0
CB A:ASP74 4.9 41.8 1.0
CB A:GLU189 5.0 36.2 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 02:14:39 2025

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