Atomistry » Calcium » PDB 7wa2-7wwn » 7wdt
Atomistry »
  Calcium »
    PDB 7wa2-7wwn »
      7wdt »

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: Fri Jul 19 05:41:01 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy