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Calcium in PDB 2vca: Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine

Enzymatic activity of Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine

All present enzymatic activity of Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine:
3.2.1.50;

Protein crystallography data

The structure of Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine, PDB code: 2vca was solved by E.Ficko-Blean, K.A.Stubbs, O.Berg, D.J.Vocadlo, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.05
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 90.773, 90.773, 252.779, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 23

Calcium Binding Sites:

The binding sites of Calcium atom in the Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine (pdb code 2vca). 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 Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine, PDB code: 2vca:

Calcium binding site 1 out of 1 in 2vca

Go back to Calcium Binding Sites List in 2vca
Calcium binding site 1 out of 1 in the Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with Beta-N-Acetyl-D-Glucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1917

b:27.8
occ:1.00
 O A:LEU48 2.3 28.3 1.0
O A:ASP53 2.3 30.8 1.0
OE2 A:GLU149 2.3 27.4 1.0
OD1 A:ASP51 2.4 30.6 1.0
O A:ALA148 2.4 28.2 1.0
O A:THR56 2.4 28.1 1.0
OG1 A:THR56 2.8 28.3 1.0
C A:THR56 3.3 28.6 1.0
CD A:GLU149 3.4 27.2 1.0
C A:ASP53 3.4 30.6 1.0
CG A:ASP51 3.4 30.0 1.0
C A:LEU48 3.5 28.5 1.0
C A:ALA148 3.6 28.1 1.0
CG A:GLU149 3.8 28.0 1.0
OD2 A:ASP51 3.8 29.9 1.0
CB A:THR56 3.9 28.6 1.0
CA A:THR56 3.9 28.9 1.0
N A:ASP53 4.0 30.1 1.0
N A:THR56 4.1 29.8 1.0
CA A:ASP53 4.1 30.3 1.0
N A:TYR57 4.2 28.5 1.0
CB A:ASP53 4.3 30.1 1.0
CA A:LEU48 4.3 28.6 1.0
CA A:ALA148 4.4 28.1 1.0
N A:ALA49 4.4 28.5 1.0
N A:ASP51 4.4 29.3 1.0
N A:LEU54 4.5 30.7 1.0
C A:ALA49 4.5 28.8 1.0
CA A:ALA49 4.5 28.9 1.0
OE1 A:GLU149 4.5 26.4 1.0
N A:GLU149 4.5 28.0 1.0
CA A:TYR57 4.6 28.4 1.0
CB A:ASP51 4.7 29.2 1.0
CA A:GLU149 4.7 28.1 1.0
CB A:LEU48 4.7 28.6 1.0
O A:ALA49 4.7 28.8 1.0
CA A:LEU54 4.7 31.1 1.0
N A:ILE50 4.8 28.9 1.0
CB A:GLU149 4.8 28.0 1.0
N A:GLY52 4.9 29.5 1.0
C A:LEU54 4.9 31.3 1.0
CA A:ASP51 4.9 29.5 1.0

Reference:

E.Ficko-Blean, K.A.Stubbs, O.Nemirovsky, D.J.Vocadlo, A.B.Boraston. Structural and Mechanistic Insight Into the Basis of Mucopolysaccharidosis Iiib. Proc.Natl.Acad.Sci.Usa V. 105 6560 2008.
ISSN: ISSN 0027-8424
PubMed: 18443291
DOI: 10.1073/PNAS.0711491105
Page generated: Tue Jul 8 08:33:19 2025

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