Atomistry » Calcium » PDB 2v5d-2vjj » 2vc9
Atomistry »
  Calcium »
    PDB 2v5d-2vjj »
      2vc9 »

Calcium in PDB 2vc9: Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with 2-Acetamido-1,2-Dideoxynojirmycin

Enzymatic activity of Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with 2-Acetamido-1,2-Dideoxynojirmycin

All present enzymatic activity of Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with 2-Acetamido-1,2-Dideoxynojirmycin:
3.2.1.50;

Protein crystallography data

The structure of Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with 2-Acetamido-1,2-Dideoxynojirmycin, PDB code: 2vc9 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) 19.70 / 2.36
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 90.960, 90.960, 252.400, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 24.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with 2-Acetamido-1,2-Dideoxynojirmycin (pdb code 2vc9). 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 2-Acetamido-1,2-Dideoxynojirmycin, PDB code: 2vc9:

Calcium binding site 1 out of 1 in 2vc9

Go back to Calcium Binding Sites List in 2vc9
Calcium binding site 1 out of 1 in the Family 89 Glycoside Hydrolase From Clostridium Perfringens in Complex with 2-Acetamido-1,2-Dideoxynojirmycin


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 2-Acetamido-1,2-Dideoxynojirmycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1912

b:34.2
occ:1.00
 O A:LEU48 2.2 34.8 1.0
O A:ASP53 2.3 35.5 1.0
OD1 A:ASP51 2.4 33.0 1.0
O A:THR56 2.4 33.5 1.0
O A:ALA148 2.4 32.9 1.0
OE2 A:GLU149 2.5 34.0 1.0
OG1 A:THR56 2.7 33.6 1.0
C A:THR56 3.2 34.0 1.0
CG A:ASP51 3.4 32.3 1.0
C A:LEU48 3.4 34.7 1.0
C A:ASP53 3.4 35.2 1.0
CD A:GLU149 3.5 33.3 1.0
C A:ALA148 3.6 32.8 1.0
OD2 A:ASP51 3.8 31.9 1.0
CB A:THR56 3.8 34.1 1.0
CA A:THR56 3.9 34.1 1.0
CG A:GLU149 3.9 32.9 1.0
N A:ASP53 4.0 34.5 1.0
N A:THR56 4.1 34.7 1.0
CA A:ASP53 4.1 34.7 1.0
N A:TYR57 4.1 33.9 1.0
CB A:ASP53 4.2 34.5 1.0
CA A:LEU48 4.3 34.6 1.0
N A:ASP51 4.4 32.8 1.0
N A:ALA49 4.4 34.6 1.0
CA A:ALA148 4.4 32.9 1.0
CA A:TYR57 4.4 33.6 1.0
CA A:ALA49 4.5 34.4 1.0
N A:LEU54 4.5 35.5 1.0
C A:ALA49 4.5 34.1 1.0
N A:GLU149 4.6 32.9 1.0
OE1 A:GLU149 4.6 30.3 1.0
CB A:LEU48 4.7 34.5 1.0
CB A:ASP51 4.7 32.2 1.0
N A:ILE50 4.7 33.7 1.0
CA A:GLU149 4.8 33.1 1.0
CA A:LEU54 4.8 35.9 1.0
CA A:ASP51 4.9 32.8 1.0
CB A:GLU149 4.9 33.3 1.0
O A:ALA49 5.0 34.1 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 08:33:04 2025

Last articles

Na in 7A74
Na in 7A70
Na in 7A56
Na in 7A3K
Na in 7A68
Na in 7A3I
Na in 7A5Z
Na in 7A2N
Na in 7A2K
Na in 7A36
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy