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Calcium in PDB 2vyo: Chitin Deacetylase Family Member From Encephalitozoon Cuniculi

Enzymatic activity of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi

All present enzymatic activity of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi:
3.5.1.41;

Protein crystallography data

The structure of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi, PDB code: 2vyo was solved by J.E.Urch, R.Hurtado-Guerrero, C.Texier, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.975, 81.916, 39.201, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 21.5

Other elements in 2vyo:

The structure of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Chitin Deacetylase Family Member From Encephalitozoon Cuniculi (pdb code 2vyo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Chitin Deacetylase Family Member From Encephalitozoon Cuniculi, PDB code: 2vyo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2vyo

Go back to Calcium Binding Sites List in 2vyo
Calcium binding site 1 out of 4 in the Chitin Deacetylase Family Member From Encephalitozoon Cuniculi


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1221

b:18.2
occ:1.00
O A:LYS176 2.3 17.9 1.0
O A:HOH2007 2.3 23.0 1.0
OG A:SER25 2.4 16.1 1.0
O A:HOH2105 2.5 20.4 1.0
CB A:SER25 3.5 15.6 1.0
C A:LYS176 3.5 16.5 1.0
CA A:LYS176 4.3 17.5 1.0
OD1 A:ASN24 4.4 22.9 1.0
O A:HOH2106 4.5 24.0 1.0
N A:HIS177 4.6 16.0 1.0
CB A:LYS176 4.7 18.8 1.0
CA A:SER25 4.7 15.4 1.0
CA A:HIS177 4.8 16.2 1.0
N A:SER25 4.8 16.7 1.0

Calcium binding site 2 out of 4 in 2vyo

Go back to Calcium Binding Sites List in 2vyo
Calcium binding site 2 out of 4 in the Chitin Deacetylase Family Member From Encephalitozoon Cuniculi


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1222

b:19.1
occ:0.75
O A:ACT1226 2.4 25.1 1.0
OD2 A:ASP49 2.4 21.8 1.0
O A:HOH2046 2.4 24.4 1.0
CG A:ASP49 3.3 21.7 1.0
C A:ACT1226 3.5 25.4 1.0
OD1 A:ASP49 3.6 23.4 1.0
CL A:CL1227 4.0 39.9 1.0
CH3 A:ACT1226 4.1 25.3 1.0
CA A:CA1225 4.2 19.1 0.8
O A:HOH2021 4.3 25.5 1.0
OXT A:ACT1226 4.5 25.2 1.0
OE2 A:GLU79 4.6 24.0 1.0
CB A:ASP49 4.7 19.6 1.0
CD A:GLU79 4.8 20.1 1.0

Calcium binding site 3 out of 4 in 2vyo

Go back to Calcium Binding Sites List in 2vyo
Calcium binding site 3 out of 4 in the Chitin Deacetylase Family Member From Encephalitozoon Cuniculi


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1225

b:19.1
occ:0.75
CL A:CL1227 2.3 39.9 1.0
OD1 A:ASP49 2.4 23.4 1.0
O A:HOH2048 2.4 26.6 1.0
O A:HOH2152 2.5 27.9 1.0
OXT A:ACT1226 2.5 25.2 1.0
O A:ACT1226 2.6 25.1 1.0
O A:HOH2023 2.7 24.1 1.0
C A:ACT1226 3.0 25.4 1.0
CG A:ASP49 3.4 21.7 1.0
O A:HOH2022 3.8 27.5 1.0
OD2 A:ASP49 4.0 21.8 1.0
O A:HOH2026 4.1 27.2 1.0
CA A:CA1222 4.2 19.1 0.8
CH3 A:ACT1226 4.5 25.3 1.0
CB A:ASP49 4.5 19.6 1.0
O A:GLU79 4.6 18.6 1.0
CA A:ASP49 4.6 19.9 1.0
O A:ASP49 4.7 21.0 1.0
O A:HOH2153 4.8 27.7 1.0
NZ A:LYS54 5.0 30.9 1.0

Calcium binding site 4 out of 4 in 2vyo

Go back to Calcium Binding Sites List in 2vyo
Calcium binding site 4 out of 4 in the Chitin Deacetylase Family Member From Encephalitozoon Cuniculi


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Chitin Deacetylase Family Member From Encephalitozoon Cuniculi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1228

b:18.4
occ:0.50
OD1 A:ASP101 2.1 36.8 1.0
O A:HOH2063 2.2 31.2 1.0
O A:HOH2064 2.3 34.1 1.0
O A:HOH2061 2.6 42.4 1.0
CG A:ASP101 3.2 35.6 1.0
OD2 A:ASP101 3.9 39.1 1.0
CB A:ASP101 4.1 33.3 1.0
CA A:ASP101 4.2 32.5 1.0
OD1 A:ASN105 4.5 31.4 1.0
OE1 A:GLU104 4.5 20.5 1.0
CD A:GLU104 4.9 17.2 1.0

Reference:

J.E.Urch, R.Hurtado-Guerrero, D.Brosson, Z.Liu, V.G.H.Eijsink, C.Texier, D.M.F.Van Aalten. Structural and Functional Characterization of A Putative Polysaccharide Deacetylase of the Human Parasite Encephalitozoon Cuniculi. Protein Sci. V. 18 1197 2009.
ISSN: ISSN 0961-8368
PubMed: 19472335
DOI: 10.1002/PRO.128
Page generated: Wed Oct 28 07:58:34 2020

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