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Calcium in PDB 3ilr: Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product

Enzymatic activity of Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product

All present enzymatic activity of Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product:
4.2.2.7;

Protein crystallography data

The structure of Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product, PDB code: 3ilr was solved by M.L.Garron, M.Cygler, D.Shaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.81 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 75.736, 109.604, 43.858, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 20.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product (pdb code 3ilr). 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 Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product, PDB code: 3ilr:

Calcium binding site 1 out of 1 in 3ilr

Go back to Calcium Binding Sites List in 3ilr
Calcium binding site 1 out of 1 in the Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Heparinase I From Bacteroides Thetaiotaomicron in Complex with Tetrasaccharide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:10.9
occ:1.00
 O A:TRP248 2.3 10.7 1.0
OD1 A:ASP346 2.3 11.5 1.0
OE2 A:GLU222 2.4 12.3 1.0
O A:HOH386 2.4 12.4 1.0
O A:ASN345 2.4 10.5 1.0
O A:HOH388 2.5 10.8 1.0
OE1 A:GLU222 2.6 12.8 1.0
CD A:GLU222 2.8 10.9 1.0
C A:ASN345 3.4 10.4 1.0
C A:TRP248 3.4 10.8 1.0
CG A:ASP346 3.5 10.6 1.0
CA A:ASP346 3.8 10.9 1.0
NH2 A:ARG344 4.0 12.0 1.0
N A:ASP346 4.0 10.6 1.0
O A:LYS247 4.0 12.8 1.0
CB A:ASP346 4.2 9.6 1.0
CA A:TRP248 4.3 10.9 1.0
CG A:GLU222 4.3 9.6 1.0
N A:LEU249 4.4 11.2 1.0
CD2 A:LEU158 4.4 13.3 1.0
CA A:LEU249 4.4 11.5 1.0
N A:THR250 4.5 11.2 1.0
OD2 A:ASP346 4.5 11.4 1.0
CE3 A:TRP248 4.6 13.8 1.0
CA A:ASN345 4.6 10.4 1.0
O A:HOH389 4.6 11.9 1.0
OG1 A:THR250 4.7 11.8 1.0
O A:HOH410 4.7 14.4 1.0
CB A:ASN345 4.9 10.5 1.0
N A:ASN345 4.9 10.2 1.0
C A:LEU249 4.9 11.8 1.0
CD2 A:TRP248 5.0 12.9 1.0
CZ3 A:TRP248 5.0 15.8 1.0
CZ A:ARG344 5.0 10.8 1.0
C A:LYS247 5.0 11.5 1.0

Reference:

Y.H.Han, M.L.Garron, H.Y.Kim, W.S.Kim, Z.Zhang, K.S.Ryu, D.Shaya, Z.Xiao, C.Cheong, Y.S.Kim, R.J.Linhardt, Y.H.Jeon, M.Cygler. Structural Snapshots of Heparin Depolymerization By Heparin Lyase I. J.Biol.Chem. V. 284 34019 2009.
ISSN: ISSN 0021-9258
PubMed: 19801541
DOI: 10.1074/JBC.M109.025338
Page generated: Sat Dec 12 04:15:40 2020

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