Calcium in PDB 3in9: Crystal Structure of Heparin Lyase I Complexed with Disaccharide Heparin

The structure of Crystal Structure of Heparin Lyase I Complexed with Disaccharide Heparin, PDB code: 3in9 was solved by Y.H.Han, K.S.Ryu, H.Y.Kim, Y.H.Jeon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.77 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.789, 63.531, 65.204, 90.00, 115.47, 90.00
R / Rfree (%)	18.3 / 21.7

The binding sites of Calcium atom in the Crystal Structure of Heparin Lyase I Complexed with Disaccharide Heparin (pdb code 3in9). 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 Crystal Structure of Heparin Lyase I Complexed with Disaccharide Heparin, PDB code: 3in9:

Calcium binding site 1 out of 1 in the Crystal Structure of Heparin Lyase I Complexed with Disaccharide Heparin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Heparin Lyase I Complexed with Disaccharide Heparin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca379 b:18.7 occ:1.00 OD1 A:ASP346 2.5 17.7 1.0 O A:TRP248 2.5 16.1 1.0 O A:ASN345 2.6 14.3 1.0 O A:HOH395 2.6 16.8 1.0 OE1 A:GLU222 2.7 19.9 1.0 OE2 A:GLU222 2.7 22.7 1.0 OD1 A:ASP155 2.8 25.3 1.0 CD A:GLU222 3.0 22.1 1.0 C A:ASN345 3.6 15.8 1.0 CG A:ASP346 3.7 18.2 1.0 C A:TRP248 3.7 18.9 1.0 CG A:ASP155 3.8 24.0 1.0 CA A:ASP346 3.9 16.7 1.0 N A:ASP346 4.1 15.9 1.0 NH2 A:ARG344 4.2 17.8 1.0 O A:LYS247 4.2 18.7 1.0 CB A:ASP346 4.3 16.4 1.0 CD2 A:LEU158 4.3 17.5 1.0 CE3 A:TRP248 4.4 27.3 1.0 CB A:ASP155 4.5 21.1 1.0 CA A:TRP248 4.5 18.6 1.0 CG A:GLU222 4.5 19.7 1.0 N A:THR250 4.6 17.8 1.0 N A:LEU249 4.6 17.7 1.0 OG1 A:THR250 4.6 18.4 1.0 CA A:LEU249 4.6 19.2 1.0 OD2 A:ASP346 4.7 18.2 1.0 CZ3 A:TRP248 4.7 31.6 1.0 N A:ASP155 4.7 18.5 1.0 OD2 A:ASP155 4.7 22.4 1.0 CA A:ASN345 4.7 15.0 1.0 CB A:ASN345 4.9 14.3 1.0 N A:ASN345 4.9 15.2 1.0

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