Zinc in PDB 3hy9: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound, PDB code: 3hy9 was solved by H.-S.Shieh, J.M.Williams, N.Caspers, K.J.Mathis, M.D.Tortorella, A.Tomasselli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.02 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.692, 44.444, 76.458, 90.00, 90.19, 90.00
R / Rfree (%)	15.9 / 23.8

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound (pdb code 3hy9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound, PDB code: 3hy9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:14.3 occ:1.00 O4 A:098801 2.0 24.8 1.0 NE2 A:HIS410 2.0 9.7 1.0 O1 A:098801 2.1 23.7 1.0 NE2 A:HIS414 2.1 13.6 1.0 NE2 A:HIS420 2.1 15.4 1.0 C3 A:098801 2.7 24.2 1.0 N2 A:098801 2.9 22.2 1.0 CD2 A:HIS410 3.0 11.0 1.0 CD2 A:HIS420 3.0 15.1 1.0 CE1 A:HIS410 3.1 10.7 1.0 CD2 A:HIS414 3.1 13.6 1.0 CE1 A:HIS414 3.1 13.9 1.0 CE1 A:HIS420 3.2 14.2 1.0 C5 A:098801 4.1 25.4 1.0 O A:HOH5037 4.1 16.8 1.0 ND1 A:HIS410 4.2 9.5 1.0 CG A:HIS410 4.2 11.0 1.0 ND1 A:HIS414 4.2 12.4 1.0 CG A:HIS414 4.2 11.8 1.0 C12 A:098801 4.2 25.1 1.0 CG A:HIS420 4.2 14.4 1.0 ND1 A:HIS420 4.2 14.4 1.0 C11 A:098801 4.4 26.6 1.0 OE2 A:GLU411 4.5 13.8 1.0 OE1 A:GLU411 4.6 11.3 1.0 CE A:MET439 4.8 14.7 1.0 N6 A:098801 4.8 26.3 1.0 O A:HOH5171 4.8 36.9 1.0 CD A:GLU411 4.9 14.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with An Amino-2-Indanol Compound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:12.3 occ:1.00 O4 B:098801 1.9 17.6 1.0 NE2 B:HIS414 2.1 9.7 1.0 NE2 B:HIS420 2.1 12.9 1.0 NE2 B:HIS410 2.1 10.4 1.0 O1 B:098801 2.3 15.0 1.0 C3 B:098801 2.7 19.6 1.0 N2 B:098801 3.0 17.9 1.0 CD2 B:HIS410 3.0 8.0 1.0 CD2 B:HIS414 3.0 9.9 1.0 CD2 B:HIS420 3.0 10.1 1.0 CE1 B:HIS414 3.1 9.8 1.0 CE1 B:HIS420 3.2 10.3 1.0 CE1 B:HIS410 3.2 8.8 1.0 C5 B:098801 4.2 22.6 1.0 O B:HOH6021 4.2 13.7 1.0 CG B:HIS414 4.2 9.1 1.0 CG B:HIS410 4.2 9.7 1.0 ND1 B:HIS414 4.2 11.5 1.0 CG B:HIS420 4.2 11.6 1.0 OE2 B:GLU411 4.2 12.7 1.0 ND1 B:HIS420 4.2 10.8 1.0 ND1 B:HIS410 4.3 10.0 1.0 C12 B:098801 4.5 22.2 1.0 C11 B:098801 4.6 24.6 1.0 OE1 B:GLU411 4.7 10.1 1.0 CE B:MET439 4.8 10.7 1.0 CD B:GLU411 4.8 11.9 1.0 N6 B:098801 4.9 23.4 1.0

M.D.Tortorella, A.G.Tomasselli, K.J.Mathis, M.E.Schnute, S.S.Woodard, G.Munie, J.M.Williams, N.Caspers, A.J.Wittwer, A.M.Malfait, H.S.Shieh. Structural and Inhibition Analysis Reveals the Mechanism of Selectivity of A Series of Aggrecanase Inhibitors J.Biol.Chem. V. 284 24185 2009.
ISSN: ISSN 0021-9258
PubMed: 19586907
DOI: 10.1074/JBC.M109.029116