Zinc in PDB 3hyg: 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: 3hyg 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)	26.41 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.818, 44.491, 76.655, 90.00, 90.26, 90.00
R / Rfree (%)	18.1 / 21

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 3hyg). 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: 3hyg:
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:9.2 occ:1.00 NE2 A:HIS420 2.1 8.8 1.0 NE2 A:HIS410 2.1 8.3 1.0 O26 A:099801 2.1 12.4 1.0 NE2 A:HIS414 2.1 8.1 1.0 O25 A:099801 2.1 13.0 1.0 C16 A:099801 2.7 12.9 1.0 N21 A:099801 2.9 12.9 1.0 CD2 A:HIS420 3.0 8.5 1.0 CD2 A:HIS410 3.0 8.8 1.0 CE1 A:HIS414 3.1 7.7 1.0 CD2 A:HIS414 3.1 8.3 1.0 CE1 A:HIS420 3.1 11.0 1.0 CE1 A:HIS410 3.1 7.8 1.0 O A:HOH5025 4.1 14.3 1.0 C11 A:099801 4.2 13.1 1.0 ND1 A:HIS420 4.2 9.7 1.0 CG A:HIS420 4.2 9.0 1.0 ND1 A:HIS410 4.2 7.7 1.0 CG A:HIS410 4.2 7.4 1.0 ND1 A:HIS414 4.2 7.6 1.0 CG A:HIS414 4.2 6.8 1.0 OE1 A:GLU411 4.4 10.7 1.0 C10 A:099801 4.5 12.3 1.0 C20 A:099801 4.6 12.4 1.0 O A:HOH5131 4.6 30.0 1.0 OE2 A:GLU411 4.8 12.2 1.0 CE A:MET439 4.8 8.4 1.0 O A:HOH5235 4.9 37.1 1.0 CD A:GLU411 5.0 11.5 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:7.3 occ:1.00 O26 B:099801 2.1 11.5 1.0 NE2 B:HIS414 2.1 6.8 1.0 NE2 B:HIS420 2.1 6.3 1.0 NE2 B:HIS410 2.1 6.0 1.0 O25 B:099801 2.2 10.3 1.0 C16 B:099801 2.8 8.9 1.0 N21 B:099801 2.9 11.9 1.0 CE1 B:HIS420 3.1 8.5 1.0 CE1 B:HIS414 3.1 7.2 1.0 CD2 B:HIS414 3.1 7.1 1.0 CD2 B:HIS410 3.1 6.1 1.0 CD2 B:HIS420 3.1 6.4 1.0 CE1 B:HIS410 3.1 5.9 1.0 O B:HOH6276 3.3 41.4 1.0 ND1 B:HIS420 4.2 8.4 1.0 ND1 B:HIS414 4.2 7.6 1.0 ND1 B:HIS410 4.2 6.4 1.0 C11 B:099801 4.2 10.0 1.0 CG B:HIS414 4.2 6.1 1.0 CG B:HIS410 4.2 6.1 1.0 CG B:HIS420 4.2 7.6 1.0 O B:HOH6023 4.3 12.2 1.0 OE1 B:GLU411 4.5 9.1 1.0 C20 B:099801 4.6 8.6 1.0 C10 B:099801 4.6 10.4 1.0 O B:HOH6085 4.7 20.0 1.0 CE B:MET439 4.8 7.9 1.0 OE2 B:GLU411 4.8 11.7 1.0 O B:HOH6221 4.8 34.4 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