Zinc in PDB 3hy7: Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat, PDB code: 3hy7 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)	26.31 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.606, 44.464, 76.349, 90.00, 89.81, 90.00
R / Rfree (%)	17.3 / 22.4

The structure of Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat 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 Marimastat (pdb code 3hy7). 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 Marimastat, PDB code: 3hy7:
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 Marimastat


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 Marimastat within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:13.8 occ:1.00 NE2 A:HIS410 2.1 11.8 1.0 NE2 A:HIS414 2.1 12.2 1.0 NE2 A:HIS420 2.1 14.8 1.0 O4 A:097801 2.1 17.7 1.0 O3 A:097801 2.3 13.5 1.0 C12 A:097801 2.8 14.8 1.0 CD2 A:HIS410 3.0 12.7 1.0 N3 A:097801 3.0 13.7 1.0 CD2 A:HIS414 3.0 11.7 1.0 CD2 A:HIS420 3.1 13.8 1.0 CE1 A:HIS410 3.1 14.2 1.0 CE1 A:HIS420 3.1 14.9 1.0 CE1 A:HIS414 3.1 11.7 1.0 ND1 A:HIS410 4.2 12.0 1.0 CG A:HIS410 4.2 11.9 1.0 ND1 A:HIS420 4.2 15.3 1.0 ND1 A:HIS414 4.2 12.1 1.0 CG A:HIS414 4.2 11.2 1.0 O A:HOH5007 4.2 14.5 1.0 CG A:HIS420 4.2 14.0 1.0 C13 A:097801 4.2 15.4 1.0 OE1 A:GLU411 4.5 14.1 1.0 O A:HOH5152 4.6 35.3 1.0 C14 A:097801 4.7 17.3 1.0 OE2 A:GLU411 4.7 14.7 1.0 C15 A:097801 4.7 16.1 1.0 CE A:MET439 4.8 12.1 1.0 O5 A:097801 4.8 16.6 1.0 CD A:GLU411 5.0 14.1 1.0 O A:HOH5051 5.0 24.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Adamts-5 in Complex with Marimastat


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 Marimastat within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:13.2 occ:1.00 NE2 B:HIS410 2.1 12.1 1.0 O4 B:097801 2.1 14.9 1.0 NE2 B:HIS414 2.1 11.1 1.0 NE2 B:HIS420 2.1 14.0 1.0 O3 B:097801 2.2 9.8 1.0 C12 B:097801 2.8 14.8 1.0 N3 B:097801 3.0 9.6 1.0 CD2 B:HIS410 3.0 12.0 1.0 CD2 B:HIS414 3.0 11.5 1.0 CE1 B:HIS410 3.1 13.8 1.0 CD2 B:HIS420 3.1 13.3 1.0 CE1 B:HIS414 3.1 11.0 1.0 CE1 B:HIS420 3.1 14.0 1.0 ND1 B:HIS410 4.2 12.4 1.0 CG B:HIS410 4.2 12.6 1.0 ND1 B:HIS414 4.2 10.9 1.0 O B:HOH5012 4.2 18.1 1.0 ND1 B:HIS420 4.2 13.4 1.0 CG B:HIS414 4.2 10.1 1.0 CG B:HIS420 4.2 14.0 1.0 C13 B:097801 4.2 15.5 1.0 OE1 B:GLU411 4.5 14.1 1.0 O B:HOH5259 4.6 42.1 1.0 C14 B:097801 4.7 16.7 1.0 C15 B:097801 4.7 16.1 1.0 CE B:MET439 4.8 13.0 1.0 OE2 B:GLU411 4.8 16.5 1.0 O5 B:097801 4.8 15.9 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