Zinc in PDB 3b8z: High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)

The structure of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2), PDB code: 3b8z was solved by H.-S.Shieh, J.M.Williams, 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)	26.53 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.057, 44.487, 76.380, 90.00, 90.07, 90.00
R / Rfree (%)	18.5 / 21.4

The structure of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Calcium	(Ca)	6 atoms

The binding sites of Zinc atom in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) (pdb code 3b8z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2), PDB code: 3b8z:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:10.9 occ:1.00 NE2 A:HIS410 2.1 9.2 1.0 O4 A:294801 2.1 23.5 1.0 NE2 A:HIS420 2.1 12.3 1.0 NE2 A:HIS414 2.1 9.7 1.0 O1 A:294801 2.2 16.2 1.0 C3 A:294801 2.8 22.5 1.0 N2 A:294801 2.9 22.0 1.0 CD2 A:HIS410 3.0 10.4 1.0 CE1 A:HIS414 3.0 8.7 1.0 CE1 A:HIS420 3.0 13.3 1.0 CE1 A:HIS410 3.1 8.0 1.0 CD2 A:HIS420 3.1 11.2 1.0 CD2 A:HIS414 3.1 9.5 1.0 ND1 A:HIS420 4.2 12.2 1.0 ND1 A:HIS410 4.2 9.8 1.0 ND1 A:HIS414 4.2 8.4 1.0 CG A:HIS410 4.2 8.6 1.0 CG A:HIS420 4.2 11.0 1.0 C5 A:294801 4.2 22.6 1.0 OE2 A:GLU411 4.2 12.2 1.0 CG A:HIS414 4.2 9.0 1.0 O A:HOH929 4.3 18.4 1.0 C15 A:294801 4.6 15.7 1.0 C14 A:294801 4.8 16.8 1.0 C10 A:294801 4.8 25.2 1.0 OE1 A:GLU411 4.8 12.7 1.0 CE A:MET439 4.8 8.3 1.0 CD A:GLU411 4.9 13.3 1.0 C16 A:294801 5.0 16.1 1.0 C9 A:294801 5.0 27.4 1.0

Zinc binding site 2 out of 2 in the High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn901 b:10.8 occ:1.00 O4 B:294801 2.0 22.8 1.0 NE2 B:HIS410 2.1 9.8 1.0 NE2 B:HIS414 2.1 9.4 1.0 NE2 B:HIS420 2.1 13.6 1.0 O1 B:294801 2.3 18.4 1.0 C3 B:294801 2.7 22.3 1.0 N2 B:294801 2.9 22.6 1.0 CE1 B:HIS420 3.0 14.9 1.0 CE1 B:HIS414 3.1 9.4 1.0 CD2 B:HIS410 3.1 10.3 1.0 CE1 B:HIS410 3.1 10.6 1.0 CD2 B:HIS414 3.1 9.7 1.0 CD2 B:HIS420 3.1 11.5 1.0 ND1 B:HIS420 4.2 13.1 1.0 ND1 B:HIS414 4.2 8.6 1.0 ND1 B:HIS410 4.2 9.6 1.0 C5 B:294801 4.2 22.0 1.0 CG B:HIS410 4.2 9.5 1.0 CG B:HIS414 4.2 9.2 1.0 CG B:HIS420 4.2 10.9 1.0 OE2 B:GLU411 4.3 11.3 1.0 O B:HOH932 4.4 17.8 1.0 C15 B:294801 4.6 13.6 1.0 C10 B:294801 4.7 24.3 1.0 C14 B:294801 4.7 15.7 1.0 CE B:MET439 4.8 9.1 1.0 OE1 B:GLU411 4.8 10.1 1.0 O B:HOH1079 4.9 34.3 1.0 O B:HOH1150 4.9 27.5 1.0 CD B:GLU411 4.9 10.3 1.0 C16 B:294801 4.9 14.0 1.0 C9 B:294801 4.9 26.8 1.0

H.S.Shieh, K.J.Mathis, J.M.Williams, R.L.Hills, J.F.Wiese, T.E.Benson, J.R.Kiefer, M.H.Marino, J.N.Carroll, J.W.Leone, A.M.Malfait, E.C.Arner, M.D.Tortorella, A.Tomasselli. High Resolution Crystal Structure of the Catalytic Domain of Adamts-5 (Aggrecanase-2). J.Biol.Chem. V. 283 1501 2008.
ISSN: ISSN 0021-9258
PubMed: 17991750
DOI: 10.1074/JBC.M705879200