Zinc in PDB 6bh8: Crystal Structure of ZMPSTE24 in Complex with Phosphoramidon

All present enzymatic activity of Crystal Structure of ZMPSTE24 in Complex with Phosphoramidon:
3.4.24.84;

The structure of Crystal Structure of ZMPSTE24 in Complex with Phosphoramidon, PDB code: 6bh8 was solved by B.R.Goblirsch, B.T.Arachea, M.C.Wiener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.03 / 3.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.329, 84.661, 132.017, 90.00, 96.26, 90.00
R / Rfree (%)	33.8 / 37.1

The binding sites of Zinc atom in the Crystal Structure of ZMPSTE24 in Complex with Phosphoramidon (pdb code 6bh8). 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 ZMPSTE24 in Complex with Phosphoramidon, PDB code: 6bh8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of ZMPSTE24 in Complex with Phosphoramidon


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 ZMPSTE24 in Complex with Phosphoramidon within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:0.1 occ:1.00 OE2 A:GLU415 1.8 0.9 1.0 O1P A:RDF502 1.8 0.9 1.0 NE2 A:HIS339 2.0 0.7 1.0 NE2 A:HIS335 2.0 97.9 1.0 O2P A:RDF502 2.1 0.5 1.0 P A:RDF502 2.4 49.2 1.0 CD A:GLU415 2.7 0.5 1.0 OE1 A:GLU415 2.9 0.1 1.0 CE1 A:HIS339 2.9 0.7 1.0 CE1 A:HIS335 3.0 90.1 1.0 HE1 A:HIS339 3.1 0.5 1.0 CD2 A:HIS335 3.1 0.1 1.0 CD2 A:HIS339 3.1 0.5 1.0 HE1 A:HIS335 3.2 0.2 1.0 HD2 A:HIS335 3.3 0.1 1.0 HD2 A:HIS339 3.3 0.7 1.0 O1 A:RDF502 3.6 0.4 1.0 N A:RDF502 3.6 0.9 1.0 CA A:RDF502 3.9 0.9 1.0 HA A:GLU415 3.9 82.6 1.0 CG A:GLU415 4.0 76.8 1.0 ND1 A:HIS339 4.0 0.1 1.0 HB3 A:ALA418 4.0 0.6 1.0 ND1 A:HIS335 4.1 91.5 1.0 CG A:HIS339 4.2 88.9 1.0 CG A:HIS335 4.2 0.2 1.0 HG2 A:GLU415 4.2 92.2 1.0 C A:RDF502 4.3 0.1 1.0 HB1 A:ALA418 4.4 0.6 1.0 O A:RDF502 4.4 0.4 1.0 O5 A:RDF502 4.5 0.7 1.0 CB A:ALA418 4.6 87.1 1.0 C1 A:RDF502 4.6 0.3 1.0 HB2 A:ALA418 4.6 0.6 1.0 HG3 A:GLU415 4.6 92.2 1.0 HA A:GLU336 4.7 0.3 1.0 CA A:GLU415 4.8 68.8 1.0 C5 A:RDF502 4.8 0.6 1.0 HD1 A:HIS339 4.8 1.0 1.0 OE2 A:GLU336 4.9 0.8 1.0 HD1 A:HIS335 4.9 0.8 1.0 CB A:GLU415 4.9 97.2 1.0 HB3 A:GLU415 5.0 0.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of ZMPSTE24 in Complex with Phosphoramidon


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 ZMPSTE24 in Complex with Phosphoramidon within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:0.5 occ:1.00 OE2 B:GLU415 1.8 0.5 1.0 O1P B:RDF502 1.8 0.2 1.0 NE2 B:HIS339 2.0 0.3 1.0 NE2 B:HIS335 2.0 0.7 1.0 O2P B:RDF502 2.1 0.7 1.0 P B:RDF502 2.4 0.5 1.0 CD B:GLU415 2.7 0.9 1.0 OE1 B:GLU415 2.9 0.0 1.0 CE1 B:HIS339 2.9 0.7 1.0 CE1 B:HIS335 3.0 0.1 1.0 CD2 B:HIS335 3.1 0.5 1.0 HE1 B:HIS339 3.1 0.9 1.0 CD2 B:HIS339 3.1 0.1 1.0 HE1 B:HIS335 3.2 0.8 1.0 HD2 B:HIS335 3.3 0.2 1.0 HD2 B:HIS339 3.3 0.8 1.0 O1 B:RDF502 3.6 0.9 1.0 N B:RDF502 3.6 0.1 1.0 CA B:RDF502 3.9 0.5 1.0 HA B:GLU415 3.9 0.6 1.0 CG B:GLU415 4.0 0.3 1.0 ND1 B:HIS339 4.0 85.2 1.0 HB3 B:ALA418 4.1 0.8 1.0 ND1 B:HIS335 4.1 1.0 1.0 CG B:HIS339 4.2 90.5 1.0 CG B:HIS335 4.2 0.1 1.0 HG2 B:GLU415 4.2 0.6 1.0 C B:RDF502 4.3 0.9 1.0 HB1 B:ALA418 4.4 0.8 1.0 O B:RDF502 4.4 0.6 1.0 O5 B:RDF502 4.5 0.5 1.0 CB B:ALA418 4.6 0.1 1.0 C1 B:RDF502 4.6 0.5 1.0 HB2 B:ALA418 4.6 0.8 1.0 HG3 B:GLU415 4.6 0.6 1.0 HA B:GLU336 4.7 0.6 1.0 CA B:GLU415 4.8 97.9 1.0 C5 B:RDF502 4.8 0.0 1.0 HD1 B:HIS339 4.8 0.3 1.0 OE2 B:GLU336 4.9 0.5 1.0 HD1 B:HIS335 4.9 0.0 1.0 CB B:GLU415 4.9 0.2 1.0 HB3 B:GLU415 5.0 0.7 1.0

B.R.Goblirsch, B.T.Arachea, D.J.Councell, M.C.Wiener. Phosphoramidon Inhibits the Integral Membrane Protein Zinc Metalloprotease ZMPSTE24. Acta Crystallogr D Struct V. 74 739 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30082509
DOI: 10.1107/S2059798318003431