Zinc in PDB 1a85: MMP8 with Malonic and Asparagine Based Inhibitor

All present enzymatic activity of MMP8 with Malonic and Asparagine Based Inhibitor:
3.4.24.34;

The structure of MMP8 with Malonic and Asparagine Based Inhibitor, PDB code: 1a85 was solved by H.Brandstetter, E.G.V.Roedern, F.Grams, R.A.Engh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.140, 69.430, 72.620, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of MMP8 with Malonic and Asparagine Based Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the MMP8 with Malonic and Asparagine Based Inhibitor (pdb code 1a85). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the MMP8 with Malonic and Asparagine Based Inhibitor, PDB code: 1a85:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the MMP8 with Malonic and Asparagine Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of MMP8 with Malonic and Asparagine Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn998 b:10.7 occ:1.00 OD2 A:ASP149 1.9 13.2 1.0 ND1 A:HIS175 2.0 7.1 1.0 NE2 A:HIS147 2.0 10.7 1.0 NE2 A:HIS162 2.1 12.5 1.0 CD2 A:HIS147 2.9 10.3 1.0 CG A:ASP149 2.9 14.3 1.0 CE1 A:HIS162 3.0 12.6 1.0 CE1 A:HIS175 3.0 7.0 1.0 CG A:HIS175 3.1 7.0 1.0 CE1 A:HIS147 3.2 10.6 1.0 CD2 A:HIS162 3.2 11.7 1.0 OD1 A:ASP149 3.3 14.2 1.0 CB A:HIS175 3.4 7.4 1.0 CZ A:PHE164 4.1 17.7 1.0 CG A:HIS147 4.1 11.1 1.0 ND1 A:HIS162 4.1 12.1 1.0 O A:SER151 4.2 17.3 1.0 NE2 A:HIS175 4.2 7.1 1.0 CD2 A:HIS175 4.2 7.3 1.0 ND1 A:HIS147 4.2 10.3 1.0 CG A:HIS162 4.3 11.5 1.0 CB A:ASP149 4.3 15.1 1.0 CE1 A:PHE164 4.3 18.1 1.0 CZ A:PHE153 4.5 11.6 1.0 CE2 A:PHE153 4.6 11.7 1.0 CA A:HIS175 4.9 7.3 1.0

Zinc binding site 2 out of 2 in the MMP8 with Malonic and Asparagine Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MMP8 with Malonic and Asparagine Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn999 b:8.1 occ:1.00 NE2 A:HIS207 2.0 7.0 1.0 NE2 A:HIS197 2.0 6.0 1.0 OH A:0DY1 2.2 11.9 1.0 NE2 A:HIS201 2.2 6.0 1.0 O1 A:0DY1 2.3 12.9 1.0 N A:0DY1 2.9 12.7 1.0 C1 A:0DY1 3.0 13.9 1.0 CD2 A:HIS207 3.0 6.7 1.0 CE1 A:HIS197 3.0 6.1 1.0 HOH A:0DY1 3.0 20.0 0.0 CE1 A:HIS207 3.0 6.3 1.0 CD2 A:HIS197 3.1 6.0 1.0 CE1 A:HIS201 3.2 6.3 1.0 CD2 A:HIS201 3.2 6.0 1.0 HN A:0DY1 3.9 20.0 0.0 HN1 A:0DY1 4.0 20.0 0.0 CG A:HIS207 4.1 7.2 1.0 ND1 A:HIS207 4.1 6.9 1.0 ND1 A:HIS197 4.1 6.0 1.0 CG A:HIS197 4.2 6.0 1.0 OE2 A:GLU198 4.3 6.9 1.0 ND1 A:HIS201 4.3 6.0 1.0 CG A:HIS201 4.4 6.0 1.0 CA A:0DY1 4.5 14.4 1.0 H A:0DY1 4.8 20.0 0.0 N2 A:0DY1 4.8 17.9 1.0 CB2 A:0DY1 5.0 18.6 1.0

H.Brandstetter, R.A.Engh, E.G.Von Roedern, L.Moroder, R.Huber, W.Bode, F.Grams. Structure of Malonic Acid-Based Inhibitors Bound to Human Neutrophil Collagenase. A New Binding Mode Explains Apparently Anomalous Data. Protein Sci. V. 7 1303 1998.
ISSN: ISSN 0961-8368
PubMed: 9655333