Calcium in PDB 1a86: MMP8 with Malonic and Aspartic Acid Based Inhibitor

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

The structure of MMP8 with Malonic and Aspartic Acid Based Inhibitor, PDB code: 1a86 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 Aspartic Acid Based Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the MMP8 with Malonic and Aspartic Acid Based Inhibitor (pdb code 1a86). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the MMP8 with Malonic and Aspartic Acid Based Inhibitor, PDB code: 1a86:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the MMP8 with Malonic and Aspartic Acid Based Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP8 with Malonic and Aspartic Acid Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca996 b:7.3 occ:1.00 O A:GLY169 2.1 15.9 1.0 O A:GLY171 2.2 10.8 1.0 O A:ASP137 2.3 11.8 1.0 OD1 A:ASP173 2.4 7.2 1.0 C A:GLY169 3.4 16.1 1.0 CG A:ASP173 3.4 7.9 1.0 C A:GLY171 3.5 11.6 1.0 C A:ASP137 3.5 12.3 1.0 OD2 A:ASP173 3.8 8.4 1.0 C A:ILE170 4.0 13.6 1.0 O A:ILE170 4.0 13.2 1.0 N A:GLY171 4.0 12.9 1.0 N A:ASP173 4.2 8.7 1.0 CA A:GLY169 4.2 17.1 1.0 CA A:GLY171 4.3 12.1 1.0 N A:GLY169 4.3 17.9 1.0 N A:ILE170 4.3 15.3 1.0 O A:GLY167 4.3 18.3 1.0 CA A:ASP137 4.4 13.8 1.0 N A:ILE138 4.4 11.3 1.0 N A:GLY172 4.5 10.9 1.0 CA A:ILE138 4.5 10.4 1.0 CA A:ILE170 4.5 14.2 1.0 O A:ALA136 4.5 17.6 1.0 CB A:ASP173 4.6 7.7 1.0 CA A:GLY172 4.6 9.8 1.0 ND2 A:ASN139 4.6 12.4 1.0 C A:GLY172 4.6 9.5 1.0 CH2 A:TRP88 4.8 21.9 1.0 C A:GLN168 4.8 18.6 1.0 CA A:ASP173 4.8 8.2 1.0 N A:ASN139 4.9 9.7 1.0

Calcium binding site 2 out of 2 in the MMP8 with Malonic and Aspartic Acid Based Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP8 with Malonic and Aspartic Acid Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca997 b:6.0 occ:1.00 O A:GLY155 2.1 10.3 1.0 OE2 A:GLU180 2.2 8.2 1.0 O A:ILE159 2.2 10.5 1.0 O A:ASN157 2.2 10.2 1.0 OD2 A:ASP177 2.4 9.1 1.0 OD1 A:ASP154 2.5 6.2 1.0 C A:ILE159 3.4 9.6 1.0 C A:GLY155 3.4 10.0 1.0 CG A:ASP177 3.4 9.4 1.0 C A:ASN157 3.4 10.5 1.0 CD A:GLU180 3.4 7.5 1.0 CG A:ASP154 3.6 8.0 1.0 N A:ILE159 3.8 9.0 1.0 N A:ASN157 3.9 11.4 1.0 N A:GLY155 4.0 8.7 1.0 C A:PRO156 4.0 11.4 1.0 CB A:ASP177 4.1 8.4 1.0 C A:GLY158 4.1 9.6 1.0 CA A:ILE159 4.2 9.8 1.0 OE1 A:GLU180 4.2 6.4 1.0 CA A:ASN157 4.2 11.0 1.0 OD2 A:ASP154 4.2 6.2 1.0 OD1 A:ASP177 4.3 8.5 1.0 C A:ASP154 4.3 8.9 1.0 N A:PRO156 4.3 10.2 1.0 CA A:GLY155 4.3 9.6 1.0 N A:ASP154 4.3 8.9 1.0 N A:LEU160 4.4 8.9 1.0 O A:PRO156 4.4 12.1 1.0 CG A:GLU180 4.4 8.4 1.0 N A:GLY158 4.4 9.9 1.0 CA A:PRO156 4.4 11.0 1.0 CA A:GLY158 4.5 9.4 1.0 CA A:LEU160 4.6 8.2 1.0 CA A:ASP154 4.7 8.8 1.0 O A:ASP154 4.7 9.3 1.0 O A:GLY158 4.8 8.6 1.0 CB A:ASP154 4.8 7.8 1.0 CD1 A:LEU160 4.8 9.1 1.0 CG1 A:ILE159 5.0 10.1 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