Calcium in PDB 3tt4: Human MMP8 in Complex with L-Glutamate Motif Inhibitor

All present enzymatic activity of Human MMP8 in Complex with L-Glutamate Motif Inhibitor:
3.4.24.34;

The structure of Human MMP8 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3tt4 was solved by E.A.Stura, V.Dive, L.Devel, B.Czarny, F.Beau, L.Vera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.69 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	32.719, 69.369, 70.312, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.8

The structure of Human MMP8 in Complex with L-Glutamate Motif Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Calcium atom in the Human MMP8 in Complex with L-Glutamate Motif Inhibitor (pdb code 3tt4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Human MMP8 in Complex with L-Glutamate Motif Inhibitor, PDB code: 3tt4:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Human MMP8 in Complex with L-Glutamate Motif Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human MMP8 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:15.6 occ:1.00 OD1 A:ASP154 2.3 13.9 1.0 OD2 A:ASP177 2.3 14.7 1.0 O A:GLY155 2.4 22.2 1.0 O A:ASN157 2.4 18.0 1.0 O A:ILE159 2.4 16.5 1.0 OE2 A:GLU180 2.4 20.6 1.0 CG A:ASP177 3.4 14.6 1.0 CG A:ASP154 3.4 14.5 1.0 C A:ILE159 3.5 15.3 1.0 C A:GLY155 3.5 19.6 1.0 C A:ASN157 3.6 17.5 1.0 CD A:GLU180 3.7 16.4 1.0 N A:ILE159 3.8 16.8 1.0 CB A:ASP177 3.9 12.6 1.0 N A:ASN157 3.9 19.6 1.0 OD2 A:ASP154 4.0 14.8 1.0 N A:GLY155 4.1 14.3 1.0 CA A:ILE159 4.1 15.7 1.0 C A:PRO156 4.2 20.5 1.0 N A:ASP154 4.2 12.0 1.0 C A:ASP154 4.2 14.3 1.0 C A:GLY158 4.3 17.1 1.0 CA A:ASN157 4.3 18.7 1.0 OD1 A:ASP177 4.4 13.1 1.0 CA A:PRO156 4.4 20.4 1.0 N A:PRO156 4.4 19.3 1.0 CB A:ILE159 4.4 17.3 1.0 OE1 A:GLU180 4.4 20.5 1.0 N A:LEU160 4.5 14.4 1.0 CA A:GLY155 4.5 17.1 1.0 CA A:ASP154 4.5 13.8 1.0 CG A:GLU180 4.6 17.9 1.0 N A:GLY158 4.6 15.5 1.0 CB A:ASP154 4.6 12.4 1.0 CA A:GLY158 4.7 16.2 1.0 CA A:LEU160 4.7 13.6 1.0 O A:PRO156 4.7 21.1 1.0 O A:ASP154 4.7 14.7 1.0 O A:GLY158 4.9 18.7 1.0

Calcium binding site 2 out of 2 in the Human MMP8 in Complex with L-Glutamate Motif Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human MMP8 in Complex with L-Glutamate Motif Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:25.5 occ:1.00 O A:GLY171 2.3 18.3 1.0 O A:HOH33 2.4 17.8 1.0 O A:HOH34 2.5 18.4 1.0 O A:ASP137 2.5 22.3 1.0 OD1 A:ASP173 2.5 14.6 1.0 O A:GLY169 2.6 26.1 1.0 CG A:ASP173 3.5 19.3 1.0 C A:GLY171 3.5 19.4 1.0 C A:ASP137 3.5 21.8 1.0 C A:GLY169 3.7 25.6 1.0 C A:ILE170 3.9 20.9 1.0 OD2 A:ASP173 3.9 20.6 1.0 O A:ILE170 4.0 20.6 1.0 N A:GLY171 4.1 19.6 1.0 N A:ASP173 4.3 14.0 1.0 CA A:GLY171 4.3 18.3 1.0 CA A:ILE170 4.3 22.7 1.0 CA A:ASP137 4.3 23.1 1.0 O A:HOH338 4.3 39.5 1.0 O A:ALA136 4.4 27.3 1.0 N A:ILE138 4.4 19.0 1.0 N A:ILE170 4.5 23.6 1.0 O A:GLY167 4.5 20.6 1.0 ND2 A:ASN139 4.5 28.6 1.0 N A:GLY172 4.5 18.8 1.0 N A:GLY169 4.6 25.8 1.0 CA A:ILE138 4.6 16.8 1.0 CA A:GLY172 4.6 16.3 1.0 CA A:GLY169 4.7 25.9 1.0 C A:GLY172 4.7 15.0 1.0 CB A:ASP173 4.7 14.1 1.0 N A:ASN139 4.7 16.8 1.0 O A:HOH36 4.7 35.3 1.0 O A:HOH335 4.7 30.7 1.0 CH2 A:TRP88 4.8 19.4 1.0 CA A:ASP173 4.9 14.5 1.0 C A:GLN168 4.9 25.7 1.0

L.Devel, F.Beau, M.Amoura, L.Vera, E.Cassar-Lajeunesse, S.Garcia, B.Czarny, E.A.Stura, V.Dive. Simple Pseudo-Dipeptides with A P2' Glutamate: A Novel Inhibitor Family of Matrix Metalloproteases and Other Metzincins. J.Biol.Chem. V. 287 26647 2012.
ISSN: ISSN 0021-9258
PubMed: 22689580
DOI: 10.1074/JBC.M112.380782