Calcium in PDB 5ue4: Prommp-9DESFNII Complexed to JNJ0966 Inhibitor

All present enzymatic activity of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor:
3.4.24.35;

The structure of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor, PDB code: 5ue4 was solved by R.S.Alexander, J.Spurlino, C.Milligan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.820, 72.945, 77.537, 90.00, 106.91, 90.00
R / Rfree (%)	19.9 / 22.4

The structure of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor (pdb code 5ue4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor, PDB code: 5ue4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:28.0 occ:1.00 O A:GLY183 2.3 30.7 1.0 OE2 A:GLU208 2.4 29.6 1.0 O A:LEU187 2.4 25.8 1.0 O A:ASP185 2.4 30.0 1.0 OD1 A:ASP182 2.4 29.1 1.0 OD2 A:ASP205 2.4 26.4 1.0 CG A:ASP205 3.5 27.0 1.0 CG A:ASP182 3.5 29.8 1.0 C A:ASP185 3.5 32.0 1.0 C A:LEU187 3.5 28.5 1.0 C A:GLY183 3.5 31.6 1.0 CD A:GLU208 3.6 29.8 1.0 N A:ASP185 3.8 31.3 1.0 N A:LEU187 3.9 26.5 1.0 OD2 A:ASP182 4.0 32.4 1.0 C A:LYS184 4.0 31.9 1.0 N A:GLY183 4.1 29.1 1.0 CB A:ASP205 4.1 26.1 1.0 CA A:ASP185 4.1 29.7 1.0 CA A:LEU187 4.3 27.4 1.0 C A:ASP182 4.3 28.1 1.0 C A:GLY186 4.3 29.7 1.0 N A:ASP182 4.4 29.1 1.0 OE1 A:GLU208 4.4 27.4 1.0 OD1 A:ASP205 4.4 25.1 1.0 CG A:GLU208 4.4 26.9 1.0 CA A:GLY183 4.4 29.6 1.0 O A:LYS184 4.4 33.2 1.0 CA A:LYS184 4.4 32.6 1.0 N A:LYS184 4.4 29.0 1.0 N A:LEU188 4.5 24.1 1.0 N A:GLY186 4.5 30.1 1.0 CD1 A:LEU187 4.6 32.5 1.0 CA A:LEU188 4.6 24.9 1.0 O A:HOH455 4.6 35.2 1.0 CA A:ASP182 4.6 31.1 1.0 CB A:ASP182 4.7 30.0 1.0 CA A:GLY186 4.7 31.2 1.0 O A:ASP182 4.7 32.5 1.0 CG A:LEU187 4.8 32.6 1.0 O A:GLY186 4.9 27.0 1.0

Calcium binding site 2 out of 5 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:39.5 occ:1.00 O A:GLN199 2.4 30.5 1.0 O A:ASP165 2.5 29.5 1.0 O A:HOH460 2.5 33.6 1.0 O A:GLY197 2.5 37.7 1.0 O A:HOH417 2.6 31.3 1.0 OD1 A:ASP201 2.6 30.2 1.0 C A:ASP165 3.5 29.7 1.0 CG A:ASP201 3.5 32.9 1.0 C A:GLN199 3.6 29.4 1.0 C A:GLY197 3.7 36.6 1.0 OD2 A:ASP201 4.0 31.2 1.0 O A:ILE198 4.0 33.7 1.0 O A:ALA164 4.0 34.9 1.0 C A:ILE198 4.0 33.3 1.0 N A:ASP201 4.1 26.9 1.0 O A:HOH420 4.2 39.8 1.0 N A:GLN199 4.3 31.8 1.0 CA A:GLY200 4.3 26.6 1.0 C A:GLY200 4.3 27.2 1.0 CA A:ASP165 4.3 29.6 1.0 N A:GLY200 4.4 28.6 1.0 O A:GLY195 4.4 34.9 1.0 N A:ILE166 4.4 25.7 1.0 N A:GLY197 4.5 36.4 1.0 CA A:GLN199 4.5 32.3 1.0 N A:VAL167 4.5 27.0 1.0 CA A:ILE198 4.5 36.0 1.0 N A:ILE198 4.5 31.7 1.0 CA A:GLY197 4.6 36.0 1.0 CA A:ILE166 4.6 28.8 1.0 CB A:ASP201 4.7 28.4 1.0 CA A:ASP201 4.7 27.1 1.0 CG2 A:VAL167 4.9 30.9 1.0 C A:PRO196 4.9 36.9 1.0 O A:HOH442 4.9 39.5 1.0 C A:ALA164 5.0 32.9 1.0 O A:GLY200 5.0 27.6 1.0

Calcium binding site 3 out of 5 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:37.4 occ:1.00 O A:GLU208 2.3 28.6 1.0 OD2 A:ASP131 2.4 28.4 1.0 O A:HOH450 2.6 30.9 1.0 O A:ASP206 2.6 28.0 1.0 OD1 A:ASP206 2.6 27.3 1.0 CG A:ASP131 3.2 30.3 1.0 C A:ASP206 3.4 29.9 1.0 C A:GLU208 3.4 27.9 1.0 OD1 A:ASP131 3.5 32.0 1.0 CG A:ASP206 3.5 29.0 1.0 CA A:ASP206 3.9 27.1 1.0 OG A:SER129 3.9 26.5 1.0 CD1 A:TRP210 4.1 24.3 1.0 N A:GLU208 4.2 26.2 1.0 CA A:LEU209 4.2 25.2 1.0 N A:LEU209 4.2 25.5 1.0 CB A:ASP206 4.2 29.4 1.0 OD2 A:ASP206 4.3 33.2 1.0 N A:ASP207 4.4 28.1 1.0 C A:ASP207 4.4 28.8 1.0 CA A:GLU208 4.4 27.9 1.0 N A:TRP210 4.5 26.0 1.0 CB A:ASP131 4.6 26.1 1.0 CA A:ASP207 4.7 29.1 1.0 NE1 A:TRP210 4.8 25.7 1.0 C A:LEU209 4.8 26.8 1.0 O A:ASP207 4.9 28.6 1.0

Calcium binding site 4 out of 5 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:31.4 occ:1.00 O B:LEU187 2.3 27.6 1.0 OE2 B:GLU208 2.3 34.5 1.0 OD2 B:ASP205 2.4 30.9 1.0 O B:GLY183 2.4 33.0 1.0 OD1 B:ASP182 2.4 32.1 1.0 O B:ASP185 2.4 34.2 1.0 C B:LEU187 3.4 28.9 1.0 CG B:ASP205 3.4 28.3 1.0 CD B:GLU208 3.5 34.0 1.0 CG B:ASP182 3.5 35.0 1.0 C B:ASP185 3.5 32.2 1.0 C B:GLY183 3.6 36.7 1.0 N B:ASP185 3.9 33.1 1.0 N B:LEU187 3.9 28.0 1.0 OD2 B:ASP182 4.0 35.3 1.0 CB B:ASP205 4.1 28.0 1.0 C B:LYS184 4.1 35.1 1.0 CA B:LEU187 4.1 30.0 1.0 CA B:ASP185 4.2 36.1 1.0 CG B:GLU208 4.2 29.6 1.0 N B:GLY183 4.2 34.2 1.0 C B:GLY186 4.3 33.5 1.0 N B:ASP182 4.3 31.3 1.0 C B:ASP182 4.3 34.1 1.0 OD1 B:ASP205 4.4 30.9 1.0 OE1 B:GLU208 4.4 32.8 1.0 CB B:LEU187 4.4 32.3 1.0 N B:LEU188 4.4 25.8 1.0 CA B:LYS184 4.5 36.4 1.0 N B:LYS184 4.5 35.5 1.0 O B:LYS184 4.5 36.5 1.0 CA B:GLY183 4.5 33.0 1.0 N B:GLY186 4.5 32.0 1.0 CA B:LEU188 4.6 25.2 1.0 O B:HOH480 4.6 40.6 1.0 O B:ASP182 4.7 39.4 1.0 CA B:GLY186 4.7 32.5 1.0 CA B:ASP182 4.7 35.8 1.0 CB B:ASP182 4.7 36.8 1.0 O B:GLY186 4.9 31.1 1.0 CD2 B:LEU188 5.0 27.2 1.0

Calcium binding site 5 out of 5 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:39.3 occ:1.00 O B:GLN199 2.4 26.6 1.0 O B:ASP165 2.5 25.9 1.0 O B:HOH435 2.5 37.2 1.0 O B:GLY197 2.6 37.0 1.0 OD1 B:ASP201 2.6 30.0 1.0 O B:HOH420 2.6 35.0 1.0 CG B:ASP201 3.5 31.7 1.0 C B:GLN199 3.5 27.0 1.0 C B:ASP165 3.6 26.9 1.0 C B:GLY197 3.7 37.4 1.0 O B:HOH453 3.9 44.4 1.0 OD2 B:ASP201 3.9 33.0 1.0 C B:ILE198 4.0 33.5 1.0 O B:ILE198 4.1 30.3 1.0 N B:ASP201 4.1 26.5 1.0 N B:GLN199 4.1 28.8 1.0 O B:HOH437 4.1 39.3 1.0 O B:ALA164 4.2 31.6 1.0 CA B:GLY200 4.2 25.4 1.0 C B:GLY200 4.3 27.2 1.0 N B:GLY200 4.3 28.4 1.0 O B:GLY195 4.4 32.1 1.0 CA B:ASP165 4.4 25.7 1.0 N B:ILE166 4.4 22.5 1.0 CA B:ILE198 4.5 33.5 1.0 CA B:GLN199 4.5 28.4 1.0 N B:ILE198 4.5 29.6 1.0 N B:VAL167 4.5 26.5 1.0 CA B:ILE166 4.5 25.4 1.0 N B:GLY197 4.6 40.1 1.0 CA B:GLY197 4.6 41.3 1.0 CB B:ASP201 4.7 28.1 1.0 CA B:ASP201 4.7 26.0 1.0 CG2 B:VAL167 4.8 28.7 1.0 C B:PRO196 4.9 35.1 1.0 CH2 B:TRP116 5.0 29.7 1.0

R.H.Scannevin, R.Alexander, T.M.Haarlander, S.L.Burke, M.Singer, C.Huo, Y.M.Zhang, D.Maguire, J.Spurlino, I.Deckman, K.I.Carroll, F.Lewandowski, E.Devine, K.Dzordzorme, B.Tounge, C.Milligan, S.Bayoumy, R.Williams, C.Schalk-Hihi, K.Leonard, P.Jackson, M.Todd, L.C.Kuo, K.J.Rhodes. Discovery of A Highly Selective Chemical Inhibitor of Matrix Metalloproteinase-9 (Mmp-9) That Allosterically Inhibits Zymogen Activation. J. Biol. Chem. V. 292 17963 2017.
ISSN: ESSN 1083-351X
PubMed: 28860188
DOI: 10.1074/JBC.M117.806075