Zinc 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:

Calcium

(Ca)

5 atoms

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

Zinc binding site 1 out of 4 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.8 occ:1.00 NE2 A:HIS230 2.0 20.7 1.0 NE2 A:HIS236 2.0 22.9 1.0 NE2 A:HIS226 2.0 19.0 1.0 SG A:CYS99 2.3 22.5 1.0 CD2 A:HIS226 2.9 21.1 1.0 CB A:CYS99 2.9 22.4 1.0 CD2 A:HIS236 2.9 21.2 1.0 CD2 A:HIS230 3.0 21.0 1.0 CE1 A:HIS230 3.0 24.8 1.0 CE1 A:HIS236 3.1 23.1 1.0 CE1 A:HIS226 3.1 21.6 1.0 CB A:VAL101 4.0 24.1 1.0 CG A:HIS226 4.1 20.1 1.0 CG A:HIS236 4.1 24.7 1.0 CG A:HIS230 4.1 21.7 1.0 ND1 A:HIS230 4.1 23.0 1.0 ND1 A:HIS236 4.1 24.6 1.0 ND1 A:HIS226 4.2 19.1 1.0 CG2 A:VAL101 4.3 23.8 1.0 OE2 A:GLU227 4.3 23.2 1.0 CA A:CYS99 4.4 21.0 1.0 OE1 A:GLU227 4.5 23.2 1.0 CD A:GLU227 4.7 23.7 1.0 CE A:MET244 4.7 24.9 1.0 N A:VAL101 4.8 25.9 1.0 CG1 A:VAL101 4.8 24.8 1.0 C A:CYS99 4.9 24.2 1.0 CA A:PRO246 4.9 23.7 1.0 CA A:VAL101 5.0 25.3 1.0

Zinc binding site 2 out of 4 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.9 occ:1.00 OD2 A:ASP177 2.0 34.5 1.0 ND1 A:HIS203 2.1 34.1 1.0 NE2 A:HIS190 2.1 30.5 1.0 NE2 A:HIS175 2.2 28.8 1.0 CG A:ASP177 2.9 34.3 1.0 CE1 A:HIS190 3.0 29.5 1.0 CD2 A:HIS175 3.0 31.0 1.0 CE1 A:HIS203 3.1 32.4 1.0 CG A:HIS203 3.1 30.6 1.0 CD2 A:HIS190 3.2 28.8 1.0 CE1 A:HIS175 3.2 32.6 1.0 OD1 A:ASP177 3.2 33.5 1.0 CB A:HIS203 3.4 26.3 1.0 ND1 A:HIS190 4.2 28.6 1.0 NE2 A:HIS203 4.2 30.4 1.0 CZ A:PHE192 4.2 30.2 1.0 CG A:HIS175 4.2 30.8 1.0 CD2 A:HIS203 4.2 32.3 1.0 ND1 A:HIS175 4.3 29.1 1.0 CE2 A:PHE192 4.3 35.3 1.0 O A:TYR179 4.3 30.5 1.0 CB A:ASP177 4.3 35.1 1.0 CG A:HIS190 4.3 25.8 1.0 CZ A:PHE181 4.4 27.4 1.0 CE2 A:PHE181 4.7 29.9 1.0 O A:HOH429 4.9 32.0 1.0 CA A:HIS203 4.9 26.5 1.0 CE1 A:PHE181 4.9 27.9 1.0 CB A:TYR179 4.9 31.6 1.0

Zinc binding site 3 out of 4 in the Prommp-9DESFNII Complexed to JNJ0966 Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:24.1 occ:1.00 NE2 B:HIS236 2.0 26.0 1.0 NE2 B:HIS230 2.0 21.0 1.0 NE2 B:HIS226 2.1 19.9 1.0 SG B:CYS99 2.3 25.0 1.0 CB B:CYS99 2.9 25.4 1.0 CD2 B:HIS236 2.9 23.2 1.0 CD2 B:HIS230 3.0 21.8 1.0 CD2 B:HIS226 3.0 22.3 1.0 CE1 B:HIS236 3.0 24.8 1.0 CE1 B:HIS230 3.0 23.6 1.0 CE1 B:HIS226 3.2 24.1 1.0 CB B:VAL101 4.0 24.5 1.0 CG B:HIS236 4.0 28.9 1.0 ND1 B:HIS236 4.1 26.3 1.0 CG B:HIS230 4.1 23.3 1.0 ND1 B:HIS230 4.1 24.3 1.0 CG B:HIS226 4.2 21.5 1.0 ND1 B:HIS226 4.3 20.1 1.0 CG2 B:VAL101 4.3 23.7 1.0 OE2 B:GLU227 4.3 24.5 1.0 CA B:CYS99 4.4 27.7 1.0 OE1 B:GLU227 4.4 23.2 1.0 CE B:MET244 4.6 22.0 1.0 CD B:GLU227 4.7 23.9 1.0 CG1 B:VAL101 4.7 25.0 1.0 N B:VAL101 4.8 26.0 1.0 CA B:PRO246 4.9 27.1 1.0 C B:CYS99 4.9 24.6 1.0 CA B:VAL101 5.0 27.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Prommp-9DESFNII Complexed to JNJ0966 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:30.1 occ:1.00 OD2 B:ASP177 2.0 33.4 1.0 NE2 B:HIS190 2.1 28.6 1.0 NE2 B:HIS175 2.1 29.3 1.0 ND1 B:HIS203 2.2 34.9 1.0 CG B:ASP177 2.9 35.6 1.0 CE1 B:HIS190 3.0 25.5 1.0 CE1 B:HIS175 3.0 31.3 1.0 CD2 B:HIS175 3.1 30.6 1.0 CE1 B:HIS203 3.1 30.6 1.0 CD2 B:HIS190 3.1 27.6 1.0 CG B:HIS203 3.2 26.3 1.0 OD1 B:ASP177 3.2 32.9 1.0 CB B:HIS203 3.5 28.1 1.0 ND1 B:HIS190 4.1 28.4 1.0 ND1 B:HIS175 4.1 32.5 1.0 CG B:HIS175 4.2 29.6 1.0 CG B:HIS190 4.2 25.2 1.0 NE2 B:HIS203 4.3 32.3 1.0 O B:TYR179 4.3 32.8 1.0 CB B:ASP177 4.3 35.6 1.0 CD2 B:HIS203 4.3 29.7 1.0 CE2 B:PHE192 4.3 30.7 1.0 O B:HOH459 4.5 37.9 1.0 CZ B:PHE181 4.5 28.7 1.0 CZ B:PHE192 4.5 31.2 1.0 CE2 B:PHE181 4.8 30.0 1.0 O B:HOH445 4.8 36.6 1.0 CA B:HIS203 5.0 26.4 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