Zinc in PDB 5ue3: Prommp-9DESFNII

All present enzymatic activity of Prommp-9DESFNII:
3.4.24.35;

The structure of Prommp-9DESFNII, PDB code: 5ue3 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)	32.84 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.300, 73.200, 77.500, 90.00, 106.30, 90.00
R / Rfree (%)	15.5 / 18.4

The structure of Prommp-9DESFNII also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Zinc atom in the Prommp-9DESFNII (pdb code 5ue3). 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, PDB code: 5ue3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Prommp-9DESFNII within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.8 occ:1.00 NE2 A:HIS230 2.0 9.6 1.0 NE2 A:HIS236 2.0 10.4 1.0 NE2 A:HIS226 2.0 10.1 1.0 SG A:CYS99 2.3 9.6 1.0 CD2 A:HIS236 2.9 9.2 1.0 CB A:CYS99 3.0 11.4 1.0 CD2 A:HIS230 3.0 9.8 1.0 CE1 A:HIS230 3.0 12.7 1.0 CD2 A:HIS226 3.0 8.2 1.0 CE1 A:HIS236 3.1 9.9 1.0 CE1 A:HIS226 3.1 8.6 1.0 CB A:VAL101 4.0 9.7 1.0 CG A:HIS236 4.1 8.3 1.0 ND1 A:HIS230 4.1 12.2 1.0 ND1 A:HIS236 4.1 9.4 1.0 CG A:HIS230 4.1 10.1 1.0 ND1 A:HIS226 4.2 9.1 1.0 CG A:HIS226 4.2 7.7 1.0 CG2 A:VAL101 4.2 10.9 1.0 OE2 A:GLU227 4.3 11.6 1.0 CA A:CYS99 4.4 9.4 1.0 OE1 A:GLU227 4.5 10.6 1.0 CE A:MET244 4.7 11.3 1.0 CD A:GLU227 4.7 9.3 1.0 CG1 A:VAL101 4.8 10.8 1.0 N A:VAL101 4.8 11.1 1.0 C A:CYS99 4.9 11.4 1.0 CA A:PRO246 5.0 10.8 1.0 CA A:VAL101 5.0 10.2 1.0

Zinc binding site 2 out of 4 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Prommp-9DESFNII within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.0 occ:1.00 OD2 A:ASP177 2.0 13.4 1.0 ND1 A:HIS203 2.0 12.3 1.0 NE2 A:HIS175 2.1 11.6 1.0 NE2 A:HIS190 2.1 12.9 1.0 CG A:ASP177 2.9 15.3 1.0 CE1 A:HIS203 3.0 13.4 1.0 CE1 A:HIS190 3.0 10.0 1.0 CD2 A:HIS175 3.0 13.4 1.0 CE1 A:HIS175 3.1 15.4 1.0 CG A:HIS203 3.1 12.2 1.0 CD2 A:HIS190 3.2 13.7 1.0 OD1 A:ASP177 3.3 16.0 1.0 CB A:HIS203 3.4 14.0 1.0 NE2 A:HIS203 4.1 15.0 1.0 ND1 A:HIS190 4.1 12.3 1.0 ND1 A:HIS175 4.2 14.1 1.0 CG A:HIS175 4.2 12.4 1.0 CD2 A:HIS203 4.2 13.0 1.0 CZ A:PHE192 4.2 17.6 1.0 O A:TYR179 4.2 13.8 1.0 CG A:HIS190 4.3 10.9 1.0 CE2 A:PHE192 4.3 16.4 1.0 CB A:ASP177 4.3 16.2 1.0 CZ A:PHE181 4.5 13.1 1.0 CE2 A:PHE181 4.8 13.8 1.0 O A:HOH464 4.9 16.6 1.0 CB A:TYR179 4.9 12.6 1.0 CA A:HIS203 4.9 10.6 1.0 O A:HOH493 4.9 30.3 1.0 CE1 A:PHE181 5.0 12.6 1.0

Zinc binding site 3 out of 4 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Prommp-9DESFNII within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.4 occ:1.00 NE2 B:HIS230 2.0 9.7 1.0 NE2 B:HIS226 2.0 9.9 1.0 NE2 B:HIS236 2.0 10.6 1.0 SG B:CYS99 2.3 12.0 1.0 CD2 B:HIS236 3.0 11.5 1.0 CD2 B:HIS230 3.0 10.8 1.0 CB B:CYS99 3.0 11.2 1.0 CD2 B:HIS226 3.0 10.4 1.0 CE1 B:HIS230 3.0 9.8 1.0 CE1 B:HIS236 3.1 9.9 1.0 CE1 B:HIS226 3.1 9.2 1.0 CB B:VAL101 3.9 11.1 1.0 CG B:HIS236 4.1 12.4 1.0 CG B:HIS230 4.1 11.2 1.0 ND1 B:HIS230 4.1 12.1 1.0 CG B:HIS226 4.1 8.0 1.0 ND1 B:HIS236 4.1 12.8 1.0 ND1 B:HIS226 4.2 9.5 1.0 CG2 B:VAL101 4.2 13.7 1.0 OE2 B:GLU227 4.3 12.2 1.0 CA B:CYS99 4.4 12.6 1.0 OE1 B:GLU227 4.5 11.7 1.0 CE B:MET244 4.7 10.6 1.0 CD B:GLU227 4.7 10.1 1.0 CG1 B:VAL101 4.7 14.2 1.0 N B:VAL101 4.8 13.2 1.0 C B:CYS99 4.9 13.2 1.0 CA B:VAL101 5.0 12.4 1.0 CA B:PRO246 5.0 15.1 1.0

Zinc binding site 4 out of 4 in the Prommp-9DESFNII


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Prommp-9DESFNII within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:14.7 occ:1.00 OD2 B:ASP177 2.0 14.4 1.0 NE2 B:HIS175 2.0 12.6 1.0 ND1 B:HIS203 2.1 17.2 1.0 NE2 B:HIS190 2.1 13.3 1.0 CG B:ASP177 2.9 18.4 1.0 CD2 B:HIS175 3.0 16.7 1.0 CE1 B:HIS190 3.0 13.8 1.0 CE1 B:HIS203 3.0 16.3 1.0 CE1 B:HIS175 3.0 13.9 1.0 CG B:HIS203 3.1 13.5 1.0 CD2 B:HIS190 3.1 14.4 1.0 OD1 B:ASP177 3.3 19.6 1.0 CB B:HIS203 3.4 11.0 1.0 ND1 B:HIS175 4.1 17.4 1.0 CG B:HIS175 4.1 16.7 1.0 ND1 B:HIS190 4.1 13.6 1.0 NE2 B:HIS203 4.1 14.5 1.0 CZ B:PHE192 4.2 14.9 1.0 CD2 B:HIS203 4.2 15.4 1.0 CG B:HIS190 4.2 11.3 1.0 CB B:ASP177 4.2 18.7 1.0 CE2 B:PHE192 4.3 15.6 1.0 O B:TYR179 4.3 17.3 1.0 CZ B:PHE181 4.4 14.3 1.0 O B:HOH529 4.4 23.7 1.0 CE2 B:PHE181 4.7 15.4 1.0 CB B:TYR179 4.9 17.8 1.0 O B:HOH460 4.9 22.3 1.0 CA B:HIS203 4.9 9.5 1.0 CE1 B:PHE181 5.0 15.2 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