Zinc in PDB 1hv5: Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor

The structure of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor, PDB code: 1hv5 was solved by A.L.Gall, M.Ruff, R.Kannan, P.Cuniasse, A.Yiotakis, V.Dive, M.C.Rio, P.Basset, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.89 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	140.100, 148.500, 91.400, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 26.2

The structure of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor (pdb code 1hv5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor, PDB code: 1hv5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5501 b:24.3 occ:1.00 OD2 A:ASP170 2.1 32.5 1.0 NE2 A:HIS168 2.2 30.1 1.0 ND1 A:HIS196 2.2 23.1 1.0 NE2 A:HIS183 2.4 16.4 1.0 CD2 A:HIS168 2.9 28.9 1.0 CG A:ASP170 3.1 32.0 1.0 CE1 A:HIS196 3.2 24.1 1.0 CG A:HIS196 3.2 22.2 1.0 CE1 A:HIS168 3.3 29.0 1.0 CE1 A:HIS183 3.3 17.8 1.0 OD1 A:ASP170 3.4 30.7 1.0 CD2 A:HIS183 3.4 17.9 1.0 CB A:HIS196 3.5 20.2 1.0 CE2 A:PHE185 4.0 36.3 1.0 O A:LEU172 4.0 32.0 1.0 CG A:HIS168 4.1 29.4 1.0 ND1 A:HIS168 4.3 28.7 1.0 NE2 A:HIS196 4.3 24.4 1.0 CD2 A:HIS196 4.4 22.7 1.0 CB A:ASP170 4.4 31.4 1.0 CE2 A:PHE174 4.4 19.5 1.0 ND1 A:HIS183 4.5 19.4 1.0 CB A:LEU172 4.5 31.9 1.0 CZ A:PHE174 4.5 19.4 1.0 CG A:HIS183 4.5 18.9 1.0 CD2 A:PHE185 4.7 34.9 1.0 C A:LEU172 4.9 30.5 1.0 CZ A:PHE185 5.0 36.2 1.0 CA A:HIS196 5.0 19.2 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5502 b:19.6 occ:1.00 NE2 A:HIS223 2.2 21.9 1.0 NE2 A:HIS229 2.3 25.5 1.0 NE2 A:HIS219 2.3 16.4 1.0 O1P A:RXP6001 2.4 29.8 1.0 CE1 A:HIS223 3.0 24.0 1.0 O2P A:RXP6001 3.0 30.5 1.0 CD2 A:HIS219 3.2 16.4 1.0 CD2 A:HIS229 3.2 25.1 1.0 P A:RXP6001 3.2 31.8 1.0 CE1 A:HIS229 3.3 26.1 1.0 CE1 A:HIS219 3.3 15.5 1.0 CD2 A:HIS223 3.4 24.2 1.0 C23 A:RXP6001 4.2 35.6 1.0 ND1 A:HIS223 4.2 25.5 1.0 O A:HOH6149 4.3 40.3 1.0 CG A:HIS219 4.4 16.3 1.0 ND1 A:HIS229 4.4 27.3 1.0 ND1 A:HIS219 4.4 17.3 1.0 C22 A:RXP6001 4.4 34.8 1.0 CG A:HIS229 4.4 27.3 1.0 CG A:HIS223 4.4 24.1 1.0 C21 A:RXP6001 4.5 28.7 1.0 C20 A:RXP6001 4.5 27.1 1.0 O A:HOH6035 4.7 53.2 1.0 O A:HOH6374 4.7 0.5 1.0 C13 A:RXP6001 4.7 26.9 1.0 CE A:MET237 4.8 23.3 1.0 OE1 A:GLU220 4.8 20.0 1.0 O A:SER238 4.8 24.7 1.0 C39 A:RXP6001 4.9 24.9 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5504 b:25.1 occ:1.00 NE2 B:HIS183 2.3 21.9 1.0 ND1 B:HIS196 2.3 25.7 1.0 NE2 B:HIS168 2.4 29.2 1.0 OD2 B:ASP170 2.5 38.8 1.0 CE1 B:HIS183 3.0 22.9 1.0 CD2 B:HIS168 3.1 28.6 1.0 CG B:HIS196 3.3 25.6 1.0 CE1 B:HIS196 3.3 27.3 1.0 CD2 B:HIS183 3.4 23.4 1.0 CG B:ASP170 3.4 38.7 1.0 CE1 B:HIS168 3.5 29.4 1.0 CB B:HIS196 3.5 24.1 1.0 OD1 B:ASP170 3.7 37.4 1.0 O B:LEU172 4.1 35.2 1.0 ND1 B:HIS183 4.2 24.1 1.0 CG B:HIS168 4.3 30.7 1.0 NE2 B:HIS196 4.4 27.8 1.0 CD2 B:HIS196 4.4 27.2 1.0 CE2 B:PHE185 4.4 39.1 1.0 CG B:HIS183 4.5 24.0 1.0 ND1 B:HIS168 4.5 30.1 1.0 CE2 B:PHE174 4.5 26.1 1.0 CZ B:PHE174 4.5 24.7 1.0 CB B:LEU172 4.6 37.4 1.0 CB B:ASP170 4.8 38.5 1.0 O B:HOH6027 4.9 62.1 1.0 CD2 B:PHE185 5.0 38.5 1.0 CA B:HIS196 5.0 24.2 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn5505 b:26.3 occ:1.00 NE2 B:HIS223 2.3 24.1 1.0 NE2 B:HIS229 2.4 40.0 1.0 O1P B:RXP6002 2.4 40.0 1.0 NE2 B:HIS219 2.4 23.9 1.0 O B:HOH6300 2.8 98.3 1.0 O2P B:RXP6002 2.8 39.4 1.0 P B:RXP6002 3.1 40.7 1.0 CD2 B:HIS223 3.2 25.4 1.0 CE1 B:HIS223 3.3 25.9 1.0 CE1 B:HIS219 3.3 25.6 1.0 CD2 B:HIS229 3.3 40.6 1.0 CE1 B:HIS229 3.4 41.6 1.0 CD2 B:HIS219 3.4 24.7 1.0 C21 B:RXP6002 4.2 39.7 1.0 C20 B:RXP6002 4.3 38.1 1.0 C22 B:RXP6002 4.4 45.1 1.0 CG B:HIS223 4.4 26.1 1.0 O B:HOH6144 4.4 0.0 1.0 ND1 B:HIS223 4.4 25.6 1.0 C23 B:RXP6002 4.4 46.7 1.0 C13 B:RXP6002 4.5 36.7 1.0 ND1 B:HIS219 4.5 26.8 1.0 ND1 B:HIS229 4.5 42.5 1.0 CG B:HIS229 4.5 43.0 1.0 CG B:HIS219 4.6 25.6 1.0 O B:HOH6208 4.7 44.0 1.0 O B:SER238 4.7 36.2 1.0 O B:HOH6103 4.8 66.1 1.0 OE1 B:GLU220 4.8 27.9 1.0 C39 B:RXP6002 4.9 37.0 1.0 CA B:PRO239 5.0 37.4 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn5507 b:24.0 occ:1.00 NE2 C:HIS183 2.3 21.3 1.0 OD2 C:ASP170 2.3 32.1 1.0 NE2 C:HIS168 2.3 24.0 1.0 ND1 C:HIS196 2.4 21.4 1.0 CD2 C:HIS168 3.0 24.1 1.0 CG C:ASP170 3.1 31.6 1.0 CE1 C:HIS183 3.1 21.0 1.0 OD1 C:ASP170 3.2 29.6 1.0 CG C:HIS196 3.3 22.0 1.0 CD2 C:HIS183 3.3 22.4 1.0 CE1 C:HIS196 3.4 23.0 1.0 CE1 C:HIS168 3.5 23.1 1.0 CB C:HIS196 3.5 20.3 1.0 O C:LEU172 3.9 32.7 1.0 CE2 C:PHE185 4.2 35.1 1.0 CG C:HIS168 4.2 25.0 1.0 ND1 C:HIS183 4.3 21.8 1.0 CG C:HIS183 4.4 23.5 1.0 ND1 C:HIS168 4.4 23.9 1.0 CD2 C:HIS196 4.5 22.4 1.0 NE2 C:HIS196 4.5 24.4 1.0 CE2 C:PHE174 4.5 24.0 1.0 CB C:ASP170 4.5 30.9 1.0 CB C:LEU172 4.5 30.4 1.0 CZ C:PHE174 4.6 24.7 1.0 CD2 C:PHE185 4.7 34.5 1.0 C C:LEU172 4.9 31.4 1.0 O C:HOH6104 4.9 26.7 1.0 CA C:HIS196 5.0 20.1 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn5508 b:16.8 occ:1.00 NE2 C:HIS219 2.3 21.0 1.0 NE2 C:HIS223 2.3 19.7 1.0 NE2 C:HIS229 2.3 27.9 1.0 O1P C:RXP6003 2.4 35.2 1.0 O2P C:RXP6003 2.9 33.8 1.0 P C:RXP6003 3.1 34.2 1.0 CE1 C:HIS223 3.2 21.8 1.0 CE1 C:HIS219 3.2 21.9 1.0 CD2 C:HIS219 3.2 20.8 1.0 CD2 C:HIS223 3.3 21.3 1.0 CD2 C:HIS229 3.3 26.0 1.0 CE1 C:HIS229 3.3 27.3 1.0 C23 C:RXP6003 3.9 39.4 1.0 O C:HOH6155 4.1 53.3 1.0 C22 C:RXP6003 4.1 38.1 1.0 ND1 C:HIS219 4.3 22.4 1.0 ND1 C:HIS223 4.3 21.9 1.0 C21 C:RXP6003 4.3 33.0 1.0 CG C:HIS219 4.4 21.1 1.0 CG C:HIS223 4.4 21.3 1.0 ND1 C:HIS229 4.4 27.4 1.0 CG C:HIS229 4.4 27.0 1.0 C20 C:RXP6003 4.5 30.9 1.0 C13 C:RXP6003 4.6 29.8 1.0 O C:SER238 4.6 27.7 1.0 OE1 C:GLU220 4.6 21.9 1.0 N4 C:RXP6003 4.6 41.6 1.0 CE C:MET237 4.7 25.8 1.0 C39 C:RXP6003 5.0 27.5 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn5510 b:22.1 occ:1.00 NE2 D:HIS183 2.3 21.3 1.0 NE2 D:HIS168 2.3 29.5 1.0 ND1 D:HIS196 2.4 24.4 1.0 OD2 D:ASP170 2.6 37.2 1.0 OD1 D:ASP170 2.9 35.2 1.0 O D:HOH1632 2.9 98.0 1.0 CD2 D:HIS168 3.0 31.3 1.0 CG D:ASP170 3.1 36.8 1.0 CE1 D:HIS183 3.1 22.3 1.0 CG D:HIS196 3.3 24.2 1.0 CE1 D:HIS196 3.3 25.8 1.0 CD2 D:HIS183 3.3 22.4 1.0 CE1 D:HIS168 3.4 30.4 1.0 CB D:HIS196 3.5 21.5 1.0 CE2 D:PHE185 3.9 33.4 1.0 O D:LEU172 4.0 35.2 1.0 CG D:HIS168 4.2 32.6 1.0 ND1 D:HIS183 4.3 22.9 1.0 ND1 D:HIS168 4.4 31.8 1.0 CE2 D:PHE174 4.4 26.4 1.0 CG D:HIS183 4.4 24.0 1.0 NE2 D:HIS196 4.4 27.3 1.0 CD2 D:HIS196 4.5 25.4 1.0 CB D:ASP170 4.5 37.4 1.0 CZ D:PHE174 4.6 25.1 1.0 CD2 D:PHE185 4.6 32.9 1.0 CB D:LEU172 4.8 35.8 1.0 CZ D:PHE185 4.8 33.1 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn5511 b:18.4 occ:1.00 NE2 D:HIS229 2.2 25.9 1.0 NE2 D:HIS223 2.3 20.0 1.0 NE2 D:HIS219 2.4 14.9 1.0 O1P D:RXP6004 2.4 24.4 1.0 O2P D:RXP6004 2.8 23.8 1.0 P D:RXP6004 3.1 24.7 1.0 CD2 D:HIS229 3.2 26.1 1.0 CE1 D:HIS229 3.2 26.3 1.0 CD2 D:HIS223 3.3 20.6 1.0 CE1 D:HIS223 3.3 19.7 1.0 CD2 D:HIS219 3.3 15.7 1.0 CE1 D:HIS219 3.3 15.0 1.0 C23 D:RXP6004 4.0 28.6 1.0 C22 D:RXP6004 4.3 28.1 1.0 C21 D:RXP6004 4.3 24.0 1.0 ND1 D:HIS229 4.3 27.8 1.0 CG D:HIS229 4.3 28.4 1.0 O D:HOH757 4.3 21.1 1.0 O D:HOH686 4.4 56.7 1.0 ND1 D:HIS223 4.4 20.5 1.0 CG D:HIS223 4.4 20.9 1.0 ND1 D:HIS219 4.4 16.0 1.0 C20 D:RXP6004 4.5 22.5 1.0 CG D:HIS219 4.5 15.9 1.0 C13 D:RXP6004 4.5 22.5 1.0 O D:SER238 4.7 22.8 1.0 OE1 D:GLU220 4.8 19.9 1.0 CA D:PRO239 5.0 23.0 1.0 C39 D:RXP6004 5.0 22.5 1.0

Zinc binding site 9 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn5513 b:24.0 occ:1.00 OD2 E:ASP170 2.3 37.2 1.0 ND1 E:HIS196 2.3 21.0 1.0 NE2 E:HIS183 2.3 23.3 1.0 NE2 E:HIS168 2.3 31.5 1.0 CD2 E:HIS168 2.9 30.2 1.0 CG E:ASP170 3.1 36.6 1.0 CE1 E:HIS183 3.2 23.8 1.0 OD1 E:ASP170 3.2 35.0 1.0 CG E:HIS196 3.2 21.4 1.0 CE1 E:HIS196 3.3 21.9 1.0 CD2 E:HIS183 3.3 23.6 1.0 CB E:HIS196 3.5 20.0 1.0 CE1 E:HIS168 3.5 30.9 1.0 O E:LEU172 4.1 33.8 1.0 CG E:HIS168 4.1 31.3 1.0 CE2 E:PHE185 4.2 41.9 1.0 ND1 E:HIS183 4.3 24.2 1.0 NE2 E:HIS196 4.4 22.2 1.0 CD2 E:HIS196 4.4 21.6 1.0 CE2 E:PHE174 4.4 22.6 1.0 CG E:HIS183 4.4 23.3 1.0 ND1 E:HIS168 4.4 31.6 1.0 CB E:ASP170 4.5 36.8 1.0 CB E:LEU172 4.6 35.2 1.0 CD2 E:PHE185 4.6 40.0 1.0 CZ E:PHE174 4.6 22.3 1.0 CD1 E:LEU172 5.0 35.6 1.0 CA E:HIS196 5.0 19.1 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn5514 b:21.0 occ:1.00 O1P E:RXP6005 2.1 38.9 1.0 NE2 E:HIS223 2.2 23.6 1.0 NE2 E:HIS219 2.4 21.4 1.0 NE2 E:HIS229 2.4 31.4 1.0 O2P E:RXP6005 2.8 40.4 1.0 P E:RXP6005 2.9 39.2 1.0 CE1 E:HIS223 3.2 25.4 1.0 CD2 E:HIS229 3.2 32.4 1.0 CD2 E:HIS223 3.2 25.8 1.0 CD2 E:HIS219 3.2 20.6 1.0 CE1 E:HIS219 3.4 20.5 1.0 CE1 E:HIS229 3.4 31.1 1.0 O E:HOH6108 3.5 71.4 1.0 C23 E:RXP6005 4.0 44.4 1.0 C21 E:RXP6005 4.1 37.9 1.0 C22 E:RXP6005 4.1 43.2 1.0 ND1 E:HIS223 4.3 25.4 1.0 C20 E:RXP6005 4.3 36.2 1.0 CG E:HIS223 4.4 25.2 1.0 CG E:HIS229 4.4 33.1 1.0 CG E:HIS219 4.4 20.8 1.0 ND1 E:HIS219 4.4 21.4 1.0 O E:HOH6137 4.5 25.9 1.0 ND1 E:HIS229 4.5 32.8 1.0 O E:HOH6218 4.5 81.6 1.0 O E:SER238 4.6 31.6 1.0 C13 E:RXP6005 4.7 34.2 1.0 N4 E:RXP6005 4.9 48.9 1.0 CE E:MET237 4.9 28.8 1.0 OE1 E:GLU220 4.9 22.4 1.0 CA E:PRO239 5.0 30.0 1.0

A.L.Gall, M.Ruff, R.Kannan, P.Cuniasse, A.Yiotakis, V.Dive, M.C.Rio, P.Basset, D.Moras. Crystal Structure of the Stromelysin-3 (Mmp-11) Catalytic Domain Complexed with A Phosphinic Inhibitor Mimicking the Transition-State. J.Mol.Biol. V. 307 577 2001.
ISSN: ISSN 0022-2836
PubMed: 11254383
DOI: 10.1006/JMBI.2001.4493