Zinc in PDB 1uea: Mmp-3/Timp-1 Complex

All present enzymatic activity of Mmp-3/Timp-1 Complex:
3.4.24.17;

The structure of Mmp-3/Timp-1 Complex, PDB code: 1uea was solved by W.Bode, K.Maskos, F.-X.Gomis-Rueth, H.Nagase, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.80
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	80.620, 80.620, 157.620, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / n/a

The structure of Mmp-3/Timp-1 Complex also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Zinc atom in the Mmp-3/Timp-1 Complex (pdb code 1uea). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Mmp-3/Timp-1 Complex, PDB code: 1uea:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:37.8 occ:0.96 NE2 A:HIS211 2.0 29.3 1.0 NE2 A:HIS201 2.1 29.7 1.0 O B:CYS1 2.1 30.1 1.0 N B:CYS1 2.2 24.6 1.0 NE2 A:HIS205 2.3 25.9 1.0 C B:CYS1 2.7 28.2 1.0 CD2 A:HIS211 2.9 28.6 1.0 CA B:CYS1 3.0 27.6 1.0 CD2 A:HIS201 3.0 27.1 1.0 CE1 A:HIS211 3.1 29.1 1.0 CD2 A:HIS205 3.2 24.9 1.0 CE1 A:HIS201 3.2 31.7 1.0 CE1 A:HIS205 3.4 25.1 1.0 CB B:CYS1 3.8 30.8 1.0 N B:THR2 3.8 26.6 1.0 CG A:HIS211 4.1 25.5 1.0 ND1 A:HIS211 4.2 26.6 1.0 CG A:HIS201 4.2 25.2 1.0 OE2 A:GLU202 4.3 20.4 1.0 ND1 A:HIS201 4.3 30.7 1.0 CG A:HIS205 4.4 23.0 1.0 CA B:THR2 4.4 28.6 1.0 ND1 A:HIS205 4.5 26.1 1.0 OE1 A:GLU202 4.5 21.0 1.0 O B:SER68 4.6 28.9 1.0 CB A:PRO221 4.7 25.4 1.0 CD A:GLU202 4.8 21.1 1.0 CA B:SER68 4.8 24.5 1.0 CA A:PRO221 4.9 27.9 1.0 CB B:THR2 4.9 28.9 1.0 O B:GLU67 4.9 21.9 1.0

Zinc binding site 2 out of 4 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:43.9 occ:1.00 OD2 A:ASP153 1.8 38.9 1.0 NE2 A:HIS166 1.8 36.4 1.0 NE2 A:HIS151 2.1 41.3 1.0 CE1 A:HIS166 2.4 34.7 1.0 ND1 A:HIS179 2.5 36.9 1.0 CG A:ASP153 2.5 41.4 1.0 OD1 A:ASP153 2.6 40.7 1.0 CD2 A:HIS151 2.9 44.1 1.0 CD2 A:HIS166 3.1 33.7 1.0 CE1 A:HIS151 3.3 43.7 1.0 CE1 A:HIS179 3.3 37.4 1.0 CG A:HIS179 3.4 36.5 1.0 ND1 A:HIS166 3.7 31.1 1.0 CB A:HIS179 3.8 32.5 1.0 CB A:ASP153 4.0 45.2 1.0 CG A:HIS166 4.0 29.3 1.0 O A:TYR155 4.0 34.4 1.0 OH A:TYR168 4.2 41.9 1.0 CG A:HIS151 4.2 44.7 1.0 ND1 A:HIS151 4.3 44.4 1.0 NE2 A:HIS179 4.4 38.4 1.0 CE1 A:TYR168 4.4 35.0 1.0 CD2 A:HIS179 4.4 37.6 1.0 CE2 A:PHE157 4.6 35.2 1.0 CZ A:PHE157 4.7 32.5 1.0 CZ A:TYR168 4.8 38.5 1.0 C A:TYR155 5.0 35.8 1.0

Zinc binding site 3 out of 4 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1 b:35.5 occ:0.97 NE2 C:HIS211 1.8 33.5 1.0 O D:CYS1 2.1 32.8 1.0 N D:CYS1 2.2 29.4 1.0 NE2 C:HIS201 2.2 30.4 1.0 NE2 C:HIS205 2.2 28.2 1.0 CE1 C:HIS211 2.7 33.1 1.0 C D:CYS1 2.8 32.3 1.0 CD2 C:HIS211 2.9 31.0 1.0 CA D:CYS1 3.0 29.8 1.0 CD2 C:HIS201 3.0 29.9 1.0 CD2 C:HIS205 3.1 27.5 1.0 CE1 C:HIS201 3.3 30.3 1.0 CE1 C:HIS205 3.3 30.9 1.0 CB D:CYS1 3.7 28.5 1.0 ND1 C:HIS211 3.9 29.4 1.0 CG C:HIS211 4.0 28.8 1.0 N D:THR2 4.0 33.2 1.0 CG C:HIS201 4.2 28.3 1.0 CG C:HIS205 4.3 27.9 1.0 ND1 C:HIS201 4.3 27.9 1.0 OE2 C:GLU202 4.3 44.7 1.0 ND1 C:HIS205 4.4 30.3 1.0 CA D:SER68 4.4 23.3 1.0 O D:SER68 4.6 19.8 1.0 OE1 C:GLU202 4.7 42.1 1.0 CA D:THR2 4.7 32.8 1.0 O D:GLU67 4.8 19.4 1.0 CD C:GLU202 4.8 40.6 1.0 C D:SER68 4.9 20.0 1.0 CB C:PRO221 5.0 29.1 1.0 N D:SER68 5.0 24.5 1.0

Zinc binding site 4 out of 4 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn2 b:46.8 occ:0.97 OD2 C:ASP153 1.8 34.8 1.0 NE2 C:HIS166 1.8 35.0 1.0 NE2 C:HIS151 2.1 39.6 1.0 ND1 C:HIS179 2.2 35.0 1.0 CG C:ASP153 2.8 34.1 1.0 CE1 C:HIS166 2.8 32.4 1.0 CD2 C:HIS166 3.0 31.9 1.0 CD2 C:HIS151 3.0 44.0 1.0 CE1 C:HIS151 3.1 42.3 1.0 OD1 C:ASP153 3.1 33.7 1.0 CE1 C:HIS179 3.2 35.6 1.0 CG C:HIS179 3.2 33.8 1.0 CB C:HIS179 3.5 33.7 1.0 ND1 C:HIS166 3.9 28.6 1.0 CB C:ASP153 4.1 37.5 1.0 CG C:HIS166 4.1 32.6 1.0 CG C:HIS151 4.1 42.6 1.0 ND1 C:HIS151 4.2 42.0 1.0 OH C:TYR168 4.2 26.9 1.0 NE2 C:HIS179 4.4 37.2 1.0 O C:TYR155 4.4 38.8 1.0 CD2 C:HIS179 4.4 33.7 1.0 CE1 C:TYR168 4.5 20.4 1.0 CE2 C:PHE157 4.6 44.5 1.0 CZ C:PHE157 4.7 41.6 1.0 CZ C:TYR168 4.9 23.3 1.0 O C:HOH1110 5.0 41.3 1.0 CA C:HIS179 5.0 31.6 1.0

F.X.Gomis-Ruth, K.Maskos, M.Betz, A.Bergner, R.Huber, K.Suzuki, N.Yoshida, H.Nagase, K.Brew, G.P.Bourenkov, H.Bartunik, W.Bode. Mechanism of Inhibition of the Human Matrix Metalloproteinase Stromelysin-1 By Timp-1. Nature V. 389 77 1997.
ISSN: ISSN 0028-0836
PubMed: 9288970
DOI: 10.1038/37995