Calcium 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:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Mmp-3/Timp-1 Complex (pdb code 1uea). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Mmp-3/Timp-1 Complex, PDB code: 1uea:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca3 b:42.4 occ:0.89 OD1 A:ASP158 2.1 36.5 1.0 OD2 A:ASP181 2.2 35.7 1.0 O A:GLY161 2.3 41.9 1.0 O A:GLY159 2.3 51.0 1.0 OE2 A:GLU184 2.5 45.6 1.0 O A:VAL163 2.5 36.3 1.0 CG A:ASP181 3.2 40.4 1.0 CG A:ASP158 3.2 37.8 1.0 C A:VAL163 3.4 35.8 1.0 C A:GLY161 3.5 44.1 1.0 C A:GLY159 3.5 44.4 1.0 CD A:GLU184 3.7 43.4 1.0 OD2 A:ASP158 3.8 37.5 1.0 N A:GLY161 3.8 42.4 1.0 N A:VAL163 3.8 40.1 1.0 OD1 A:ASP181 4.0 43.0 1.0 C A:PRO160 4.0 40.7 1.0 C A:ASP158 4.0 43.2 1.0 CB A:ASP181 4.1 41.8 1.0 N A:GLY159 4.1 41.8 1.0 CA A:VAL163 4.2 35.7 1.0 CA A:GLY161 4.2 42.0 1.0 O A:ASP158 4.3 45.0 1.0 N A:LEU164 4.3 34.2 1.0 N A:ASP158 4.4 43.1 1.0 CB A:ASP158 4.4 40.0 1.0 CA A:PRO160 4.4 39.7 1.0 N A:PRO160 4.4 41.3 1.0 CA A:ASP158 4.4 42.0 1.0 CG A:GLU184 4.4 41.3 1.0 C A:ASN162 4.5 46.8 1.0 CA A:GLY159 4.5 42.6 1.0 O A:PRO160 4.5 42.9 1.0 N A:ASN162 4.5 44.8 1.0 CA A:LEU164 4.6 30.0 1.0 O A:HOH1465 4.6 37.0 1.0 OE1 A:GLU184 4.6 44.7 1.0 CB A:VAL163 4.8 37.9 1.0 CD1 A:LEU164 4.8 29.3 1.0 CA A:ASN162 4.8 46.2 1.0

Calcium binding site 2 out of 6 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4 b:34.0 occ:0.93 O A:GLY173 2.2 35.6 1.0 O A:ASP141 2.3 34.0 1.0 O A:ASN175 2.3 36.9 1.0 OD1 A:ASP177 2.5 33.1 1.0 C A:GLY173 3.3 39.4 1.0 CG A:ASP177 3.5 31.2 1.0 C A:ASP141 3.5 34.6 1.0 C A:ASN175 3.5 31.0 1.0 N A:ASN175 3.8 35.1 1.0 OD2 A:ASP177 3.8 34.0 1.0 C A:ILE174 3.8 37.6 1.0 O A:ALA140 4.1 46.4 1.0 CA A:ASP141 4.2 36.3 1.0 CA A:ASN175 4.2 32.6 1.0 N A:ILE174 4.2 39.0 1.0 CA A:ILE174 4.2 38.7 1.0 O A:ILE174 4.2 35.3 1.0 CA A:GLY173 4.3 38.4 1.0 N A:ASP177 4.3 22.0 1.0 N A:GLY173 4.5 40.3 1.0 O A:GLY171 4.5 31.3 1.0 N A:GLY176 4.6 28.2 1.0 N A:ILE142 4.6 29.4 1.0 CG A:MSE143 4.6 46.0 1.0 CB A:ASP177 4.7 23.7 1.0 CA A:GLY176 4.8 23.9 1.0 N A:MSE143 4.8 33.9 1.0 C A:GLY176 4.8 22.6 1.0 CA A:ILE142 4.9 25.7 1.0 O A:HOH1223 4.9 68.3 1.0 CB A:ASN175 4.9 32.0 1.0 C A:PRO172 4.9 39.6 1.0 CA A:ASP177 5.0 24.4 1.0 O A:HOH1024 5.0 25.2 1.0 C A:ALA140 5.0 43.9 1.0 CH2 A:TRP92 5.0 12.3 1.0

Calcium binding site 3 out of 6 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca5 b:56.2 occ:0.57 O A:ASP182 1.6 53.8 1.0 O A:GLU184 1.7 39.1 1.0 O A:HOH1337 2.4 65.9 1.0 OD1 A:ASP107 2.7 62.5 1.0 C A:GLU184 2.8 39.6 1.0 C A:ASP182 2.9 48.9 1.0 OD2 A:ASP107 3.0 65.7 1.0 CG A:ASP107 3.2 64.0 1.0 N A:GLU184 3.2 41.0 1.0 C A:ASP183 3.3 45.5 1.0 OD1 A:ASP182 3.6 31.0 1.0 CA A:GLU184 3.7 39.5 1.0 N A:ASP183 3.7 46.8 1.0 O A:ASP183 3.7 48.9 1.0 CA A:ASP183 3.8 44.9 1.0 N A:GLN185 3.8 41.6 1.0 CA A:ASP182 3.9 45.4 1.0 CA A:GLN185 4.1 42.9 1.0 CG A:ASP182 4.5 36.0 1.0 OE1 A:GLN185 4.6 64.0 1.0 CD1 A:TRP186 4.6 35.6 1.0 CB A:ASP182 4.6 41.4 1.0 N A:TRP186 4.6 40.3 1.0 CB A:ASP107 4.7 59.7 1.0 O A:ASP181 4.8 45.3 1.0 CB A:GLU184 4.8 42.3 1.0 C A:GLN185 4.9 40.6 1.0 OG1 A:THR105 5.0 46.7 1.0

Calcium binding site 4 out of 6 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca3 b:44.2 occ:1.02 OD1 C:ASP158 2.3 49.2 1.0 O C:VAL163 2.3 41.0 1.0 OD2 C:ASP181 2.4 54.6 1.0 O C:GLY161 2.4 57.4 1.0 O C:GLY159 2.5 44.7 1.0 OE2 C:GLU184 2.6 47.0 1.0 C C:VAL163 3.5 44.0 1.0 CD C:GLU184 3.5 44.2 1.0 CG C:ASP181 3.5 50.7 1.0 CG C:ASP158 3.5 48.1 1.0 C C:GLY161 3.6 57.8 1.0 C C:GLY159 3.7 48.8 1.0 C C:PRO160 3.8 49.0 1.0 N C:GLY161 3.9 52.6 1.0 NH2 C:ARG149 4.1 41.0 0.0 N C:VAL163 4.1 49.8 1.0 O C:PRO160 4.1 49.5 1.0 CB C:ASP181 4.1 45.9 1.0 OE1 C:GLU184 4.2 45.7 1.0 CA C:PRO160 4.2 46.7 1.0 OD2 C:ASP158 4.2 50.6 1.0 C C:ASP158 4.2 54.0 1.0 O C:ASP158 4.3 59.5 1.0 CG C:GLU184 4.3 43.4 1.0 CA C:VAL163 4.3 45.8 1.0 CA C:GLY161 4.3 55.3 1.0 N C:PRO160 4.4 46.7 1.0 N C:LEU164 4.4 43.0 1.0 N C:ASP158 4.4 44.6 1.0 OD1 C:ASP181 4.5 51.9 1.0 N C:GLY159 4.5 53.3 1.0 C C:ASN162 4.5 54.0 1.0 CA C:LEU164 4.6 40.6 1.0 CA C:ASP158 4.6 49.0 1.0 CB C:ASP158 4.7 48.3 1.0 N C:ASN162 4.7 60.3 1.0 CD1 C:LEU164 4.7 35.0 1.0 CA C:GLY159 4.8 50.7 1.0 CB C:VAL163 4.8 43.0 1.0 CB C:ASN162 4.9 70.5 1.0 CA C:ASN162 4.9 60.8 1.0

Calcium binding site 5 out of 6 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca4 b:35.4 occ:1.10 O C:ASP141 2.0 26.4 1.0 O C:ASN175 2.5 28.4 1.0 O C:GLY173 2.5 14.1 1.0 OD1 C:ASP177 2.5 26.2 1.0 C C:ASP141 3.1 25.9 1.0 CG C:ASP177 3.6 25.8 1.0 O C:ALA140 3.6 30.6 1.0 CA C:ASP141 3.7 26.0 1.0 C C:ASN175 3.7 22.7 1.0 C C:GLY173 3.7 15.8 1.0 OD2 C:ASP177 4.0 27.8 1.0 N C:ASP177 4.1 15.9 1.0 N C:ILE142 4.2 22.4 1.0 O C:HOH1014 4.3 24.8 1.0 N C:MSE143 4.4 17.9 1.0 C C:ILE174 4.4 18.2 1.0 CA C:GLY176 4.4 17.1 1.0 CG C:MSE143 4.5 30.9 1.0 O C:ILE174 4.5 16.3 1.0 C C:GLY176 4.5 16.8 1.0 N C:ASN175 4.5 15.3 1.0 O C:GLY171 4.5 29.5 1.0 C C:ALA140 4.5 29.8 1.0 N C:GLY176 4.5 23.3 1.0 N C:GLY173 4.6 11.0 1.0 CA C:ILE142 4.6 17.8 1.0 CA C:GLY173 4.6 12.9 1.0 N C:ASP141 4.6 24.5 1.0 N C:ILE174 4.7 18.5 1.0 CA C:ASN175 4.7 20.2 1.0 CB C:ASP177 4.8 18.8 1.0 CB C:ASP141 4.8 32.4 1.0 CA C:ILE174 4.8 17.9 1.0 CA C:ASP177 4.8 21.0 1.0 C C:PRO172 4.9 16.8 1.0 CB C:MSE143 4.9 24.0 1.0 CH2 C:TRP92 5.0 21.1 1.0

Calcium binding site 6 out of 6 in the Mmp-3/Timp-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Mmp-3/Timp-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca5 b:58.8 occ:0.63 O C:GLU184 1.7 43.3 1.0 O C:ASP182 1.7 49.2 1.0 OD2 C:ASP107 2.7 38.9 1.0 OE1 C:GLN185 2.8 51.3 1.0 C C:GLU184 2.9 39.3 1.0 OD1 C:ASP107 2.9 41.8 1.0 C C:ASP182 2.9 45.7 1.0 CG C:ASP107 3.2 42.6 1.0 N C:GLU184 3.3 37.5 1.0 OD1 C:ASP182 3.4 43.0 1.0 CA C:GLU184 3.8 38.3 1.0 C C:ASP183 3.8 41.0 1.0 CA C:ASP182 3.9 44.0 1.0 N C:GLN185 3.9 38.9 1.0 N C:ASP183 3.9 44.8 1.0 CD C:GLN185 4.0 52.4 1.0 CA C:GLN185 4.1 36.3 1.0 CA C:ASP183 4.1 42.6 1.0 CD1 C:TRP186 4.1 27.5 1.0 CG C:ASP182 4.3 44.7 1.0 NE1 C:TRP186 4.4 26.8 1.0 CB C:ASP182 4.5 45.5 1.0 CB C:ASP107 4.7 44.3 1.0 O C:ASP183 4.7 46.0 1.0 OG1 C:THR105 4.7 50.4 1.0 O C:ASP181 4.8 35.6 1.0 N C:TRP186 4.8 39.2 1.0 NE2 C:GLN185 4.8 54.7 1.0 CB C:GLU184 4.8 40.2 1.0 O C:HOH1388 5.0 47.1 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