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Calcium in PDB 1utz: Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid

Enzymatic activity of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid

All present enzymatic activity of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid, PDB code: 1utz was solved by R.Morales, S.Perrier, J.M.Florent, J.Beltra, S.Dufour, I.De Mendez, P.Manceau, A.Tertre, F.Moreau, D.Compere, A.C.Dublanchet, M.O'gara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.50
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 123.224, 123.224, 168.200, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Other elements in 1utz:

The structure of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid (pdb code 1utz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid, PDB code: 1utz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1utz

Go back to Calcium Binding Sites List in 1utz
Calcium binding site 1 out of 4 in the Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1270

b:28.9
occ:1.00
 O A:ILE180 2.2 26.8 1.0
O A:GLY176 2.3 26.8 1.0
O A:GLY178 2.3 26.9 1.0
OD2 A:ASP175 2.3 27.9 1.0
OD1 A:ASP198 2.4 24.3 1.0
OE2 A:GLU201 2.4 31.2 1.0
C A:ILE180 3.3 25.9 1.0
CG A:ASP198 3.5 25.2 1.0
C A:GLY178 3.5 28.6 1.0
CG A:ASP175 3.5 26.7 1.0
C A:GLY176 3.5 28.2 1.0
CD A:GLU201 3.6 31.3 1.0
N A:GLY178 3.9 27.6 1.0
N A:ILE180 3.9 27.4 1.0
N A:GLY176 4.0 29.4 1.0
OD1 A:ASP175 4.1 28.5 1.0
CB A:ASP198 4.1 24.9 1.0
C A:LYS177 4.1 29.2 1.0
C A:GLY179 4.1 28.4 1.0
CA A:ILE180 4.2 27.0 1.0
C A:ASP175 4.2 29.1 1.0
CA A:GLY178 4.3 26.4 1.0
N A:ASP175 4.3 28.1 1.0
N A:LEU181 4.3 24.8 1.0
CG A:GLU201 4.4 32.3 1.0
OD2 A:ASP198 4.4 22.5 1.0
N A:LYS177 4.4 28.6 1.0
CA A:GLY176 4.4 27.2 1.0
CA A:LYS177 4.4 29.0 1.0
OE1 A:GLU201 4.4 32.5 1.0
CA A:LEU181 4.5 25.1 1.0
N A:GLY179 4.5 28.4 1.0
O A:GLY179 4.6 28.8 1.0
CA A:ASP175 4.6 28.3 1.0
CA A:GLY179 4.6 28.0 1.0
CB A:ASP175 4.6 27.6 1.0
O A:LYS177 4.7 31.2 1.0
CB A:ILE180 4.7 28.1 1.0
O A:ASP175 4.7 30.1 1.0

Calcium binding site 2 out of 4 in 1utz

Go back to Calcium Binding Sites List in 1utz
Calcium binding site 2 out of 4 in the Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1271

b:46.4
occ:1.00
 OD1 A:ASP124 2.3 30.9 1.0
O A:GLU199 2.3 31.5 1.0
O A:GLU201 2.4 31.4 1.0
OE2 A:GLU199 2.4 27.6 1.0
CG A:ASP124 3.0 30.3 1.0
OD2 A:ASP124 3.1 33.1 1.0
C A:GLU199 3.4 29.7 1.0
CD A:GLU199 3.5 28.2 1.0
C A:GLU201 3.6 30.9 1.0
CG A:GLU199 3.9 26.6 1.0
O A:HOH2043 4.0 38.7 1.0
OG1 A:THR122 4.0 27.1 1.0
CA A:PHE202 4.1 26.5 1.0
CA A:GLU199 4.1 27.7 1.0
CD1 A:TRP203 4.2 25.6 1.0
O A:HOH2044 4.3 58.4 1.0
N A:GLU201 4.3 30.3 1.0
N A:PHE202 4.3 28.3 1.0
C A:ASP200 4.4 30.6 1.0
CB A:ASP124 4.4 29.3 1.0
N A:ASP200 4.5 29.4 1.0
O A:HOH2012 4.5 35.0 1.0
N A:TRP203 4.6 25.6 1.0
OE1 A:GLU199 4.6 29.6 1.0
CB A:GLU199 4.6 26.1 1.0
CA A:ASP200 4.7 30.6 1.0
NE1 A:TRP203 4.7 26.1 1.0
CA A:GLU201 4.7 29.8 1.0
O A:ASP200 4.8 32.4 1.0
CD1 A:PHE202 4.9 31.7 1.0
C A:PHE202 4.9 26.4 1.0

Calcium binding site 3 out of 4 in 1utz

Go back to Calcium Binding Sites List in 1utz
Calcium binding site 3 out of 4 in the Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1269

b:30.9
occ:1.00
 O B:GLY176 2.1 33.0 1.0
O B:GLY178 2.3 30.8 1.0
OE2 B:GLU201 2.3 34.4 1.0
O B:ILE180 2.4 27.9 1.0
OD1 B:ASP198 2.4 30.4 1.0
OD2 B:ASP175 2.4 31.4 1.0
C B:GLY176 3.3 33.4 1.0
CG B:ASP198 3.4 29.9 1.0
C B:GLY178 3.5 31.6 1.0
CD B:GLU201 3.5 35.9 1.0
C B:ILE180 3.5 28.7 1.0
CG B:ASP175 3.6 31.9 1.0
N B:GLY178 3.7 32.3 1.0
N B:GLY176 3.9 33.6 1.0
N B:ILE180 4.0 28.5 1.0
CB B:ASP198 4.1 27.5 1.0
C B:LYS177 4.1 33.9 1.0
C B:ASP175 4.1 32.6 1.0
CA B:GLY178 4.2 31.8 1.0
OD1 B:ASP175 4.2 33.7 1.0
CA B:GLY176 4.2 32.8 1.0
CG B:GLU201 4.2 35.1 1.0
N B:ASP175 4.3 30.1 1.0
CA B:ILE180 4.3 29.2 1.0
C B:GLY179 4.3 28.8 1.0
N B:LYS177 4.3 34.0 1.0
CA B:LYS177 4.4 34.5 1.0
OD2 B:ASP198 4.4 30.1 1.0
OE1 B:GLU201 4.4 40.6 1.0
N B:GLY179 4.5 30.7 1.0
CA B:ASP175 4.5 30.8 1.0
N B:LEU181 4.5 30.0 1.0
CB B:ILE180 4.6 28.8 1.0
O B:ASP175 4.6 33.3 1.0
CB B:ASP175 4.6 31.4 1.0
O B:LYS177 4.7 34.9 1.0
O B:GLY179 4.7 28.7 1.0
CA B:GLY179 4.7 29.2 1.0
CA B:LEU181 4.7 29.5 1.0

Calcium binding site 4 out of 4 in 1utz

Go back to Calcium Binding Sites List in 1utz
Calcium binding site 4 out of 4 in the Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Mmp-12 Complexed to (2R)-3-({[4-[(Pyridin-4-Yl) Phenyl]-Thien-2-Yl}Carboxamido)(Phenyl)Propanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1270

b:47.9
occ:1.00
 O B:GLU199 2.2 31.6 1.0
OD1 B:ASP124 2.4 36.3 1.0
O B:GLU201 2.4 31.6 1.0
OE2 B:GLU199 2.4 34.5 1.0
OD2 B:ASP124 3.0 39.3 1.0
CG B:ASP124 3.0 37.9 1.0
C B:GLU199 3.3 31.5 1.0
CD B:GLU199 3.5 34.1 1.0
C B:GLU201 3.6 30.5 1.0
CG B:GLU199 3.9 32.7 1.0
CA B:GLU199 4.1 30.6 1.0
OG1 B:THR122 4.1 33.4 1.0
N B:GLU201 4.1 30.9 1.0
CA B:PHE202 4.2 29.1 1.0
CD1 B:TRP203 4.3 24.4 1.0
C B:ASP200 4.3 30.8 1.0
N B:ASP200 4.3 31.5 1.0
N B:PHE202 4.3 29.7 1.0
CB B:ASP124 4.5 37.0 1.0
CA B:ASP200 4.5 31.2 1.0
CA B:GLU201 4.6 30.8 1.0
OE1 B:GLU199 4.6 36.6 1.0
CB B:GLU199 4.6 32.6 1.0
N B:TRP203 4.7 26.8 1.0
NE1 B:TRP203 4.7 24.8 1.0
O B:ASP200 4.8 32.1 1.0

Reference:

R.Morales, S.Perrier, J.M.Florent, J.Beltra, S.Dufour, I.De Mendez, P.Manceau, A.Tertre, F.Moreau, D.Compere, A.C.Dublanchet, M.O'gara. Crystal Structures of Novel Non-Peptidic, Non-Zinc Chelating Inhibitors Bound to Mmp-12 J.Mol.Biol. V. 341 1063 2004.
ISSN: ISSN 0022-2836
PubMed: 15289103
DOI: 10.1016/J.JMB.2004.06.039
Page generated: Thu Jul 11 23:40:18 2024

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