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Zinc 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:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1utz

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1268

b:23.8
occ:1.00
 NE2 A:HIS228 2.1 26.1 1.0
O2 A:HAE1267 2.1 23.3 1.0
NE2 A:HIS222 2.2 16.4 1.0
NE2 A:HIS218 2.2 20.0 1.0
O A:HAE1267 2.2 22.9 1.0
C2 A:HAE1267 2.8 23.7 1.0
N A:HAE1267 2.9 21.1 1.0
CE1 A:HIS228 3.0 22.5 1.0
CD2 A:HIS218 3.0 20.4 1.0
CD2 A:HIS222 3.1 17.0 1.0
CD2 A:HIS228 3.1 25.7 1.0
CE1 A:HIS222 3.2 17.1 1.0
CE1 A:HIS218 3.2 21.9 1.0
O A:HOH2072 3.9 35.7 1.0
ND1 A:HIS228 4.1 23.7 1.0
CG A:HIS228 4.2 24.8 1.0
CG A:HIS218 4.2 22.6 1.0
OE2 A:GLU219 4.2 23.8 1.0
O A:HOH2071 4.2 27.5 1.0
CG A:HIS222 4.2 18.3 1.0
ND1 A:HIS222 4.3 17.3 1.0
ND1 A:HIS218 4.3 20.7 1.0
C1 A:HAE1267 4.3 22.3 1.0
C4 A:PF31265 4.7 25.0 1.0
S1 A:PF31265 4.8 26.3 1.0
OE1 A:GLU219 4.9 21.9 1.0
CD A:GLU219 4.9 23.1 1.0

Zinc binding site 2 out of 4 in 1utz

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1269

b:24.2
occ:1.00
 OD2 A:ASP170 1.9 28.4 1.0
ND1 A:HIS196 2.0 21.6 1.0
NE2 A:HIS183 2.0 24.7 1.0
NE2 A:HIS168 2.1 20.2 1.0
CE1 A:HIS183 2.8 26.5 1.0
CG A:ASP170 2.8 26.9 1.0
CD2 A:HIS168 2.9 21.4 1.0
CE1 A:HIS196 2.9 22.6 1.0
CG A:HIS196 3.0 23.5 1.0
OD1 A:ASP170 3.1 23.7 1.0
CD2 A:HIS183 3.2 24.0 1.0
CE1 A:HIS168 3.2 24.0 1.0
CB A:HIS196 3.4 22.0 1.0
ND1 A:HIS183 4.0 26.4 1.0
NE2 A:HIS196 4.1 21.3 1.0
CG A:HIS168 4.1 23.1 1.0
CD2 A:HIS196 4.1 21.9 1.0
CB A:ASP170 4.2 27.2 1.0
CG A:HIS183 4.2 24.3 1.0
ND1 A:HIS168 4.2 22.1 1.0
CE1 A:PHE185 4.3 27.3 1.0
O A:HIS172 4.3 27.6 1.0
CZ A:PHE174 4.6 26.0 1.0
CZ A:PHE185 4.7 26.0 1.0
CE2 A:PHE174 4.9 23.6 1.0
CA A:HIS196 4.9 23.0 1.0
O A:HOH2027 4.9 30.9 1.0
CB A:HIS172 5.0 28.5 1.0

Zinc binding site 3 out of 4 in 1utz

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1267

b:27.3
occ:1.00
 O B:HAE1266 2.0 23.8 1.0
NE2 B:HIS228 2.0 24.9 1.0
NE2 B:HIS218 2.0 21.3 1.0
NE2 B:HIS222 2.2 20.3 1.0
O2 B:HAE1266 2.3 27.6 1.0
N B:HAE1266 2.8 23.4 1.0
C2 B:HAE1266 2.9 26.9 1.0
CE1 B:HIS218 2.9 21.3 1.0
CD2 B:HIS228 3.0 24.8 1.0
CE1 B:HIS228 3.0 23.9 1.0
CD2 B:HIS222 3.1 22.1 1.0
CD2 B:HIS218 3.1 22.2 1.0
CE1 B:HIS222 3.2 20.3 1.0
O B:HOH2059 4.0 31.9 1.0
ND1 B:HIS218 4.1 23.3 1.0
ND1 B:HIS228 4.1 23.1 1.0
CG B:HIS228 4.2 24.2 1.0
O B:HOH2040 4.2 84.0 1.0
CG B:HIS218 4.2 24.4 1.0
CG B:HIS222 4.3 21.0 1.0
OE2 B:GLU219 4.3 27.8 1.0
ND1 B:HIS222 4.3 22.4 1.0
C1 B:HAE1266 4.4 28.2 1.0
C4 B:PF31265 4.7 28.6 1.0
S1 B:PF31265 4.7 26.7 1.0

Zinc binding site 4 out of 4 in 1utz

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Zinc 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 Zinc with other atoms in the Zn 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:Zn1268

b:26.3
occ:1.00
 OD2 B:ASP170 1.9 24.3 1.0
ND1 B:HIS196 1.9 23.5 1.0
NE2 B:HIS183 1.9 22.8 1.0
NE2 B:HIS168 2.0 26.9 1.0
CE1 B:HIS183 2.8 21.7 1.0
CE1 B:HIS196 2.8 23.9 1.0
CD2 B:HIS168 2.9 25.9 1.0
CG B:ASP170 2.9 25.0 1.0
CG B:HIS196 3.0 25.2 1.0
CE1 B:HIS168 3.0 26.5 1.0
CD2 B:HIS183 3.1 22.0 1.0
OD1 B:ASP170 3.2 22.6 1.0
CB B:HIS196 3.4 24.3 1.0
ND1 B:HIS183 3.9 22.5 1.0
NE2 B:HIS196 4.0 26.2 1.0
CD2 B:HIS196 4.1 23.8 1.0
CG B:HIS168 4.1 26.8 1.0
ND1 B:HIS168 4.1 26.1 1.0
CG B:HIS183 4.1 21.5 1.0
CB B:ASP170 4.2 24.6 1.0
O B:HIS172 4.3 25.4 1.0
CE1 B:PHE185 4.4 26.5 1.0
CZ B:PHE174 4.6 26.1 1.0
CZ B:PHE185 4.8 28.6 1.0
CE2 B:PHE174 4.9 24.2 1.0
CA B:HIS196 4.9 24.3 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: Wed Oct 16 19:37:24 2024

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