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Zinc in PDB 1ros: Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid

Enzymatic activity of Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid

All present enzymatic activity of Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid, PDB code: 1ros 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) 24.30 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 123.200, 123.200, 59.500, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.9

Other elements in 1ros:

The structure of Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid (pdb code 1ros). 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 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid, PDB code: 1ros:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1ros

Go back to Zinc Binding Sites List in 1ros
Zinc binding site 1 out of 4 in the Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic 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 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:15.8
occ:1.00
 O5 A:DEO1 1.9 15.0 1.0
NE2 A:HIS228 2.1 13.8 1.0
NE2 A:HIS222 2.1 12.8 1.0
NE2 A:HIS218 2.1 12.0 1.0
C28 A:DEO1 2.5 16.1 1.0
O6 A:DEO1 2.6 13.2 1.0
CE1 A:HIS218 2.9 14.2 1.0
CE1 A:HIS222 3.0 14.4 1.0
CE1 A:HIS228 3.0 9.6 1.0
CD2 A:HIS228 3.0 11.1 1.0
CD2 A:HIS222 3.1 12.7 1.0
CD2 A:HIS218 3.1 14.0 1.0
C11 A:DEO1 4.1 17.8 1.0
ND1 A:HIS218 4.1 11.7 1.0
ND1 A:HIS228 4.1 9.4 1.0
ND1 A:HIS222 4.1 12.9 1.0
C3 A:DEO1 4.2 14.5 1.0
O A:HOH430 4.2 16.7 1.0
CG A:HIS228 4.2 9.6 1.0
CG A:HIS222 4.2 11.3 1.0
C2 A:DEO1 4.2 17.7 1.0
CG A:HIS218 4.2 14.1 1.0
C8 A:DEO1 4.3 16.0 1.0
C1 A:DEO1 4.4 12.9 1.0
N1 A:DEO1 4.4 16.6 1.0
C15 A:DEO1 4.5 15.6 1.0
C4 A:DEO1 4.6 15.2 1.0
OE2 A:GLU219 4.7 15.4 1.0
C7 A:DEO1 4.7 15.3 1.0
C12 A:DEO1 4.7 15.1 1.0
O1 A:DEO1 4.8 16.9 1.0
C10 A:DEO1 4.8 20.0 1.0
C16 A:DEO1 4.8 16.0 1.0
C14 A:DEO1 4.9 14.7 1.0
O2 A:DEO1 4.9 19.4 1.0

Zinc binding site 2 out of 4 in 1ros

Go back to Zinc Binding Sites List in 1ros
Zinc binding site 2 out of 4 in the Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic 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 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:16.6
occ:1.00
 NE2 A:HIS168 1.9 15.1 1.0
NE2 A:HIS183 2.0 14.7 1.0
OD2 A:ASP170 2.0 20.3 1.0
ND1 A:HIS196 2.1 17.3 1.0
CD2 A:HIS168 2.8 14.7 1.0
CE1 A:HIS183 2.9 15.6 1.0
CG A:ASP170 3.0 17.4 1.0
CE1 A:HIS196 3.0 15.6 1.0
CE1 A:HIS168 3.1 15.9 1.0
CD2 A:HIS183 3.1 14.0 1.0
CG A:HIS196 3.1 16.4 1.0
OD1 A:ASP170 3.3 15.4 1.0
CB A:HIS196 3.4 14.4 1.0
CG A:HIS168 4.0 16.4 1.0
ND1 A:HIS183 4.0 12.9 1.0
ND1 A:HIS168 4.1 13.8 1.0
CG A:HIS183 4.1 12.5 1.0
NE2 A:HIS196 4.2 18.3 1.0
CD2 A:HIS196 4.2 15.3 1.0
CB A:ASP170 4.3 17.7 1.0
O A:HIS172 4.3 17.0 1.0
CE1 A:PHE185 4.4 17.2 1.0
CZ A:PHE174 4.6 16.5 1.0
CZ A:PHE185 4.7 16.6 1.0
CE2 A:PHE174 4.7 17.3 1.0
CA A:HIS196 4.9 14.7 1.0

Zinc binding site 3 out of 4 in 1ros

Go back to Zinc Binding Sites List in 1ros
Zinc binding site 3 out of 4 in the Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic 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 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:15.8
occ:1.00
 O5 B:DEO1 1.9 15.0 1.0
NE2 B:HIS218 2.0 11.4 1.0
NE2 B:HIS228 2.0 13.7 1.0
NE2 B:HIS222 2.1 14.0 1.0
C28 B:DEO1 2.6 16.1 1.0
O6 B:DEO1 2.6 13.2 1.0
CE1 B:HIS218 2.8 13.2 1.0
CE1 B:HIS228 3.0 11.4 1.0
CE1 B:HIS222 3.0 15.1 1.0
CD2 B:HIS228 3.0 12.5 1.0
CD2 B:HIS222 3.1 12.7 1.0
CD2 B:HIS218 3.1 11.6 1.0
ND1 B:HIS218 4.0 11.7 1.0
C11 B:DEO1 4.1 17.8 1.0
ND1 B:HIS228 4.1 10.9 1.0
O B:HOH529 4.1 23.3 1.0
CG B:HIS218 4.1 11.6 1.0
ND1 B:HIS222 4.1 12.5 1.0
CG B:HIS228 4.2 10.8 1.0
C3 B:DEO1 4.2 14.5 1.0
CG B:HIS222 4.2 11.4 1.0
C2 B:DEO1 4.3 17.7 1.0
C8 B:DEO1 4.3 16.0 1.0
C15 B:DEO1 4.4 15.6 1.0
N1 B:DEO1 4.4 16.6 1.0
C1 B:DEO1 4.5 12.9 1.0
C4 B:DEO1 4.6 15.2 1.0
C12 B:DEO1 4.7 15.1 1.0
O1 B:DEO1 4.8 16.9 1.0
OE2 B:GLU219 4.8 16.2 1.0
C16 B:DEO1 4.8 16.0 1.0
C7 B:DEO1 4.8 15.3 1.0
C10 B:DEO1 4.8 20.0 1.0
C14 B:DEO1 4.8 14.7 1.0
CE B:MET236 4.9 15.6 1.0

Zinc binding site 4 out of 4 in 1ros

Go back to Zinc Binding Sites List in 1ros
Zinc binding site 4 out of 4 in the Crystal Structure of Mmp-12 Complexed to 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic 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 2-(1,3-Dioxo-1,3-Dihydro-2H- Isoindol-2-Yl)Ethyl-4-(4-Ethoxy[1,1-Biphenyl]-4-Yl)-4-Oxobutanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:16.0
occ:1.00
 OD2 B:ASP170 1.9 18.1 1.0
NE2 B:HIS168 2.0 14.9 1.0
ND1 B:HIS196 2.0 8.9 1.0
NE2 B:HIS183 2.1 17.9 1.0
CD2 B:HIS168 2.8 15.2 1.0
CG B:ASP170 2.8 15.6 1.0
CE1 B:HIS183 2.9 18.2 1.0
CE1 B:HIS196 2.9 10.1 1.0
CG B:HIS196 3.1 9.9 1.0
CE1 B:HIS168 3.1 13.6 1.0
OD1 B:ASP170 3.1 16.8 1.0
CD2 B:HIS183 3.2 14.8 1.0
CB B:HIS196 3.5 11.9 1.0
CG B:HIS168 4.0 15.4 1.0
ND1 B:HIS183 4.1 14.2 1.0
NE2 B:HIS196 4.1 10.6 1.0
ND1 B:HIS168 4.1 15.0 1.0
CD2 B:HIS196 4.2 10.0 1.0
CB B:ASP170 4.2 17.9 1.0
CG B:HIS183 4.2 13.6 1.0
O B:HIS172 4.3 16.6 1.0
CE1 B:PHE185 4.4 17.5 1.0
CE2 B:PHE174 4.6 18.5 1.0
CZ B:PHE174 4.7 16.9 1.0
CZ B:PHE185 4.8 17.6 1.0
CA B:HIS196 4.9 11.9 1.0
O B:HOH507 5.0 14.3 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 18:38:31 2024

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