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Calcium 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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1ros

Go back to Calcium Binding Sites List in 1ros
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca402

b:16.7
occ:1.00
 OE2 A:GLU201 2.2 19.9 1.0
O A:GLY176 2.3 18.6 1.0
O A:ILE180 2.3 16.4 1.0
OD1 A:ASP198 2.3 16.8 1.0
OD2 A:ASP175 2.4 18.3 1.0
O A:GLY178 2.4 19.0 1.0
CG A:ASP198 3.4 18.3 1.0
CD A:GLU201 3.4 15.8 1.0
C A:ILE180 3.5 15.2 1.0
C A:GLY176 3.5 18.1 1.0
CG A:ASP175 3.6 19.0 1.0
C A:GLY178 3.6 18.6 1.0
N A:GLY178 3.9 17.5 1.0
CB A:ASP198 3.9 17.6 1.0
N A:GLY176 4.0 19.4 1.0
N A:ILE180 4.0 17.3 1.0
OE1 A:GLU201 4.2 16.8 1.0
C A:LYS177 4.2 18.2 1.0
OD1 A:ASP175 4.2 20.5 1.0
C A:ASP175 4.2 19.0 1.0
N A:ASP175 4.3 18.5 1.0
OD2 A:ASP198 4.3 16.6 1.0
CA A:ILE180 4.3 17.0 1.0
CA A:GLY176 4.4 18.4 1.0
C A:GLY179 4.4 17.1 1.0
N A:LYS177 4.4 18.2 1.0
N A:LEU181 4.4 13.9 1.0
CG A:GLU201 4.4 14.8 1.0
CA A:GLY178 4.4 16.9 1.0
CA A:LYS177 4.4 18.1 1.0
CA A:LEU181 4.5 12.4 1.0
CA A:ASP175 4.6 18.7 1.0
N A:GLY179 4.6 18.6 1.0
CB A:ASP175 4.7 19.3 1.0
O A:ASP175 4.7 19.6 1.0
CA A:GLY179 4.7 17.7 1.0
O A:LYS177 4.8 18.8 1.0
CB A:ILE180 4.8 18.3 1.0
O A:GLY179 4.9 16.6 1.0

Calcium binding site 2 out of 6 in 1ros

Go back to Calcium Binding Sites List in 1ros
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca403

b:21.9
occ:1.00
 O A:GLY192 2.2 12.6 1.0
O A:ASP158 2.4 15.5 1.0
OD2 A:ASP194 2.5 14.5 1.0
O A:GLY190 2.6 18.3 1.0
C A:GLY192 3.4 14.6 1.0
CG A:ASP194 3.5 15.9 1.0
C A:ASP158 3.5 16.5 1.0
O A:HOH514 3.7 34.9 1.0
C A:GLY190 3.7 18.1 1.0
C A:ILE191 3.8 18.5 1.0
O A:ILE191 3.9 19.2 1.0
OD1 A:ASP194 3.9 13.7 1.0
N A:GLY192 4.0 18.3 1.0
N A:ASP194 4.1 14.1 1.0
CA A:GLY192 4.3 14.0 1.0
N A:GLY193 4.3 12.1 1.0
CA A:ILE191 4.4 21.8 1.0
O A:ALA157 4.4 15.8 1.0
CA A:GLY193 4.4 14.8 1.0
N A:ILE159 4.4 15.3 1.0
CA A:ASP158 4.4 16.0 1.0
O A:GLY188 4.5 17.5 1.0
N A:ILE191 4.5 19.6 1.0
CA A:ILE159 4.5 16.1 1.0
C A:GLY193 4.5 14.3 1.0
CB A:ASP194 4.6 12.2 1.0
N A:LEU160 4.8 17.7 1.0
CA A:ASP194 4.8 13.5 1.0
O A:HOH473 4.8 22.0 1.0
CA A:GLY190 4.8 19.1 1.0
N A:GLY190 4.9 19.2 1.0
CH2 A:TRP109 4.9 13.6 1.0
CD2 A:LEU160 4.9 22.7 1.0

Calcium binding site 3 out of 6 in 1ros

Go back to Calcium Binding Sites List in 1ros
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
A:Ca404

b:26.7
occ:1.00
 O A:GLU199 2.3 19.5 1.0
OD1 A:ASP124 2.3 19.9 1.0
OE2 A:GLU199 2.4 14.0 1.0
O A:GLU201 2.4 14.9 1.0
O A:HOH497 2.9 28.9 1.0
OD2 A:ASP124 2.9 20.2 1.0
CG A:ASP124 2.9 20.4 1.0
C A:GLU199 3.3 18.7 1.0
CD A:GLU199 3.4 17.7 1.0
C A:GLU201 3.6 15.2 1.0
CG A:GLU199 3.8 17.0 1.0
OG1 A:THR122 3.9 16.4 1.0
CA A:GLU199 4.0 18.2 1.0
CD1 A:TRP203 4.2 15.0 1.0
CA A:PHE202 4.2 15.0 1.0
N A:GLU201 4.3 17.4 1.0
CB A:ASP124 4.4 20.4 1.0
N A:PHE202 4.4 15.8 1.0
O A:HOH538 4.4 38.9 1.0
N A:ASP200 4.4 16.6 1.0
CB A:GLU199 4.5 18.0 1.0
C A:ASP200 4.5 17.6 1.0
OE1 A:GLU199 4.6 16.8 1.0
NE1 A:TRP203 4.6 13.6 1.0
CA A:GLU201 4.7 16.0 1.0
N A:TRP203 4.7 14.4 1.0
CA A:ASP200 4.7 17.5 1.0
O A:HOH462 4.8 32.2 1.0
O A:HOH519 4.9 38.7 1.0

Calcium binding site 4 out of 6 in 1ros

Go back to Calcium Binding Sites List in 1ros
Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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:Ca502

b:19.1
occ:1.00
 OE2 B:GLU201 2.1 17.5 1.0
O B:ILE180 2.3 18.3 1.0
O B:GLY176 2.3 22.1 1.0
OD1 B:ASP198 2.3 16.4 1.0
OD2 B:ASP175 2.4 17.8 1.0
O B:GLY178 2.4 20.9 1.0
CD B:GLU201 3.3 17.1 1.0
CG B:ASP198 3.3 16.1 1.0
C B:ILE180 3.4 16.9 1.0
C B:GLY176 3.5 21.5 1.0
CG B:ASP175 3.6 19.9 1.0
C B:GLY178 3.6 20.6 1.0
CB B:ASP198 3.9 17.0 1.0
N B:GLY178 3.9 21.1 1.0
N B:ILE180 4.0 18.0 1.0
N B:GLY176 4.0 22.2 1.0
OE1 B:GLU201 4.0 18.8 1.0
C B:ASP175 4.2 21.4 1.0
C B:LYS177 4.2 21.8 1.0
OD1 B:ASP175 4.2 20.5 1.0
N B:ASP175 4.3 19.4 1.0
CA B:ILE180 4.3 17.0 1.0
OD2 B:ASP198 4.3 14.1 1.0
CA B:GLY178 4.3 20.5 1.0
CG B:GLU201 4.4 14.4 1.0
CA B:GLY176 4.4 21.4 1.0
N B:LEU181 4.4 16.2 1.0
C B:GLY179 4.4 17.9 1.0
N B:LYS177 4.4 21.6 1.0
CA B:LEU181 4.5 16.1 1.0
CA B:LYS177 4.5 22.9 1.0
CA B:ASP175 4.5 20.2 1.0
O B:ASP175 4.6 21.8 1.0
N B:GLY179 4.6 20.2 1.0
CB B:ASP175 4.7 20.4 1.0
O B:LYS177 4.8 23.6 1.0
CA B:GLY179 4.8 19.1 1.0
CB B:ILE180 4.8 17.9 1.0
O B:GLY179 4.9 16.1 1.0

Calcium binding site 5 out of 6 in 1ros

Go back to Calcium Binding Sites List in 1ros
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca503

b:22.6
occ:1.00
 O B:GLY192 2.3 12.6 1.0
O B:ASP158 2.4 14.8 1.0
O B:HOH591 2.4 18.8 1.0
O B:GLY190 2.5 22.1 1.0
OD2 B:ASP194 2.7 15.4 1.0
O B:HOH569 3.4 26.9 1.0
C B:GLY192 3.4 15.4 1.0
CG B:ASP194 3.5 16.9 1.0
C B:ASP158 3.5 15.7 1.0
C B:GLY190 3.7 20.8 1.0
OD1 B:ASP194 3.9 16.1 1.0
C B:ILE191 3.9 20.7 1.0
O B:ILE191 4.0 21.1 1.0
N B:GLY192 4.1 18.9 1.0
CD1 B:LEU160 4.1 23.7 1.0
N B:ASP194 4.1 15.2 1.0
CA B:GLY192 4.3 15.4 1.0
O B:ALA157 4.3 18.0 1.0
N B:GLY193 4.4 13.0 1.0
CA B:ASP158 4.4 14.6 1.0
N B:ILE159 4.4 14.5 1.0
O B:GLY188 4.5 19.5 1.0
CA B:GLY193 4.5 15.3 1.0
CA B:ILE191 4.5 23.1 1.0
CA B:ILE159 4.5 16.1 1.0
N B:ILE191 4.6 21.7 1.0
O B:HOH537 4.6 36.5 1.0
C B:GLY193 4.6 16.1 1.0
CB B:ASP194 4.7 15.3 1.0
CA B:GLY190 4.7 22.0 1.0
N B:LEU160 4.7 17.6 1.0
CH2 B:TRP109 4.8 14.5 1.0
O B:HOH612 4.8 27.8 1.0
N B:GLY190 4.8 22.4 1.0
CA B:ASP194 4.8 14.9 1.0

Calcium binding site 6 out of 6 in 1ros

Go back to Calcium Binding Sites List in 1ros
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca504

b:26.8
occ:1.00
 OD1 B:ASP124 2.2 17.2 1.0
O B:GLU199 2.3 19.0 1.0
O B:GLU201 2.4 16.3 1.0
OE2 B:GLU199 2.4 15.9 1.0
O B:HOH565 2.8 27.2 1.0
CG B:ASP124 2.9 19.9 1.0
OD2 B:ASP124 2.9 18.4 1.0
C B:GLU199 3.4 18.3 1.0
CD B:GLU199 3.5 16.9 1.0
C B:GLU201 3.6 16.1 1.0
CG B:GLU199 3.8 16.9 1.0
OG1 B:THR122 3.9 17.6 1.0
CA B:GLU199 3.9 18.2 1.0
CA B:PHE202 4.2 16.4 1.0
CD1 B:TRP203 4.2 12.1 1.0
N B:GLU201 4.2 17.4 1.0
N B:PHE202 4.3 15.7 1.0
CB B:ASP124 4.4 19.1 1.0
N B:ASP200 4.5 16.5 1.0
CB B:GLU199 4.5 16.2 1.0
OE1 B:GLU199 4.6 16.4 1.0
C B:ASP200 4.6 18.1 1.0
N B:TRP203 4.6 15.5 1.0
CA B:GLU201 4.6 16.8 1.0
NE1 B:TRP203 4.7 11.4 1.0
CA B:ASP200 4.8 17.6 1.0
CD1 B:PHE202 5.0 17.2 1.0
C B:PHE202 5.0 15.7 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 22:14:47 2024

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