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Calcium in PDB 2wo8: MMP12 Complex with A Beta Hydroxy Carboxylic Acid

Enzymatic activity of MMP12 Complex with A Beta Hydroxy Carboxylic Acid

All present enzymatic activity of MMP12 Complex with A Beta Hydroxy Carboxylic Acid:
3.4.24.65;

Protein crystallography data

The structure of MMP12 Complex with A Beta Hydroxy Carboxylic Acid, PDB code: 2wo8 was solved by I.P.Holmes, S.Gaines, S.P.Watson, O.Lorthioir, A.Walker, S.J.Baddeley, S.Herbert, D.Egan, M.A.Convery, O.M.P.Singh, J.W.Gross, J.M.Strelow, R.H.Smith, A.J.Amour, D.Brown, S.L.Martin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.043, 65.264, 67.808, 66.47, 83.86, 71.37
R / Rfree (%) 18.416 / 24.589

Other elements in 2wo8:

The structure of MMP12 Complex with A Beta Hydroxy Carboxylic Acid also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid (pdb code 2wo8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid, PDB code: 2wo8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2wo8

Go back to Calcium Binding Sites List in 2wo8
Calcium binding site 1 out of 6 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1270

b:28.2
occ:1.00
 OD2 A:ASP198 2.3 29.1 1.0
OE2 A:GLU201 2.3 27.0 1.0
O A:GLY178 2.3 27.0 1.0
OD2 A:ASP175 2.3 29.0 1.0
O A:GLY176 2.3 27.8 1.0
O A:ILE180 2.3 27.1 1.0
CG A:ASP198 3.4 25.9 1.0
C A:ILE180 3.5 27.0 1.0
CD A:GLU201 3.5 21.3 1.0
CG A:ASP175 3.5 25.8 1.0
C A:GLY178 3.5 28.5 1.0
C A:GLY176 3.5 28.7 1.0
N A:GLY178 3.9 28.7 1.0
N A:ILE180 4.0 26.1 1.0
CB A:ASP198 4.0 24.2 1.0
C A:ASP175 4.1 30.6 1.0
N A:GLY176 4.2 30.1 1.0
N A:ASP175 4.2 32.7 1.0
C A:LYS177 4.2 28.9 1.0
OD1 A:ASP175 4.2 26.5 1.0
CA A:ILE180 4.3 27.4 1.0
O A:HOH2070 4.3 36.9 1.0
OD1 A:ASP198 4.3 22.9 1.0
OE1 A:GLU201 4.3 25.7 1.0
C A:GLY179 4.3 27.2 1.0
CA A:GLY178 4.3 28.2 1.0
O A:ASP175 4.4 31.0 1.0
CA A:LYS177 4.4 26.9 1.0
N A:LEU181 4.4 25.6 1.0
N A:LYS177 4.4 27.3 1.0
CA A:GLY176 4.5 29.0 1.0
CA A:ASP175 4.5 31.5 1.0
CG A:GLU201 4.5 23.6 1.0
CA A:LEU181 4.5 26.0 1.0
N A:GLY179 4.6 28.2 1.0
CB A:ASP175 4.6 31.8 1.0
CA A:GLY179 4.7 28.9 1.0
CB A:ILE180 4.8 28.8 1.0
O A:GLY179 4.8 28.6 1.0
O A:LYS177 4.9 29.2 1.0

Calcium binding site 2 out of 6 in 2wo8

Go back to Calcium Binding Sites List in 2wo8
Calcium binding site 2 out of 6 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1271

b:21.7
occ:1.00
 OE2 B:GLU201 2.3 25.1 1.0
O B:GLY178 2.3 23.3 1.0
OD2 B:ASP198 2.3 20.4 1.0
O B:GLY176 2.3 24.5 1.0
OD2 B:ASP175 2.3 21.1 1.0
O B:ILE180 2.3 18.1 1.0
CG B:ASP198 3.4 17.8 1.0
CG B:ASP175 3.5 22.7 1.0
C B:ILE180 3.5 19.2 1.0
CD B:GLU201 3.5 25.8 1.0
C B:GLY178 3.5 24.2 1.0
C B:GLY176 3.5 26.2 1.0
N B:GLY178 3.9 25.1 1.0
CB B:ASP198 4.0 14.9 1.0
OD1 B:ASP175 4.0 22.1 1.0
N B:GLY176 4.1 26.8 1.0
N B:ILE180 4.1 20.9 1.0
C B:ASP175 4.2 25.7 1.0
OE1 B:GLU201 4.2 20.2 1.0
C B:LYS177 4.3 24.8 1.0
C B:GLY179 4.3 21.3 1.0
N B:ASP175 4.3 22.3 1.0
OD1 B:ASP198 4.3 19.8 1.0
CA B:ILE180 4.4 20.5 1.0
CA B:GLY178 4.4 24.7 1.0
CA B:GLY176 4.4 26.2 1.0
N B:LEU181 4.4 19.3 1.0
N B:LYS177 4.5 24.6 1.0
N B:GLY179 4.5 23.6 1.0
CG B:GLU201 4.5 20.6 1.0
O B:ASP175 4.5 26.4 1.0
CA B:LYS177 4.5 24.9 1.0
CA B:LEU181 4.6 18.1 1.0
CA B:GLY179 4.6 22.9 1.0
CA B:ASP175 4.6 24.6 1.0
CB B:ASP175 4.6 23.8 1.0
O B:GLY179 4.7 20.8 1.0
O B:LYS177 4.8 23.5 1.0
CB B:ILE180 4.9 20.2 1.0

Calcium binding site 3 out of 6 in 2wo8

Go back to Calcium Binding Sites List in 2wo8
Calcium binding site 3 out of 6 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1272

b:27.4
occ:1.00
 O B:GLY192 2.3 21.2 1.0
O B:GLY190 2.3 24.8 1.0
O B:ASP158 2.3 22.3 1.0
O B:HOH2086 2.4 19.9 1.0
O B:HOH2060 2.5 23.0 1.0
OD1 B:ASP194 2.6 20.5 1.0
C B:ASP158 3.4 22.0 1.0
CG B:ASP194 3.5 17.4 1.0
C B:GLY192 3.5 21.1 1.0
C B:GLY190 3.5 23.9 1.0
OD2 B:ASP194 3.8 22.7 1.0
C B:ILE191 3.9 19.5 1.0
N B:GLY192 4.0 20.2 1.0
O B:HOH2094 4.0 28.8 1.0
O B:ALA157 4.1 27.9 1.0
O B:ILE191 4.2 19.0 1.0
N B:ASP194 4.3 15.8 1.0
CA B:ILE191 4.3 19.9 1.0
CA B:ASP158 4.3 23.2 1.0
N B:ILE191 4.3 21.2 1.0
CA B:GLY192 4.4 20.0 1.0
N B:ILE159 4.4 19.8 1.0
O B:GLY188 4.4 22.8 1.0
N B:GLY190 4.4 23.2 1.0
N B:GLY193 4.5 20.2 1.0
CA B:GLY190 4.5 22.1 1.0
CA B:GLY193 4.5 18.1 1.0
CA B:ILE159 4.5 16.4 1.0
C B:GLY193 4.7 18.1 1.0
C B:SER189 4.7 24.9 1.0
N B:LEU160 4.7 16.0 1.0
CB B:ASP194 4.8 14.9 1.0
O B:HOH2063 4.9 29.3 1.0
CA B:ASP194 4.9 16.7 1.0

Calcium binding site 4 out of 6 in 2wo8

Go back to Calcium Binding Sites List in 2wo8
Calcium binding site 4 out of 6 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1270

b:28.6
occ:1.00
 OD2 C:ASP175 2.3 29.3 1.0
OE2 C:GLU201 2.3 28.1 1.0
OD2 C:ASP198 2.3 21.8 1.0
O C:GLY176 2.3 31.3 1.0
O C:ILE180 2.3 27.2 1.0
O C:GLY178 2.3 31.9 1.0
CG C:ASP198 3.4 25.3 1.0
CG C:ASP175 3.5 32.8 1.0
C C:GLY176 3.5 32.3 1.0
C C:ILE180 3.5 28.0 1.0
C C:GLY178 3.5 33.1 1.0
CD C:GLU201 3.6 30.4 1.0
N C:ILE180 3.9 31.8 1.0
CB C:ASP198 4.0 22.3 1.0
N C:GLY178 4.0 35.1 1.0
N C:GLY176 4.0 32.1 1.0
OD1 C:ASP175 4.0 33.8 1.0
C C:LYS177 4.1 35.5 1.0
C C:ASP175 4.2 31.9 1.0
C C:GLY179 4.2 32.0 1.0
N C:ASP175 4.2 28.8 1.0
CA C:ILE180 4.2 29.8 1.0
OE1 C:GLU201 4.3 29.7 1.0
N C:LYS177 4.4 31.5 1.0
CA C:GLY176 4.4 31.6 1.0
OD1 C:ASP198 4.4 25.8 1.0
CA C:LYS177 4.4 34.8 1.0
CA C:GLY178 4.4 33.0 1.0
N C:GLY179 4.5 33.4 1.0
N C:LEU181 4.5 25.5 1.0
CG C:GLU201 4.5 25.1 1.0
CA C:ASP175 4.5 30.7 1.0
CA C:GLY179 4.5 32.5 1.0
O C:ASP175 4.6 32.4 1.0
O C:LYS177 4.6 36.5 1.0
CB C:ASP175 4.6 31.3 1.0
CA C:LEU181 4.6 23.7 1.0
O C:GLY179 4.7 32.8 1.0
CB C:ILE180 4.7 31.9 1.0

Calcium binding site 5 out of 6 in 2wo8

Go back to Calcium Binding Sites List in 2wo8
Calcium binding site 5 out of 6 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1269

b:21.7
occ:1.00
 OD2 D:ASP175 2.3 21.8 1.0
OE2 D:GLU201 2.3 23.8 1.0
O D:ILE180 2.3 21.8 1.0
OD2 D:ASP198 2.3 24.0 1.0
O D:GLY178 2.3 22.5 1.0
O D:GLY176 2.3 20.4 1.0
CG D:ASP198 3.4 18.3 1.0
C D:ILE180 3.5 20.9 1.0
CG D:ASP175 3.5 20.5 1.0
CD D:GLU201 3.5 22.9 1.0
C D:GLY178 3.5 22.8 1.0
C D:GLY176 3.6 21.2 1.0
N D:GLY178 3.9 21.2 1.0
CB D:ASP198 4.0 21.0 1.0
N D:ILE180 4.0 20.7 1.0
N D:GLY176 4.1 24.1 1.0
OD1 D:ASP175 4.1 25.7 1.0
C D:ASP175 4.2 23.6 1.0
N D:ASP175 4.2 23.9 1.0
OE1 D:GLU201 4.2 26.8 1.0
C D:LYS177 4.2 20.6 1.0
OD1 D:ASP198 4.3 18.6 1.0
CA D:GLY178 4.3 21.0 1.0
C D:GLY179 4.3 22.8 1.0
CA D:ILE180 4.3 20.8 1.0
CA D:GLY176 4.4 22.1 1.0
N D:LEU181 4.4 19.8 1.0
CA D:LEU181 4.5 18.2 1.0
CG D:GLU201 4.5 21.8 1.0
CA D:ASP175 4.5 23.4 1.0
N D:LYS177 4.5 20.9 1.0
N D:GLY179 4.6 21.8 1.0
O D:ASP175 4.6 23.3 1.0
CA D:LYS177 4.6 22.4 1.0
CB D:ASP175 4.6 23.7 1.0
O D:LYS177 4.7 21.0 1.0
CA D:GLY179 4.7 21.5 1.0
O D:GLY179 4.8 21.8 1.0
CB D:ILE180 4.9 21.1 1.0

Calcium binding site 6 out of 6 in 2wo8

Go back to Calcium Binding Sites List in 2wo8
Calcium binding site 6 out of 6 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1270

b:29.4
occ:1.00
 OD2 D:ASP124 2.3 24.9 1.0
O D:GLU199 2.3 25.7 1.0
OE2 D:GLU199 2.5 20.2 1.0
O D:HOH2153 2.5 35.3 1.0
O D:HOH2070 2.5 26.4 1.0
O D:GLU201 2.6 22.2 1.0
OD1 D:ASP124 2.8 25.9 1.0
CG D:ASP124 2.9 26.6 1.0
C D:GLU199 3.4 23.1 1.0
CD D:GLU199 3.5 26.5 1.0
C D:GLU201 3.7 21.5 1.0
CG D:GLU199 3.8 18.6 1.0
OG1 D:THR122 4.1 18.0 1.0
CA D:GLU199 4.1 20.8 1.0
CA D:PHE202 4.3 20.1 1.0
CB D:ASP124 4.3 22.5 1.0
N D:GLU201 4.4 21.9 1.0
CD1 D:TRP203 4.4 11.1 1.0
N D:PHE202 4.5 20.1 1.0
N D:ASP200 4.5 22.2 1.0
C D:ASP200 4.5 23.6 1.0
CB D:GLU199 4.6 21.6 1.0
OE1 D:GLU199 4.6 26.4 1.0
O D:HOH2046 4.7 26.8 1.0
CA D:ASP200 4.7 20.9 1.0
N D:TRP203 4.7 16.2 1.0
CA D:GLU201 4.8 20.5 1.0
NE1 D:TRP203 4.9 14.8 1.0

Reference:

I.P.Holmes, S.Gaines, S.P.Watson, O.Lorthioir, A.Walker, S.J.Baddeley, S.Herbert, D.Egan, M.A.Convery, O.M.P.Singh, J.W.Gross, J.M.Strelow, R.H.Smith, A.J.Amour, D.Brown, S.L.Martin. The Identification of Beta-Hydroxy Carboxylic Acids As Selective Mmp-12 Inhibitors. Bioorg.Med.Chem.Lett. V. 19 5760 2009.
ISSN: ISSN 0960-894X
PubMed: 19703773
DOI: 10.1016/J.BMCL.2009.07.155
Page generated: Tue Jul 8 09:08:48 2025

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