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Calcium in PDB 2wo9: 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: 2wo9 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) 19.88 / 1.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.352, 65.291, 69.356, 66.15, 83.84, 71.38
R / Rfree (%) 17.219 / 21.754

Other elements in 2wo9:

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 2wo9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid, PDB code: 2wo9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 2wo9

Go back to Calcium Binding Sites List in 2wo9
Calcium binding site 1 out of 7 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:23.3
occ:1.00
 O A:ILE180 2.3 22.5 1.0
OE2 A:GLU201 2.3 23.4 1.0
OD2 A:ASP198 2.3 23.4 1.0
O A:GLY176 2.3 22.7 1.0
O A:GLY178 2.3 23.1 1.0
OD2 A:ASP175 2.3 24.0 1.0
CG A:ASP198 3.4 20.6 1.0
C A:ILE180 3.4 22.5 1.0
CG A:ASP175 3.5 28.1 1.0
C A:GLY178 3.5 24.2 1.0
CD A:GLU201 3.5 25.4 1.0
C A:GLY176 3.6 25.3 1.0
N A:GLY178 3.9 23.4 1.0
N A:ILE180 3.9 21.7 1.0
CB A:ASP198 4.0 22.5 1.0
OD1 A:ASP175 4.1 28.8 1.0
N A:GLY176 4.1 24.8 1.0
C A:ASP175 4.2 25.2 1.0
CA A:ILE180 4.2 23.3 1.0
C A:LYS177 4.3 24.4 1.0
OE1 A:GLU201 4.3 21.0 1.0
CA A:GLY178 4.3 24.8 1.0
C A:GLY179 4.3 22.3 1.0
N A:ASP175 4.3 27.1 1.0
N A:LEU181 4.4 20.6 1.0
OD1 A:ASP198 4.4 22.3 1.0
CA A:GLY176 4.5 24.9 1.0
CA A:LYS177 4.5 23.2 1.0
CA A:LEU181 4.5 20.6 1.0
N A:LYS177 4.5 23.8 1.0
O A:HOH2096 4.6 31.4 1.0
O A:ASP175 4.6 25.4 1.0
CG A:GLU201 4.6 20.9 1.0
N A:GLY179 4.6 24.2 1.0
CA A:ASP175 4.6 27.3 1.0
CB A:ASP175 4.7 27.7 1.0
CA A:GLY179 4.7 24.7 1.0
CB A:ILE180 4.7 24.4 1.0
O A:GLY179 4.9 24.7 1.0
CD2 A:LEU181 5.0 23.0 1.0

Calcium binding site 2 out of 7 in 2wo9

Go back to Calcium Binding Sites List in 2wo9
Calcium binding site 2 out of 7 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:Ca1270

b:21.3
occ:1.00
 OE2 B:GLU201 2.3 22.9 1.0
OD2 B:ASP175 2.3 22.4 1.0
O B:ILE180 2.3 19.4 1.0
O B:GLY176 2.3 22.3 1.0
O B:GLY178 2.3 21.9 1.0
OD2 B:ASP198 2.3 20.8 1.0
CG B:ASP198 3.4 16.9 1.0
C B:ILE180 3.5 17.8 1.0
CD B:GLU201 3.5 20.0 1.0
CG B:ASP175 3.5 22.8 1.0
C B:GLY178 3.5 21.7 1.0
C B:GLY176 3.6 24.8 1.0
N B:GLY178 4.0 21.1 1.0
N B:ILE180 4.0 19.1 1.0
CB B:ASP198 4.0 19.6 1.0
OD1 B:ASP175 4.1 21.8 1.0
N B:GLY176 4.1 22.2 1.0
OE1 B:GLU201 4.2 23.3 1.0
C B:LYS177 4.3 23.7 1.0
C B:GLY179 4.3 20.0 1.0
CA B:ILE180 4.3 18.4 1.0
CA B:GLY178 4.3 23.1 1.0
C B:ASP175 4.3 22.8 1.0
N B:ASP175 4.4 23.2 1.0
CA B:GLY176 4.4 23.3 1.0
N B:LEU181 4.4 17.5 1.0
OD1 B:ASP198 4.4 16.4 1.0
CG B:GLU201 4.5 20.0 1.0
N B:LYS177 4.5 24.3 1.0
CA B:LEU181 4.5 18.9 1.0
N B:GLY179 4.6 21.2 1.0
CA B:LYS177 4.6 25.1 1.0
O B:HOH2092 4.6 44.8 1.0
CA B:ASP175 4.7 23.3 1.0
CA B:GLY179 4.7 20.7 1.0
CB B:ASP175 4.7 25.2 1.0
O B:GLY179 4.8 20.5 1.0
O B:ASP175 4.8 23.3 1.0
O B:LYS177 4.8 23.5 1.0
CB B:ILE180 4.9 19.1 1.0

Calcium binding site 3 out of 7 in 2wo9

Go back to Calcium Binding Sites List in 2wo9
Calcium binding site 3 out of 7 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:Ca1271

b:28.8
occ:1.00
 O B:GLY192 2.3 19.9 1.0
O B:GLY190 2.3 24.6 1.0
O B:ASP158 2.3 23.5 1.0
OD1 B:ASP194 2.3 24.7 1.0
O B:HOH2069 2.6 33.2 1.0
O B:HOH2103 2.7 25.1 1.0
CG B:ASP194 3.4 20.4 1.0
C B:ASP158 3.5 22.1 1.0
C B:GLY192 3.5 21.3 1.0
C B:GLY190 3.5 22.7 1.0
OD2 B:ASP194 3.8 20.3 1.0
C B:ILE191 3.8 20.2 1.0
O B:HOH2108 4.0 26.2 1.0
N B:GLY192 4.0 20.1 1.0
O B:ILE191 4.0 20.1 1.0
N B:ASP194 4.2 18.3 1.0
CA B:ILE191 4.2 19.6 1.0
O B:ALA157 4.3 26.5 1.0
N B:ILE191 4.3 20.3 1.0
CA B:GLY192 4.4 20.3 1.0
N B:ILE159 4.4 21.3 1.0
CA B:ASP158 4.4 21.5 1.0
CA B:ILE159 4.5 21.0 1.0
O B:GLY188 4.5 22.6 1.0
N B:GLY193 4.5 20.5 1.0
N B:GLY190 4.6 23.2 1.0
CA B:GLY190 4.6 22.3 1.0
CB B:ASP194 4.6 19.5 1.0
CA B:GLY193 4.6 20.1 1.0
C B:GLY193 4.6 20.6 1.0
N B:LEU160 4.7 19.3 1.0
C B:SER189 4.8 21.4 1.0
CA B:ASP194 4.8 19.5 1.0

Calcium binding site 4 out of 7 in 2wo9

Go back to Calcium Binding Sites List in 2wo9
Calcium binding site 4 out of 7 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
B:Ca1272

b:28.0
occ:1.00
 O B:GLU199 2.3 21.5 1.0
OD2 B:ASP124 2.3 25.0 1.0
O B:GLU201 2.3 22.3 1.0
OE2 B:GLU199 2.3 24.9 1.0
O B:HOH2113 2.5 35.8 1.0
O B:HOH2118 2.6 33.3 1.0
OD1 B:ASP124 2.9 25.9 1.0
CG B:ASP124 3.0 24.7 1.0
C B:GLU199 3.4 21.2 1.0
CD B:GLU199 3.4 20.5 1.0
C B:GLU201 3.5 21.0 1.0
CG B:GLU199 3.9 22.4 1.0
CA B:GLU199 4.1 19.8 1.0
OG1 B:THR122 4.1 22.7 1.0
CD1 B:TRP203 4.1 22.4 1.0
CA B:PHE202 4.2 22.4 1.0
N B:PHE202 4.3 22.1 1.0
N B:GLU201 4.3 20.5 1.0
CB B:ASP124 4.4 22.1 1.0
N B:ASP200 4.5 20.2 1.0
C B:ASP200 4.5 21.3 1.0
OE1 B:GLU199 4.6 24.7 1.0
NE1 B:TRP203 4.6 21.6 1.0
CB B:GLU199 4.6 20.7 1.0
CA B:GLU201 4.6 20.9 1.0
N B:TRP203 4.7 21.9 1.0
O B:HOH2116 4.7 39.5 1.0
CA B:ASP200 4.7 21.4 1.0
NH2 B:ARG165 5.0 33.2 1.0
O B:HOH2079 5.0 34.8 1.0

Calcium binding site 5 out of 7 in 2wo9

Go back to Calcium Binding Sites List in 2wo9
Calcium binding site 5 out of 7 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
C:Ca1271

b:23.9
occ:1.00
 O C:ILE180 2.3 23.0 1.0
OE2 C:GLU201 2.3 25.7 1.0
O C:GLY176 2.3 25.4 1.0
OD2 C:ASP198 2.3 21.5 1.0
O C:GLY178 2.3 25.6 1.0
OD2 C:ASP175 2.3 24.9 1.0
CG C:ASP198 3.4 19.5 1.0
C C:ILE180 3.5 23.2 1.0
CD C:GLU201 3.5 27.2 1.0
C C:GLY176 3.5 26.7 1.0
C C:GLY178 3.5 28.3 1.0
CG C:ASP175 3.6 28.8 1.0
N C:GLY178 3.9 26.3 1.0
N C:ILE180 4.0 23.9 1.0
CB C:ASP198 4.0 18.8 1.0
N C:GLY176 4.1 24.4 1.0
C C:LYS177 4.1 26.5 1.0
OD1 C:ASP175 4.2 25.4 1.0
OE1 C:GLU201 4.2 29.0 1.0
CA C:GLY178 4.3 27.5 1.0
CA C:ILE180 4.3 23.3 1.0
N C:ASP175 4.3 24.3 1.0
C C:ASP175 4.3 25.5 1.0
OD1 C:ASP198 4.3 21.6 1.0
C C:GLY179 4.4 25.3 1.0
CA C:LYS177 4.4 26.1 1.0
N C:LEU181 4.4 21.8 1.0
CA C:GLY176 4.4 25.8 1.0
N C:LYS177 4.4 25.8 1.0
CA C:LEU181 4.5 21.9 1.0
CG C:GLU201 4.6 24.0 1.0
N C:GLY179 4.6 28.6 1.0
CA C:ASP175 4.6 26.5 1.0
O C:LYS177 4.7 27.3 1.0
CB C:ASP175 4.7 27.6 1.0
CA C:GLY179 4.7 27.2 1.0
O C:ASP175 4.8 24.8 1.0
CB C:ILE180 4.8 23.5 1.0
CD2 C:LEU181 4.8 28.8 1.0
O C:GLY179 4.9 23.2 1.0

Calcium binding site 6 out of 7 in 2wo9

Go back to Calcium Binding Sites List in 2wo9
Calcium binding site 6 out of 7 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:Ca1269

b:20.9
occ:1.00
 OD2 D:ASP175 2.3 21.8 1.0
OE2 D:GLU201 2.3 23.4 1.0
OD2 D:ASP198 2.3 21.7 1.0
O D:ILE180 2.3 20.2 1.0
O D:GLY178 2.3 20.6 1.0
O D:GLY176 2.3 20.9 1.0
CG D:ASP198 3.4 17.8 1.0
C D:ILE180 3.5 19.4 1.0
CG D:ASP175 3.5 23.5 1.0
CD D:GLU201 3.5 21.8 1.0
C D:GLY178 3.5 21.7 1.0
C D:GLY176 3.6 23.3 1.0
N D:GLY178 3.9 22.2 1.0
N D:ILE180 4.0 21.6 1.0
OD1 D:ASP175 4.0 24.7 1.0
CB D:ASP198 4.0 20.0 1.0
N D:GLY176 4.1 22.7 1.0
OE1 D:GLU201 4.2 23.4 1.0
C D:LYS177 4.2 25.2 1.0
CA D:ILE180 4.3 20.7 1.0
CA D:GLY178 4.3 22.8 1.0
C D:GLY179 4.3 22.9 1.0
N D:ASP175 4.3 22.6 1.0
C D:ASP175 4.3 24.1 1.0
OD1 D:ASP198 4.4 21.3 1.0
N D:LEU181 4.4 18.3 1.0
CA D:GLY176 4.4 23.8 1.0
CG D:GLU201 4.5 20.9 1.0
CA D:LEU181 4.5 19.6 1.0
N D:LYS177 4.6 24.5 1.0
N D:GLY179 4.6 21.7 1.0
CA D:LYS177 4.6 25.3 1.0
CA D:ASP175 4.6 24.5 1.0
CB D:ASP175 4.6 25.2 1.0
O D:HOH2073 4.7 37.1 1.0
CA D:GLY179 4.7 22.1 1.0
O D:LYS177 4.7 26.2 1.0
O D:GLY179 4.8 22.2 1.0
O D:ASP175 4.8 25.5 1.0
CB D:ILE180 4.9 22.4 1.0

Calcium binding site 7 out of 7 in 2wo9

Go back to Calcium Binding Sites List in 2wo9
Calcium binding site 7 out of 7 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 7 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1270

b:27.0
occ:1.00
 OD2 D:ASP124 2.3 19.5 1.0
O D:GLU199 2.3 23.8 1.0
O D:GLU201 2.4 24.2 1.0
O D:HOH2012 2.4 33.6 1.0
OE2 D:GLU199 2.5 23.5 1.0
OD1 D:ASP124 2.8 22.4 1.0
CG D:ASP124 2.9 23.1 1.0
C D:GLU199 3.4 21.3 1.0
CD D:GLU199 3.6 25.5 1.0
C D:GLU201 3.6 23.5 1.0
CG D:GLU199 3.9 22.8 1.0
O D:HOH2060 4.0 36.9 1.0
CA D:GLU199 4.1 21.0 1.0
OG1 D:THR122 4.1 17.6 1.0
CA D:PHE202 4.2 21.6 1.0
CD1 D:TRP203 4.3 19.9 1.0
N D:PHE202 4.4 20.5 1.0
CB D:ASP124 4.4 18.8 1.0
N D:GLU201 4.4 20.5 1.0
N D:ASP200 4.4 20.8 1.0
C D:ASP200 4.5 22.0 1.0
CB D:GLU199 4.6 21.0 1.0
OE1 D:GLU199 4.7 22.9 1.0
CA D:GLU201 4.7 20.9 1.0
CA D:ASP200 4.7 21.1 1.0
N D:TRP203 4.7 19.5 1.0
NE1 D:TRP203 4.8 20.5 1.0
O D:HOH2063 4.8 25.4 1.0
CD1 D:PHE202 5.0 30.2 1.0
NH2 D:ARG165 5.0 30.1 1.0
O D:ASP200 5.0 23.5 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: Fri Jul 12 18:46:55 2024

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