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Calcium in PDB 2woa: 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: 2woa 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) 19.73 / 2.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.156, 65.339, 68.332, 66.11, 84.12, 71.46
R / Rfree (%) 15.3 / 21.9

Other elements in 2woa:

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 2woa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid, PDB code: 2woa:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2woa

Go back to Calcium Binding Sites List in 2woa
Calcium binding site 1 out of 9 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:Ca1272

b:34.5
occ:1.00
 OD2 A:ASP198 2.3 33.9 1.0
OE2 A:GLU201 2.3 33.5 1.0
O A:GLY178 2.3 32.1 1.0
OD2 A:ASP175 2.3 33.5 1.0
O A:GLY176 2.3 34.4 1.0
O A:ILE180 2.3 35.3 1.0
CG A:ASP198 3.3 35.3 1.0
C A:ILE180 3.5 34.1 1.0
CD A:GLU201 3.5 31.2 1.0
CG A:ASP175 3.5 33.2 1.0
C A:GLY178 3.5 33.1 1.0
C A:GLY176 3.5 34.2 1.0
N A:GLY178 3.9 34.9 1.0
CB A:ASP198 4.0 33.3 1.0
N A:ILE180 4.0 31.7 1.0
OD1 A:ASP175 4.0 35.4 1.0
OE1 A:GLU201 4.1 35.3 1.0
N A:GLY176 4.2 35.0 1.0
C A:GLY179 4.2 31.5 1.0
C A:ASP175 4.2 34.5 1.0
N A:ASP175 4.3 35.7 1.0
CA A:ILE180 4.3 33.5 1.0
OD1 A:ASP198 4.3 36.5 1.0
C A:LYS177 4.3 34.8 1.0
CA A:GLY178 4.4 34.0 1.0
N A:LEU181 4.4 33.6 1.0
N A:LYS177 4.4 34.4 1.0
CA A:GLY176 4.5 34.9 1.0
CA A:LYS177 4.5 33.3 1.0
N A:GLY179 4.5 31.4 1.0
O A:ASP175 4.5 34.6 1.0
CA A:LEU181 4.5 31.0 1.0
O A:HOH2052 4.6 34.6 1.0
CG A:GLU201 4.6 31.9 1.0
CA A:GLY179 4.6 32.2 1.0
CA A:ASP175 4.6 35.1 1.0
O A:GLY179 4.7 31.2 1.0
CB A:ASP175 4.7 34.9 1.0
CB A:ILE180 4.7 34.7 1.0

Calcium binding site 2 out of 9 in 2woa

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Calcium binding site 2 out of 9 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:Ca1272

b:32.5
occ:1.00
 OE2 B:GLU201 2.3 34.1 1.0
O B:GLY178 2.3 31.0 1.0
OD2 B:ASP198 2.3 30.1 1.0
O B:GLY176 2.3 34.4 1.0
O B:ILE180 2.3 29.6 1.0
OD2 B:ASP175 2.3 31.1 1.0
CG B:ASP198 3.4 26.1 1.0
CG B:ASP175 3.4 27.6 1.0
C B:ILE180 3.5 28.2 1.0
C B:GLY178 3.5 31.0 1.0
CD B:GLU201 3.5 36.1 1.0
C B:GLY176 3.5 33.6 1.0
N B:GLY178 3.8 29.4 1.0
OD1 B:ASP175 3.9 29.6 1.0
N B:ILE180 4.0 28.3 1.0
CB B:ASP198 4.1 25.1 1.0
C B:LYS177 4.1 32.2 1.0
N B:GLY176 4.1 34.1 1.0
OE1 B:GLU201 4.2 31.0 1.0
C B:GLY179 4.2 28.7 1.0
CA B:GLY178 4.2 30.0 1.0
C B:ASP175 4.3 32.5 1.0
OD1 B:ASP198 4.3 21.9 1.0
CA B:ILE180 4.3 28.2 1.0
N B:ASP175 4.4 31.1 1.0
N B:LEU181 4.4 28.3 1.0
CA B:LYS177 4.4 33.0 1.0
CA B:LEU181 4.4 28.4 1.0
N B:LYS177 4.4 32.8 1.0
CA B:GLY176 4.5 33.1 1.0
N B:GLY179 4.5 30.0 1.0
CG B:GLU201 4.5 30.3 1.0
CA B:GLY179 4.6 29.5 1.0
O B:ASP175 4.6 32.2 1.0
CB B:ASP175 4.6 30.1 1.0
CA B:ASP175 4.7 31.5 1.0
O B:LYS177 4.7 32.7 1.0
O B:GLY179 4.7 28.9 1.0
CB B:ILE180 5.0 28.3 1.0

Calcium binding site 3 out of 9 in 2woa

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Calcium binding site 3 out of 9 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:Ca1273

b:35.7
occ:1.00
 O B:ASP158 2.3 31.7 1.0
O B:GLY192 2.3 30.7 1.0
O B:HOH2047 2.3 33.5 1.0
O B:GLY190 2.3 32.4 1.0
OD1 B:ASP194 2.3 33.8 1.0
O B:HOH2073 2.6 23.6 1.0
CG B:ASP194 3.4 31.2 1.0
C B:ASP158 3.5 31.1 1.0
C B:GLY192 3.5 29.6 1.0
C B:GLY190 3.6 32.1 1.0
C B:ILE191 3.8 29.6 1.0
OD2 B:ASP194 3.9 31.7 1.0
N B:GLY192 3.9 29.9 1.0
O B:ILE191 4.0 29.4 1.0
O B:HOH2079 4.1 30.1 1.0
N B:ASP194 4.2 24.7 1.0
CA B:ILE191 4.2 30.3 1.0
O B:ALA157 4.2 32.5 1.0
CA B:GLY192 4.3 29.2 1.0
N B:ILE191 4.3 31.3 1.0
CA B:ASP158 4.4 31.6 1.0
N B:ILE159 4.4 29.2 1.0
O B:GLY188 4.4 28.5 1.0
N B:GLY193 4.4 29.3 1.0
CA B:ILE159 4.5 27.5 1.0
CA B:GLY193 4.5 27.7 1.0
N B:GLY190 4.6 31.5 1.0
C B:GLY193 4.6 27.2 1.0
CA B:GLY190 4.6 31.2 1.0
CB B:ASP194 4.6 24.8 1.0
N B:LEU160 4.7 27.0 1.0
C B:SER189 4.8 30.3 1.0
CA B:ASP194 4.8 24.9 1.0
O B:HOH2049 4.8 33.5 1.0
CH2 B:TRP109 4.9 30.0 1.0
O B:SER189 5.0 29.4 1.0

Calcium binding site 4 out of 9 in 2woa

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Calcium binding site 4 out of 9 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:Ca1274

b:36.1
occ:1.00
 O B:GLU201 2.3 32.5 1.0
OD2 B:ASP124 2.3 34.2 1.0
O B:GLU199 2.3 33.1 1.0
OE2 B:GLU199 2.3 30.2 1.0
O B:HOH2088 2.6 39.6 1.0
OD1 B:ASP124 3.0 35.7 1.0
CG B:ASP124 3.0 32.9 1.0
CD B:GLU199 3.4 31.4 1.0
C B:GLU199 3.4 31.3 1.0
C B:GLU201 3.5 32.9 1.0
CG B:GLU199 3.9 30.2 1.0
CA B:GLU199 4.1 29.0 1.0
OG1 B:THR122 4.1 24.1 1.0
CA B:PHE202 4.2 29.9 1.0
CD1 B:TRP203 4.2 30.7 1.0
N B:PHE202 4.3 33.1 1.0
O B:HOH2087 4.3 36.5 1.0
N B:GLU201 4.3 31.1 1.0
C B:ASP200 4.4 31.8 1.0
CB B:ASP124 4.5 27.9 1.0
N B:ASP200 4.5 31.9 1.0
O B:HOH2052 4.6 47.7 1.0
OE1 B:GLU199 4.6 30.5 1.0
NE1 B:TRP203 4.6 27.2 1.0
CB B:GLU199 4.6 28.6 1.0
CA B:GLU201 4.6 31.7 1.0
CA B:ASP200 4.7 32.2 1.0
N B:TRP203 4.7 28.4 1.0
NH2 B:ARG165 4.8 44.1 1.0
O B:HOH2053 4.9 41.7 1.0
O B:ASP200 4.9 32.5 1.0

Calcium binding site 5 out of 9 in 2woa

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Calcium binding site 5 out of 9 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:Ca1270

b:33.5
occ:1.00
 OE2 C:GLU201 2.3 32.4 1.0
O C:GLY176 2.3 35.7 1.0
O C:ILE180 2.3 33.2 1.0
OD2 C:ASP175 2.3 31.3 1.0
OD2 C:ASP198 2.3 31.7 1.0
O C:GLY178 2.3 33.6 1.0
CG C:ASP198 3.4 32.0 1.0
C C:ILE180 3.4 32.5 1.0
CD C:GLU201 3.5 32.8 1.0
C C:GLY176 3.5 36.0 1.0
CG C:ASP175 3.5 35.5 1.0
C C:GLY178 3.6 34.8 1.0
N C:ILE180 3.9 32.6 1.0
N C:GLY178 3.9 37.1 1.0
CB C:ASP198 4.0 29.4 1.0
N C:GLY176 4.0 34.0 1.0
OD1 C:ASP175 4.2 36.1 1.0
OE1 C:GLU201 4.2 34.6 1.0
C C:LYS177 4.2 36.9 1.0
CA C:ILE180 4.2 32.9 1.0
C C:ASP175 4.2 33.4 1.0
C C:GLY179 4.3 32.9 1.0
N C:ASP175 4.3 32.2 1.0
OD1 C:ASP198 4.3 33.3 1.0
N C:LEU181 4.3 31.1 1.0
CA C:GLY176 4.4 34.6 1.0
CA C:GLY178 4.4 34.9 1.0
N C:LYS177 4.4 36.0 1.0
CA C:LEU181 4.4 30.3 1.0
CA C:LYS177 4.4 38.0 1.0
CG C:GLU201 4.5 29.9 1.0
N C:GLY179 4.5 34.0 1.0
CA C:ASP175 4.6 32.9 1.0
CA C:GLY179 4.7 33.1 1.0
CB C:ASP175 4.7 32.1 1.0
O C:ASP175 4.8 34.8 1.0
O C:LYS177 4.8 35.4 1.0
O C:GLY179 4.8 32.7 1.0
CB C:ILE180 4.9 33.7 1.0

Calcium binding site 6 out of 9 in 2woa

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Calcium binding site 6 out of 9 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
C:Ca1271

b:62.2
occ:1.00
 O C:GLY190 2.6 45.9 1.0
O C:GLY192 2.7 32.5 1.0
OD1 C:ASP194 2.7 31.9 1.0
O C:ASP158 2.8 29.3 1.0
CG C:ASP194 3.5 34.0 1.0
O C:HOH2055 3.6 34.7 1.0
C C:ILE191 3.6 41.2 1.0
C C:GLY192 3.6 35.0 1.0
O C:ILE191 3.7 41.5 1.0
C C:GLY190 3.7 46.1 1.0
OD2 C:ASP194 3.8 32.1 1.0
N C:GLY192 3.9 40.2 1.0
C C:ASP158 3.9 32.2 1.0
CA C:ILE191 4.0 42.4 1.0
N C:ASP194 4.3 32.4 1.0
N C:ILE191 4.3 43.7 1.0
CA C:GLY192 4.4 37.1 1.0
O C:ALA157 4.5 37.9 1.0
N C:GLY193 4.5 34.1 1.0
CA C:GLY193 4.7 33.6 1.0
CA C:ILE159 4.7 31.8 1.0
CB C:ASP194 4.7 30.9 1.0
N C:ILE159 4.7 31.6 1.0
C C:GLY193 4.8 34.1 1.0
CA C:ASP158 4.9 34.1 1.0
CA C:ASP194 4.9 32.7 1.0
CA C:GLY190 4.9 48.0 1.0
N C:LEU160 4.9 33.0 1.0

Calcium binding site 7 out of 9 in 2woa

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Calcium binding site 7 out of 9 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
C:Ca1272

b:42.0
occ:1.00
 O C:GLU199 2.3 34.9 1.0
OE2 C:GLU199 2.3 37.4 1.0
O C:HOH2011 2.5 41.2 1.0
O C:GLU201 2.6 33.2 1.0
OD2 C:ASP124 2.7 42.6 1.0
O C:HOH2037 2.8 38.2 1.0
OD1 C:ASP124 2.8 33.4 1.0
CG C:ASP124 3.1 36.9 1.0
CD C:GLU199 3.4 36.8 1.0
C C:GLU199 3.4 33.7 1.0
CG C:GLU199 3.8 37.5 1.0
C C:GLU201 3.9 34.1 1.0
CA C:GLU199 4.1 34.3 1.0
OG1 C:THR122 4.2 30.1 1.0
CD1 C:TRP203 4.4 30.7 1.0
N C:ASP200 4.5 31.5 1.0
CA C:PHE202 4.5 36.8 1.0
N C:GLU201 4.5 31.5 1.0
OE1 C:GLU199 4.6 31.7 1.0
C C:ASP200 4.6 31.9 1.0
CB C:GLU199 4.6 35.9 1.0
NH2 C:ARG165 4.6 27.7 1.0
CB C:ASP124 4.6 35.5 1.0
N C:PHE202 4.6 35.3 1.0
CA C:ASP200 4.7 31.9 1.0
NE1 C:TRP203 4.8 29.2 1.0
CA C:GLU201 4.9 33.3 1.0

Calcium binding site 8 out of 9 in 2woa

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Calcium binding site 8 out of 9 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 8 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1269

b:30.8
occ:1.00
 O D:ILE180 2.3 27.1 1.0
OD2 D:ASP198 2.3 32.6 1.0
O D:GLY178 2.3 31.6 1.0
OE2 D:GLU201 2.3 32.7 1.0
O D:GLY176 2.3 29.7 1.0
OD2 D:ASP175 2.3 31.2 1.0
CG D:ASP198 3.4 30.9 1.0
C D:ILE180 3.5 27.9 1.0
C D:GLY178 3.5 32.3 1.0
C D:GLY176 3.5 29.4 1.0
CG D:ASP175 3.5 32.2 1.0
CD D:GLU201 3.6 31.0 1.0
N D:GLY178 3.9 30.2 1.0
CB D:ASP198 4.0 27.2 1.0
N D:GLY176 4.1 33.4 1.0
N D:ILE180 4.1 28.5 1.0
OD1 D:ASP175 4.1 29.2 1.0
C D:LYS177 4.2 31.2 1.0
C D:ASP175 4.3 32.0 1.0
CA D:GLY178 4.3 30.4 1.0
OD1 D:ASP198 4.3 27.7 1.0
OE1 D:GLU201 4.3 32.7 1.0
C D:GLY179 4.3 29.6 1.0
N D:ASP175 4.3 32.0 1.0
CA D:ILE180 4.4 27.5 1.0
N D:LEU181 4.4 27.7 1.0
CA D:GLY176 4.4 31.3 1.0
CA D:LEU181 4.5 28.0 1.0
N D:LYS177 4.5 29.9 1.0
CA D:LYS177 4.5 31.9 1.0
CG D:GLU201 4.6 28.2 1.0
N D:GLY179 4.6 29.8 1.0
O D:ASP175 4.6 31.9 1.0
CA D:ASP175 4.7 31.5 1.0
O D:GLY179 4.7 29.7 1.0
CB D:ASP175 4.7 32.0 1.0
CA D:GLY179 4.7 28.6 1.0
O D:LYS177 4.8 34.2 1.0
CB D:ILE180 5.0 26.9 1.0

Calcium binding site 9 out of 9 in 2woa

Go back to Calcium Binding Sites List in 2woa
Calcium binding site 9 out of 9 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 9 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1270

b:32.9
occ:1.00
 O D:HOH2007 2.2 34.4 1.0
OD2 D:ASP124 2.3 30.5 1.0
O D:GLU199 2.3 32.6 1.0
OE2 D:GLU199 2.4 31.5 1.0
O D:GLU201 2.4 32.3 1.0
OD1 D:ASP124 2.7 29.0 1.0
O D:HOH2067 2.8 49.5 1.0
CG D:ASP124 2.8 27.4 1.0
CD D:GLU199 3.4 31.6 1.0
C D:GLU199 3.4 30.3 1.0
C D:GLU201 3.6 30.9 1.0
O D:HOH2043 3.8 41.8 1.0
CG D:GLU199 3.8 30.7 1.0
OG1 D:THR122 4.0 27.0 1.0
CA D:GLU199 4.1 29.9 1.0
CA D:PHE202 4.2 29.5 1.0
CB D:ASP124 4.3 25.4 1.0
N D:PHE202 4.4 30.9 1.0
CD1 D:TRP203 4.4 24.1 1.0
N D:GLU201 4.4 28.4 1.0
N D:ASP200 4.5 30.9 1.0
OE1 D:GLU199 4.5 26.1 1.0
CB D:GLU199 4.6 30.2 1.0
C D:ASP200 4.6 30.7 1.0
N D:TRP203 4.7 26.4 1.0
CA D:GLU201 4.7 30.0 1.0
CA D:ASP200 4.8 30.1 1.0
NE1 D:TRP203 4.9 28.2 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 18:47:02 2024

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