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Zinc 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:

Calcium (Ca) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid, PDB code: 2wo9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2wo9

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Zinc binding site 1 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1268

b:26.2
occ:1.00
 O20 A:0681271 2.0 21.5 1.0
NE2 A:HIS228 2.1 24.2 1.0
NE2 A:HIS222 2.1 20.9 1.0
NE2 A:HIS218 2.1 23.6 1.0
C18 A:0681271 2.6 24.0 1.0
O19 A:0681271 2.7 22.3 1.0
CD2 A:HIS228 3.1 27.5 1.0
CE1 A:HIS218 3.1 23.6 1.0
CD2 A:HIS222 3.1 22.5 1.0
CE1 A:HIS228 3.1 29.7 1.0
CE1 A:HIS222 3.1 25.7 1.0
CD2 A:HIS218 3.1 20.2 1.0
C17 A:0681271 4.1 23.7 1.0
ND1 A:HIS228 4.2 30.0 1.0
ND1 A:HIS218 4.2 22.6 1.0
O A:HOH2163 4.2 30.7 1.0
CG A:HIS228 4.2 27.4 1.0
O A:HOH2162 4.2 31.0 1.0
ND1 A:HIS222 4.2 23.0 1.0
CG A:HIS218 4.2 18.5 1.0
CG A:HIS222 4.3 19.1 1.0
C3 A:0681271 4.4 24.4 1.0
C2 A:0681271 4.8 24.5 1.0
OE2 A:GLU219 4.8 23.0 1.0
O A:HOH2138 4.8 39.2 1.0
CE A:MET236 4.9 27.1 1.0
O A:HOH2108 4.9 43.6 1.0
O A:HOH2104 5.0 39.9 1.0

Zinc binding site 2 out of 8 in 2wo9

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Zinc binding site 2 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of MMP12 Complex with A Beta Hydroxy Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1269

b:29.2
occ:1.00
 OD1 A:ASP170 2.0 30.6 1.0
NE2 A:HIS183 2.1 26.9 1.0
ND1 A:HIS196 2.1 29.9 1.0
NE2 A:HIS168 2.1 23.1 1.0
CG A:ASP170 2.9 32.6 1.0
CE1 A:HIS183 3.0 25.4 1.0
CE1 A:HIS196 3.0 26.7 1.0
CD2 A:HIS168 3.1 28.0 1.0
CE1 A:HIS168 3.1 25.1 1.0
CG A:HIS196 3.1 25.0 1.0
CD2 A:HIS183 3.2 28.4 1.0
OD2 A:ASP170 3.2 32.5 1.0
CB A:HIS196 3.5 22.1 1.0
ND1 A:HIS183 4.1 26.5 1.0
NE2 A:HIS196 4.2 29.8 1.0
ND1 A:HIS168 4.2 27.3 1.0
CG A:HIS168 4.2 29.2 1.0
O A:HIS172 4.2 31.0 1.0
CE1 A:PHE185 4.2 35.1 1.0
CD2 A:HIS196 4.2 25.2 1.0
CG A:HIS183 4.3 23.8 1.0
CB A:ASP170 4.3 35.8 1.0
CZ A:PHE185 4.4 34.8 1.0
CZ A:PHE174 4.6 23.3 1.0
CE2 A:PHE174 4.7 25.6 1.0
CB A:HIS172 4.9 33.8 1.0
O A:HOH2092 5.0 36.4 1.0

Zinc binding site 3 out of 8 in 2wo9

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Zinc binding site 3 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1268

b:21.0
occ:1.00
 O12 B:0231267 2.0 22.9 1.0
NE2 B:HIS218 2.1 17.5 1.0
O16 B:0231267 2.1 17.9 1.0
NE2 B:HIS228 2.1 18.6 1.0
NE2 B:HIS222 2.1 21.8 1.0
N7 B:0231267 2.8 20.0 1.0
C11 B:0231267 2.8 20.9 1.0
CD2 B:HIS218 3.0 17.2 1.0
CD2 B:HIS228 3.1 20.4 1.0
CD2 B:HIS222 3.1 13.8 1.0
CE1 B:HIS222 3.1 20.0 1.0
CE1 B:HIS218 3.1 19.5 1.0
CE1 B:HIS228 3.2 19.9 1.0
O B:HOH2186 3.9 29.1 1.0
C3 B:0231267 4.1 18.6 1.0
CG B:HIS218 4.2 16.4 1.0
ND1 B:HIS218 4.2 15.9 1.0
CG B:HIS228 4.2 20.5 1.0
ND1 B:HIS228 4.2 21.8 1.0
ND1 B:HIS222 4.2 18.9 1.0
CG B:HIS222 4.3 18.1 1.0
O B:HOH2098 4.3 20.2 1.0
C1 B:0231267 4.5 16.8 1.0
C4 B:0231267 4.5 17.5 1.0
OE1 B:GLU219 4.7 18.6 1.0
CE B:MET236 4.8 23.4 1.0
OE2 B:GLU219 4.8 19.9 1.0
C8 B:0231267 4.9 25.3 1.0
O B:HOH2126 5.0 26.2 1.0

Zinc binding site 4 out of 8 in 2wo9

Go back to Zinc Binding Sites List in 2wo9
Zinc binding site 4 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1269

b:22.8
occ:1.00
 OD1 B:ASP170 2.0 21.0 1.0
ND1 B:HIS196 2.1 20.4 1.0
NE2 B:HIS168 2.1 23.4 1.0
NE2 B:HIS183 2.1 22.1 1.0
CG B:ASP170 2.9 21.7 1.0
CD2 B:HIS168 3.0 22.3 1.0
CE1 B:HIS183 3.0 20.2 1.0
CE1 B:HIS196 3.1 18.3 1.0
CG B:HIS196 3.2 19.5 1.0
CE1 B:HIS168 3.2 23.1 1.0
CD2 B:HIS183 3.2 21.5 1.0
OD2 B:ASP170 3.3 21.4 1.0
CB B:HIS196 3.5 17.8 1.0
CG B:HIS168 4.2 22.6 1.0
ND1 B:HIS183 4.2 21.5 1.0
NE2 B:HIS196 4.2 20.2 1.0
O B:HIS172 4.2 22.2 1.0
ND1 B:HIS168 4.2 22.1 1.0
CB B:ASP170 4.2 23.5 1.0
CD2 B:HIS196 4.3 19.1 1.0
CG B:HIS183 4.3 17.9 1.0
CE1 B:PHE185 4.5 24.6 1.0
CE2 B:PHE174 4.7 24.1 1.0
CZ B:PHE174 4.7 25.4 1.0
CB B:HIS172 4.8 22.4 1.0
CZ B:PHE185 4.8 23.5 1.0

Zinc binding site 5 out of 8 in 2wo9

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Zinc binding site 5 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1269

b:25.6
occ:1.00
 O20 C:0681272 2.0 23.7 1.0
NE2 C:HIS228 2.1 23.2 1.0
NE2 C:HIS218 2.1 20.5 1.0
NE2 C:HIS222 2.1 23.9 1.0
O19 C:0681272 2.6 20.7 1.0
C18 C:0681272 2.6 23.6 1.0
CD2 C:HIS228 3.1 26.8 1.0
CD2 C:HIS222 3.1 20.1 1.0
CE1 C:HIS218 3.1 19.2 1.0
CD2 C:HIS218 3.1 18.4 1.0
CE1 C:HIS228 3.1 27.4 1.0
CE1 C:HIS222 3.1 23.6 1.0
O C:HOH2155 4.0 35.1 1.0
C17 C:0681272 4.1 25.4 1.0
ND1 C:HIS218 4.2 19.9 1.0
ND1 C:HIS228 4.2 28.1 1.0
CG C:HIS228 4.2 28.0 1.0
ND1 C:HIS222 4.2 24.5 1.0
CG C:HIS222 4.2 21.9 1.0
CG C:HIS218 4.2 18.5 1.0
C3 C:0681272 4.3 23.0 1.0
O C:HOH2093 4.5 23.8 1.0
C2 C:0681272 4.8 23.1 1.0
O C:HOH2120 4.8 42.8 1.0
CE C:MET236 4.8 21.2 1.0
OE2 C:GLU219 4.8 24.2 1.0

Zinc binding site 6 out of 8 in 2wo9

Go back to Zinc Binding Sites List in 2wo9
Zinc binding site 6 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1270

b:24.9
occ:1.00
 OD1 C:ASP170 2.0 24.2 1.0
NE2 C:HIS183 2.1 23.1 1.0
NE2 C:HIS168 2.1 23.6 1.0
ND1 C:HIS196 2.1 22.7 1.0
CG C:ASP170 2.9 24.7 1.0
CD2 C:HIS168 3.0 21.0 1.0
CE1 C:HIS196 3.0 23.8 1.0
CE1 C:HIS183 3.0 22.1 1.0
CD2 C:HIS183 3.1 23.0 1.0
CE1 C:HIS168 3.2 21.3 1.0
OD2 C:ASP170 3.2 24.5 1.0
CG C:HIS196 3.2 21.7 1.0
CB C:HIS196 3.6 20.4 1.0
CG C:HIS168 4.2 20.7 1.0
ND1 C:HIS183 4.2 22.8 1.0
NE2 C:HIS196 4.2 24.2 1.0
CG C:HIS183 4.2 22.9 1.0
ND1 C:HIS168 4.2 19.9 1.0
CD2 C:HIS196 4.3 23.3 1.0
CE1 C:PHE185 4.3 31.2 1.0
CB C:ASP170 4.3 27.2 1.0
CZ C:PHE185 4.4 30.4 1.0
O C:HIS172 4.5 28.4 1.0
CE2 C:PHE174 4.5 22.4 1.0
CZ C:PHE174 4.6 24.1 1.0
O C:HOH2071 4.7 29.4 1.0

Zinc binding site 7 out of 8 in 2wo9

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Zinc binding site 7 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1267

b:24.2
occ:1.00
 O12 D:0231266 2.0 25.8 1.0
O16 D:0231266 2.1 21.7 1.0
NE2 D:HIS218 2.1 21.5 1.0
NE2 D:HIS228 2.1 24.3 1.0
NE2 D:HIS222 2.1 24.4 1.0
N7 D:0231266 2.8 21.2 1.0
C11 D:0231266 2.8 21.6 1.0
CD2 D:HIS218 3.0 17.0 1.0
CD2 D:HIS228 3.1 22.8 1.0
CD2 D:HIS222 3.1 18.2 1.0
CE1 D:HIS222 3.2 25.4 1.0
CE1 D:HIS228 3.2 26.5 1.0
CE1 D:HIS218 3.2 18.6 1.0
O D:HOH2143 3.8 27.2 1.0
C3 D:0231266 4.1 19.7 1.0
O D:HOH2142 4.2 18.8 1.0
CG D:HIS218 4.2 19.8 1.0
CG D:HIS228 4.2 22.6 1.0
ND1 D:HIS218 4.3 20.8 1.0
ND1 D:HIS228 4.3 25.7 1.0
ND1 D:HIS222 4.3 24.8 1.0
CG D:HIS222 4.3 25.9 1.0
C4 D:0231266 4.5 19.3 1.0
C1 D:0231266 4.6 16.7 1.0
OE1 D:GLU219 4.6 23.1 1.0
OE2 D:GLU219 4.8 20.0 1.0
C8 D:0231266 4.9 19.9 1.0
CB D:PRO238 4.9 23.1 1.0
CE D:MET236 5.0 21.4 1.0
CA D:PRO238 5.0 22.6 1.0

Zinc binding site 8 out of 8 in 2wo9

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Zinc binding site 8 out of 8 in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn1268

b:25.2
occ:1.00
 OD1 D:ASP170 2.0 21.3 1.0
NE2 D:HIS183 2.1 23.7 1.0
ND1 D:HIS196 2.1 20.0 1.0
NE2 D:HIS168 2.1 22.3 1.0
CG D:ASP170 3.0 24.8 1.0
CD2 D:HIS168 3.0 26.0 1.0
CE1 D:HIS196 3.0 21.5 1.0
CE1 D:HIS183 3.1 21.4 1.0
CD2 D:HIS183 3.1 21.3 1.0
CG D:HIS196 3.1 23.2 1.0
CE1 D:HIS168 3.2 23.4 1.0
OD2 D:ASP170 3.3 25.8 1.0
CB D:HIS196 3.5 19.4 1.0
NE2 D:HIS196 4.2 24.3 1.0
ND1 D:HIS183 4.2 19.6 1.0
CG D:HIS168 4.2 26.7 1.0
ND1 D:HIS168 4.2 25.5 1.0
CG D:HIS183 4.2 18.4 1.0
CD2 D:HIS196 4.2 21.7 1.0
CB D:ASP170 4.3 25.9 1.0
O D:HIS172 4.3 23.5 1.0
CE1 D:PHE185 4.4 28.4 1.0
CE2 D:PHE174 4.6 24.9 1.0
CZ D:PHE174 4.6 27.3 1.0
CZ D:PHE185 4.8 30.0 1.0
CA D:HIS196 5.0 20.4 1.0
CB D:HIS172 5.0 25.9 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: Thu Oct 17 04:57:11 2024

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