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Zinc 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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the MMP12 Complex with A Beta Hydroxy Carboxylic Acid, PDB code: 2wo8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2wo8

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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:28.2
occ:1.00
O3 A:0771271 2.1 31.7 1.0
O4 A:0771271 2.1 34.8 1.0
NE2 A:HIS228 2.1 29.0 1.0
NE2 A:HIS218 2.1 20.5 1.0
NE2 A:HIS222 2.1 34.8 1.0
C18 A:0771271 2.4 34.7 1.0
CE1 A:HIS228 3.0 27.8 1.0
CD2 A:HIS218 3.0 15.5 1.0
CE1 A:HIS222 3.1 30.8 1.0
CD2 A:HIS228 3.1 29.7 1.0
CD2 A:HIS222 3.2 30.2 1.0
CE1 A:HIS218 3.2 21.8 1.0
C17 A:0771271 3.9 34.5 1.0
O A:HOH2130 4.1 25.3 1.0
ND1 A:HIS228 4.1 31.2 1.0
ND1 A:HIS222 4.2 26.3 1.0
CG A:HIS228 4.2 28.4 1.0
CG A:HIS218 4.2 18.9 1.0
O A:HOH2129 4.2 43.7 1.0
ND1 A:HIS218 4.3 17.2 1.0
CG A:HIS222 4.3 25.9 1.0
C12 A:0771271 4.3 30.3 1.0
C20 A:0771271 4.6 30.6 1.0
CE A:MET236 4.8 20.1 1.0
OE2 A:GLU219 4.8 27.2 1.0

Zinc binding site 2 out of 8 in 2wo8

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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:29.6
occ:1.00
OD1 A:ASP170 2.0 37.0 1.0
NE2 A:HIS168 2.1 28.4 1.0
NE2 A:HIS183 2.1 28.7 1.0
ND1 A:HIS196 2.1 26.3 1.0
CE1 A:HIS183 3.0 28.9 1.0
CD2 A:HIS168 3.0 27.7 1.0
CG A:ASP170 3.1 39.4 1.0
CG A:HIS196 3.1 25.4 1.0
CE1 A:HIS196 3.1 26.3 1.0
CE1 A:HIS168 3.2 27.7 1.0
CD2 A:HIS183 3.2 29.3 1.0
CB A:HIS196 3.4 25.3 1.0
OD2 A:ASP170 3.5 36.8 1.0
ND1 A:HIS183 4.2 32.3 1.0
CG A:HIS168 4.2 33.7 1.0
NE2 A:HIS196 4.2 29.8 1.0
ND1 A:HIS168 4.2 25.0 1.0
CD2 A:HIS196 4.2 27.8 1.0
CE1 A:PHE185 4.2 38.0 1.0
CG A:HIS183 4.3 29.1 1.0
CB A:ASP170 4.3 40.3 1.0
CZ A:PHE185 4.4 34.3 1.0
O A:HIS172 4.4 38.6 1.0
CZ A:PHE174 4.5 17.4 1.0
CE2 A:PHE174 4.5 27.9 1.0
CA A:HIS196 4.9 25.7 1.0
O A:HOH2134 4.9 28.0 1.0

Zinc binding site 3 out of 8 in 2wo8

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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:Zn1269

b:19.5
occ:1.00
O16 B:0231268 2.0 23.3 1.0
NE2 B:HIS222 2.1 18.7 1.0
NE2 B:HIS228 2.1 20.9 1.0
NE2 B:HIS218 2.1 16.8 1.0
O12 B:0231268 2.1 20.3 1.0
C11 B:0231268 2.7 15.4 1.0
N7 B:0231268 2.8 19.0 1.0
CD2 B:HIS228 3.0 22.1 1.0
CE1 B:HIS218 3.0 12.0 1.0
CE1 B:HIS222 3.1 19.5 1.0
CD2 B:HIS222 3.1 12.3 1.0
CD2 B:HIS218 3.1 11.4 1.0
CE1 B:HIS228 3.2 22.7 1.0
O B:HOH2167 3.9 24.8 1.0
C3 B:0231268 4.1 15.4 1.0
ND1 B:HIS218 4.2 15.0 1.0
CG B:HIS228 4.2 22.4 1.0
ND1 B:HIS222 4.2 17.9 1.0
ND1 B:HIS228 4.2 24.1 1.0
CG B:HIS222 4.2 19.7 1.0
CG B:HIS218 4.3 13.4 1.0
O B:HOH2083 4.4 23.0 1.0
C4 B:0231268 4.5 14.6 1.0
C1 B:0231268 4.6 15.5 1.0
OE1 B:GLU219 4.7 19.2 1.0
CE B:MET236 4.8 14.6 1.0
C8 B:0231268 4.8 19.6 1.0
CB B:PRO238 4.9 18.4 1.0
OE2 B:GLU219 5.0 24.1 1.0

Zinc binding site 4 out of 8 in 2wo8

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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:Zn1270

b:21.1
occ:1.00
OD1 B:ASP170 2.0 22.3 1.0
NE2 B:HIS168 2.1 19.0 1.0
NE2 B:HIS183 2.1 20.7 1.0
ND1 B:HIS196 2.2 20.6 1.0
CG B:ASP170 2.9 20.5 1.0
CE1 B:HIS168 3.0 13.1 1.0
CE1 B:HIS183 3.1 22.8 1.0
CE1 B:HIS196 3.1 18.5 1.0
CD2 B:HIS183 3.1 22.3 1.0
CD2 B:HIS168 3.1 21.2 1.0
CG B:HIS196 3.1 20.7 1.0
OD2 B:ASP170 3.2 23.8 1.0
CB B:HIS196 3.5 16.9 1.0
ND1 B:HIS168 4.2 14.6 1.0
ND1 B:HIS183 4.2 22.5 1.0
NE2 B:HIS196 4.2 21.0 1.0
O B:HIS172 4.2 21.7 1.0
CG B:HIS168 4.2 19.0 1.0
CG B:HIS183 4.3 18.6 1.0
CD2 B:HIS196 4.3 16.7 1.0
CB B:ASP170 4.3 24.3 1.0
CE1 B:PHE185 4.5 20.2 1.0
CE2 B:PHE174 4.6 20.5 1.0
CZ B:PHE174 4.7 21.1 1.0
CB B:HIS172 4.9 19.0 1.0
CZ B:PHE185 4.9 18.2 1.0

Zinc binding site 5 out of 8 in 2wo8

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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:Zn1268

b:26.6
occ:1.00
O3 C:0771271 2.0 24.7 1.0
NE2 C:HIS218 2.1 16.8 1.0
NE2 C:HIS222 2.1 24.1 1.0
NE2 C:HIS228 2.1 32.0 1.0
C18 C:0771271 2.6 28.9 1.0
O4 C:0771271 2.8 27.5 1.0
CE1 C:HIS218 3.0 21.1 1.0
CE1 C:HIS222 3.0 23.0 1.0
CD2 C:HIS228 3.1 31.7 1.0
CE1 C:HIS228 3.1 34.3 1.0
CD2 C:HIS218 3.1 18.3 1.0
CD2 C:HIS222 3.2 18.8 1.0
C17 C:0771271 4.1 31.3 1.0
ND1 C:HIS218 4.2 19.6 1.0
ND1 C:HIS228 4.2 34.8 1.0
ND1 C:HIS222 4.2 22.2 1.0
CG C:HIS228 4.2 32.5 1.0
CG C:HIS218 4.2 17.0 1.0
CG C:HIS222 4.3 22.4 1.0
C12 C:0771271 4.5 28.3 1.0
O C:HOH2076 4.5 29.0 1.0
OE2 C:GLU219 4.6 17.2 1.0
O C:HOH2097 4.7 52.8 1.0
C20 C:0771271 4.7 31.7 1.0
CE C:MET236 4.8 19.9 1.0

Zinc binding site 6 out of 8 in 2wo8

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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:Zn1269

b:27.4
occ:1.00
OD1 C:ASP170 2.0 27.2 1.0
ND1 C:HIS196 2.1 23.3 1.0
NE2 C:HIS183 2.1 22.9 1.0
NE2 C:HIS168 2.1 27.4 1.0
CE1 C:HIS196 2.9 22.5 1.0
CG C:ASP170 2.9 23.9 1.0
CD2 C:HIS168 3.0 23.8 1.0
CD2 C:HIS183 3.1 25.8 1.0
CE1 C:HIS183 3.1 24.8 1.0
CE1 C:HIS168 3.2 23.2 1.0
OD2 C:ASP170 3.2 21.2 1.0
CG C:HIS196 3.2 21.4 1.0
CB C:HIS196 3.7 22.4 1.0
NE2 C:HIS196 4.1 22.2 1.0
CG C:HIS168 4.2 23.3 1.0
ND1 C:HIS168 4.2 23.9 1.0
CZ C:PHE185 4.2 27.8 1.0
CG C:HIS183 4.2 22.7 1.0
ND1 C:HIS183 4.2 24.7 1.0
CD2 C:HIS196 4.3 23.4 1.0
O C:HIS172 4.3 33.3 1.0
CB C:ASP170 4.3 29.4 1.0
CE2 C:PHE174 4.4 27.2 1.0
CE1 C:PHE185 4.4 30.8 1.0
CZ C:PHE174 4.5 27.5 1.0
O C:HOH2063 4.8 21.1 1.0

Zinc binding site 7 out of 8 in 2wo8

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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:23.7
occ:1.00
O16 D:0231266 2.0 16.8 1.0
NE2 D:HIS222 2.1 16.9 1.0
NE2 D:HIS218 2.2 19.4 1.0
NE2 D:HIS228 2.2 25.6 1.0
O12 D:0231266 2.2 20.4 1.0
C11 D:0231266 2.7 21.8 1.0
N7 D:0231266 2.8 18.8 1.0
CD2 D:HIS218 3.0 14.2 1.0
CD2 D:HIS222 3.0 23.4 1.0
CD2 D:HIS228 3.0 26.4 1.0
CE1 D:HIS222 3.1 27.1 1.0
CE1 D:HIS228 3.2 30.6 1.0
CE1 D:HIS218 3.2 17.0 1.0
O D:HOH2106 3.7 39.1 1.0
C3 D:0231266 4.1 23.6 1.0
CG D:HIS218 4.2 16.9 1.0
O D:HOH2105 4.2 25.4 1.0
CG D:HIS222 4.2 26.9 1.0
ND1 D:HIS222 4.2 24.2 1.0
CG D:HIS228 4.2 24.1 1.0
ND1 D:HIS218 4.3 16.2 1.0
ND1 D:HIS228 4.3 28.8 1.0
C1 D:0231266 4.5 18.7 1.0
C4 D:0231266 4.6 20.0 1.0
OE1 D:GLU219 4.7 27.0 1.0
C8 D:0231266 4.7 20.5 1.0
OE2 D:GLU219 4.8 21.2 1.0
CA D:PRO238 5.0 20.7 1.0
CE D:MET236 5.0 29.1 1.0

Zinc binding site 8 out of 8 in 2wo8

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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:27.4
occ:1.00
OD1 D:ASP170 2.0 24.4 1.0
NE2 D:HIS183 2.1 24.4 1.0
NE2 D:HIS168 2.1 25.8 1.0
ND1 D:HIS196 2.1 31.8 1.0
CE1 D:HIS183 2.9 16.7 1.0
CD2 D:HIS168 2.9 26.9 1.0
CG D:ASP170 3.0 26.4 1.0
CG D:HIS196 3.1 28.9 1.0
CE1 D:HIS196 3.1 34.6 1.0
CD2 D:HIS183 3.2 27.2 1.0
CE1 D:HIS168 3.3 22.5 1.0
OD2 D:ASP170 3.4 23.9 1.0
CB D:HIS196 3.4 22.5 1.0
ND1 D:HIS183 4.1 18.2 1.0
CG D:HIS168 4.1 20.7 1.0
NE2 D:HIS196 4.2 34.7 1.0
CD2 D:HIS196 4.2 32.5 1.0
ND1 D:HIS168 4.3 24.5 1.0
CG D:HIS183 4.3 20.4 1.0
CB D:ASP170 4.3 29.0 1.0
O D:HIS172 4.3 27.1 1.0
CE1 D:PHE185 4.6 34.5 1.0
CE2 D:PHE174 4.6 19.7 1.0
CZ D:PHE174 4.6 20.4 1.0
CZ D:PHE185 4.9 32.5 1.0
O D:HOH2050 4.9 33.6 1.0
CA D:HIS196 4.9 23.5 1.0
CB D:HIS172 5.0 28.1 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: Sat Sep 26 04:25:00 2020
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