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Zinc 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:

Calcium (Ca) 9 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 2woa

Go back to Zinc Binding Sites List in 2woa
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:Zn1270

b:37.9
occ:1.00
 O20 A:5761273 2.0 38.4 1.0
NE2 A:HIS218 2.1 28.2 1.0
NE2 A:HIS222 2.1 34.4 1.0
NE2 A:HIS228 2.1 36.6 1.0
C18 A:5761273 2.6 39.5 1.0
O19 A:5761273 2.7 32.9 1.0
CD2 A:HIS222 3.0 32.3 1.0
CD2 A:HIS228 3.0 35.2 1.0
CD2 A:HIS218 3.1 27.0 1.0
CE1 A:HIS218 3.1 27.5 1.0
CE1 A:HIS228 3.2 34.0 1.0
CE1 A:HIS222 3.2 37.0 1.0
C17 A:5761273 4.1 37.8 1.0
O A:HOH2056 4.2 29.3 1.0
CG A:HIS228 4.2 39.3 1.0
CG A:HIS222 4.2 32.2 1.0
CG A:HIS218 4.2 28.3 1.0
ND1 A:HIS218 4.2 25.9 1.0
ND1 A:HIS228 4.2 39.8 1.0
ND1 A:HIS222 4.2 36.3 1.0
C3 A:5761273 4.5 39.5 1.0
O A:HOH2078 4.7 37.5 1.0
CE A:MET236 4.8 25.6 1.0
C2 A:5761273 4.8 41.6 1.0
OE2 A:GLU219 4.8 33.7 1.0

Zinc binding site 2 out of 8 in 2woa

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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:Zn1271

b:38.4
occ:1.00
 OD1 A:ASP170 2.0 45.7 1.0
NE2 A:HIS168 2.1 38.6 1.0
NE2 A:HIS183 2.1 34.6 1.0
ND1 A:HIS196 2.1 31.3 1.0
CG A:ASP170 2.9 43.5 1.0
CE1 A:HIS183 3.0 34.0 1.0
CD2 A:HIS168 3.0 37.2 1.0
CE1 A:HIS196 3.1 32.7 1.0
CG A:HIS196 3.1 31.3 1.0
CE1 A:HIS168 3.2 39.0 1.0
OD2 A:ASP170 3.2 35.6 1.0
CD2 A:HIS183 3.3 35.1 1.0
CB A:HIS196 3.5 32.4 1.0
ND1 A:HIS183 4.1 33.2 1.0
CG A:HIS168 4.2 44.6 1.0
CB A:ASP170 4.2 45.6 1.0
NE2 A:HIS196 4.2 28.8 1.0
ND1 A:HIS168 4.2 38.9 1.0
CD2 A:HIS196 4.3 30.8 1.0
CG A:HIS183 4.3 31.9 1.0
O A:HIS172 4.4 42.2 1.0
CE1 A:PHE185 4.4 39.8 1.0
CZ A:PHE174 4.6 24.1 1.0
CE2 A:PHE174 4.6 30.1 1.0
CZ A:PHE185 4.6 41.7 1.0
CB A:HIS172 4.9 44.7 1.0
CA A:HIS196 5.0 32.8 1.0

Zinc binding site 3 out of 8 in 2woa

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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:Zn1270

b:31.5
occ:1.00
 O12 B:0231269 2.0 26.0 1.0
O16 B:0231269 2.0 29.0 1.0
NE2 B:HIS218 2.1 28.5 1.0
NE2 B:HIS222 2.1 26.1 1.0
NE2 B:HIS228 2.1 29.6 1.0
N7 B:0231269 2.8 27.4 1.0
C11 B:0231269 2.8 24.3 1.0
CD2 B:HIS228 3.0 28.3 1.0
CD2 B:HIS218 3.1 23.6 1.0
CD2 B:HIS222 3.1 20.6 1.0
CE1 B:HIS218 3.1 29.6 1.0
CE1 B:HIS222 3.2 29.3 1.0
CE1 B:HIS228 3.2 25.9 1.0
C3 B:0231269 4.1 25.9 1.0
CG B:HIS228 4.2 30.0 1.0
CG B:HIS218 4.2 26.7 1.0
ND1 B:HIS218 4.2 24.9 1.0
CG B:HIS222 4.2 25.4 1.0
ND1 B:HIS222 4.2 30.2 1.0
ND1 B:HIS228 4.3 33.2 1.0
O B:HOH2070 4.3 26.5 1.0
C4 B:0231269 4.4 28.1 1.0
C1 B:0231269 4.5 29.5 1.0
CE B:MET236 4.7 25.0 1.0
O B:HOH2094 4.8 45.2 1.0
C8 B:0231269 4.8 27.0 1.0
OE1 B:GLU219 4.9 27.4 1.0
OE2 B:GLU219 4.9 23.5 1.0

Zinc binding site 4 out of 8 in 2woa

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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:Zn1271

b:30.9
occ:1.00
 OD1 B:ASP170 2.0 31.5 1.0
NE2 B:HIS168 2.1 27.3 1.0
NE2 B:HIS183 2.1 24.6 1.0
ND1 B:HIS196 2.2 25.0 1.0
CG B:ASP170 2.9 30.1 1.0
CE1 B:HIS168 3.0 26.2 1.0
CE1 B:HIS183 3.0 22.5 1.0
CE1 B:HIS196 3.1 25.1 1.0
CG B:HIS196 3.1 26.4 1.0
OD2 B:ASP170 3.2 28.3 1.0
CD2 B:HIS168 3.2 27.4 1.0
CD2 B:HIS183 3.2 25.5 1.0
CB B:HIS196 3.5 22.4 1.0
ND1 B:HIS168 4.1 26.7 1.0
ND1 B:HIS183 4.2 32.3 1.0
O B:HIS172 4.2 33.9 1.0
NE2 B:HIS196 4.2 23.2 1.0
CG B:HIS168 4.2 31.3 1.0
CD2 B:HIS196 4.3 24.7 1.0
CG B:HIS183 4.3 25.4 1.0
CB B:ASP170 4.3 29.2 1.0
CE1 B:PHE185 4.5 30.6 1.0
CZ B:PHE174 4.6 26.9 1.0
CE2 B:PHE174 4.7 28.6 1.0
CB B:HIS172 4.8 31.5 1.0
CZ B:PHE185 4.9 25.7 1.0
O B:HOH2055 5.0 35.2 1.0
CA B:HIS196 5.0 24.1 1.0

Zinc binding site 5 out of 8 in 2woa

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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:34.0
occ:1.00
 O20 C:5761273 2.0 34.6 1.0
O19 C:5761273 2.1 40.1 1.0
NE2 C:HIS218 2.1 26.1 1.0
NE2 C:HIS222 2.1 30.8 1.0
NE2 C:HIS228 2.1 34.6 1.0
C18 C:5761273 2.3 37.4 1.0
CD2 C:HIS218 3.0 29.0 1.0
CD2 C:HIS228 3.0 37.1 1.0
CD2 C:HIS222 3.1 29.0 1.0
CE1 C:HIS218 3.1 24.0 1.0
CE1 C:HIS222 3.1 31.0 1.0
CE1 C:HIS228 3.2 33.6 1.0
C17 C:5761273 3.8 40.6 1.0
CG C:HIS218 4.2 27.3 1.0
ND1 C:HIS218 4.2 24.1 1.0
CG C:HIS222 4.2 30.2 1.0
ND1 C:HIS222 4.2 29.9 1.0
CG C:HIS228 4.2 34.2 1.0
ND1 C:HIS228 4.3 40.0 1.0
C3 C:5761273 4.3 34.8 1.0
O C:HOH2051 4.4 31.1 1.0
C2 C:5761273 4.5 38.6 1.0
OE2 C:GLU219 4.6 35.1 1.0
CE C:MET236 5.0 30.1 1.0

Zinc binding site 6 out of 8 in 2woa

Go back to Zinc Binding Sites List in 2woa
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:36.8
occ:1.00
 OD1 C:ASP170 2.0 39.0 1.0
NE2 C:HIS183 2.1 30.4 1.0
ND1 C:HIS196 2.1 30.9 1.0
NE2 C:HIS168 2.2 28.5 1.0
CG C:ASP170 2.9 37.2 1.0
CD2 C:HIS168 3.0 27.6 1.0
CE1 C:HIS196 3.1 36.0 1.0
CD2 C:HIS183 3.1 31.0 1.0
CE1 C:HIS183 3.1 29.3 1.0
CG C:HIS196 3.1 29.8 1.0
OD2 C:ASP170 3.2 30.5 1.0
CE1 C:HIS168 3.2 27.4 1.0
CB C:HIS196 3.5 30.8 1.0
NE2 C:HIS196 4.2 32.4 1.0
ND1 C:HIS183 4.2 32.1 1.0
CG C:HIS168 4.2 32.6 1.0
CG C:HIS183 4.2 31.1 1.0
CZ C:PHE185 4.3 38.5 1.0
CD2 C:HIS196 4.3 32.0 1.0
ND1 C:HIS168 4.3 26.3 1.0
CB C:ASP170 4.3 36.7 1.0
CE1 C:PHE185 4.4 42.1 1.0
O C:HIS172 4.5 43.6 1.0
CE2 C:PHE174 4.5 32.4 1.0
CZ C:PHE174 4.6 35.4 1.0
O C:HOH2039 4.8 31.2 1.0
CE2 C:PHE171 4.9 57.2 1.0
CA C:HIS196 5.0 30.0 1.0

Zinc binding site 7 out of 8 in 2woa

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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:33.3
occ:1.00
 O12 D:0231266 2.0 27.7 1.0
O16 D:0231266 2.0 33.3 1.0
NE2 D:HIS222 2.1 34.0 1.0
NE2 D:HIS218 2.1 27.8 1.0
NE2 D:HIS228 2.1 35.1 1.0
C11 D:0231266 2.7 28.1 1.0
N7 D:0231266 2.7 29.5 1.0
CD2 D:HIS218 3.0 19.4 1.0
CD2 D:HIS228 3.0 35.1 1.0
CE1 D:HIS222 3.1 35.0 1.0
CD2 D:HIS222 3.1 30.5 1.0
CE1 D:HIS228 3.2 36.5 1.0
CE1 D:HIS218 3.2 29.6 1.0
O D:HOH2102 3.8 33.9 1.0
C3 D:0231266 4.1 32.3 1.0
CG D:HIS218 4.2 25.3 1.0
ND1 D:HIS222 4.2 37.6 1.0
CG D:HIS228 4.2 35.3 1.0
CG D:HIS222 4.3 34.8 1.0
ND1 D:HIS218 4.3 26.0 1.0
ND1 D:HIS228 4.3 38.9 1.0
O D:HOH2103 4.3 27.8 1.0
C1 D:0231266 4.5 27.9 1.0
C4 D:0231266 4.5 29.8 1.0
OE1 D:GLU219 4.7 32.3 1.0
CB D:PRO238 4.7 28.7 1.0
C8 D:0231266 4.8 26.0 1.0
CE D:MET236 4.8 31.4 1.0
CA D:PRO238 4.9 29.5 1.0
OE2 D:GLU219 5.0 27.3 1.0

Zinc binding site 8 out of 8 in 2woa

Go back to Zinc Binding Sites List in 2woa
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:35.3
occ:1.00
 OD1 D:ASP170 2.0 35.4 1.0
NE2 D:HIS168 2.1 29.2 1.0
NE2 D:HIS183 2.1 24.6 1.0
ND1 D:HIS196 2.2 37.5 1.0
CG D:ASP170 3.0 30.7 1.0
CD2 D:HIS168 3.0 26.4 1.0
CE1 D:HIS183 3.1 23.0 1.0
CE1 D:HIS196 3.1 35.2 1.0
CD2 D:HIS183 3.1 29.6 1.0
CG D:HIS196 3.2 35.6 1.0
CE1 D:HIS168 3.2 30.0 1.0
OD2 D:ASP170 3.3 26.1 1.0
CB D:HIS196 3.5 32.0 1.0
CG D:HIS168 4.2 31.5 1.0
ND1 D:HIS183 4.2 28.1 1.0
ND1 D:HIS168 4.2 29.8 1.0
NE2 D:HIS196 4.2 38.5 1.0
O D:HIS172 4.2 33.9 1.0
CG D:HIS183 4.3 26.3 1.0
CD2 D:HIS196 4.3 36.8 1.0
CB D:ASP170 4.4 33.0 1.0
CE1 D:PHE185 4.4 31.9 1.0
CZ D:PHE174 4.5 33.5 1.0
CE2 D:PHE174 4.5 29.7 1.0
CZ D:PHE185 4.7 33.8 1.0
O D:HOH2047 4.9 32.8 1.0
CA D:HIS196 5.0 31.9 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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