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Zinc in PDB 5i2z: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24)., PDB code: 5i2z was solved by E.A.Stura, L.Rosalia, D.Cuffaro, L.Tepshi, L.Ciccone, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.41 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.990, 63.120, 78.750, 90.00, 102.37, 90.00
R / Rfree (%) 21.4 / 26.3

Other elements in 5i2z:

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). (pdb code 5i2z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24)., PDB code: 5i2z:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5i2z

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Zinc binding site 1 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:26.9
occ:1.00
 O20 A:V24301 2.1 21.0 1.0
NE2 A:HIS218 2.2 28.9 1.0
NE2 A:HIS228 2.2 38.6 1.0
NE2 A:HIS222 2.2 28.1 1.0
O19 A:V24301 2.4 26.5 1.0
C18 A:V24301 2.5 21.1 1.0
CD2 A:HIS222 3.1 20.6 1.0
CD2 A:HIS218 3.1 18.3 1.0
CD2 A:HIS228 3.2 38.6 1.0
CE1 A:HIS218 3.2 17.9 1.0
CE1 A:HIS228 3.2 30.1 1.0
CE1 A:HIS222 3.3 23.9 1.0
C17 A:V24301 3.9 37.4 1.0
ND1 A:HIS218 4.3 21.3 1.0
CG A:HIS218 4.3 28.3 1.0
CG A:HIS222 4.3 23.8 1.0
ND1 A:HIS228 4.3 30.1 1.0
CG A:HIS228 4.3 35.1 1.0
ND1 A:HIS222 4.4 20.4 1.0
NE2 A:GLN219 4.4 27.3 1.0
N16 A:V24301 4.6 61.0 1.0
O A:HOH492 4.6 35.3 1.0
C21 A:V24301 4.7 42.4 1.0
C9 A:V24301 4.8 36.7 1.0
C10 A:V24301 4.9 32.9 1.0
O A:HOH460 4.9 30.0 1.0
C24 A:V24301 5.0 68.8 1.0

Zinc binding site 2 out of 8 in 5i2z

Go back to Zinc Binding Sites List in 5i2z
Zinc binding site 2 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:25.1
occ:1.00
 OD2 A:ASP170 1.9 17.0 1.0
NE2 A:HIS168 2.1 20.1 1.0
ND1 A:HIS196 2.1 13.7 1.0
NE2 A:HIS183 2.3 22.1 1.0
CG A:ASP170 2.9 19.2 1.0
CE1 A:HIS196 2.9 16.0 1.0
CD2 A:HIS168 3.0 16.3 1.0
CE1 A:HIS168 3.1 25.2 1.0
CE1 A:HIS183 3.2 29.3 1.0
CG A:HIS196 3.2 14.4 1.0
OD1 A:ASP170 3.3 11.5 1.0
CD2 A:HIS183 3.4 24.2 1.0
CB A:HIS196 3.7 14.3 1.0
NE2 A:HIS196 4.1 18.2 1.0
CG A:HIS168 4.1 30.4 1.0
ND1 A:HIS168 4.1 31.1 1.0
CB A:ASP170 4.2 21.6 1.0
CD2 A:HIS196 4.3 18.2 1.0
CE1 A:PHE185 4.3 18.3 1.0
O A:HIS172 4.3 24.7 1.0
ND1 A:HIS183 4.4 28.4 1.0
CG A:HIS183 4.5 21.7 1.0
CZ A:PHE185 4.5 28.1 1.0
CZ A:PHE174 4.7 18.1 1.0
CE2 A:PHE174 4.8 17.3 1.0
O A:HOH438 5.0 9.2 1.0
CB A:HIS172 5.0 13.3 1.0

Zinc binding site 3 out of 8 in 5i2z

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Zinc binding site 3 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:37.3
occ:1.00
 O20 B:V24301 2.0 36.3 1.0
NE2 B:HIS222 2.1 23.9 1.0
NE2 B:HIS218 2.1 33.3 1.0
NE2 B:HIS228 2.3 40.2 1.0
C18 B:V24301 2.7 45.1 1.0
O19 B:V24301 2.8 50.2 1.0
CE1 B:HIS222 2.9 32.1 1.0
CD2 B:HIS218 3.0 22.4 1.0
CE1 B:HIS218 3.0 37.4 1.0
CD2 B:HIS222 3.1 24.1 1.0
CD2 B:HIS228 3.2 43.8 1.0
CE1 B:HIS228 3.4 25.5 1.0
C17 B:V24301 4.1 54.0 1.0
ND1 B:HIS222 4.1 34.0 1.0
ND1 B:HIS218 4.2 28.5 1.0
CG B:HIS218 4.2 28.7 1.0
CG B:HIS222 4.2 30.8 1.0
CG B:HIS228 4.3 43.8 1.0
O B:HOH682 4.3 28.5 1.0
ND1 B:HIS228 4.4 37.8 1.0
N16 B:V24301 4.6 67.0 1.0
C24 B:V24301 4.7 58.1 1.0
NE2 B:GLN219 4.7 37.5 1.0
C23 B:V24301 4.7 24.8 1.0
C21 B:V24301 4.8 44.3 1.0
C11 B:V24301 4.9 39.0 1.0
CE B:MET236 4.9 17.1 1.0
C12 B:V24301 4.9 38.2 1.0

Zinc binding site 4 out of 8 in 5i2z

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Zinc binding site 4 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:24.6
occ:1.00
 OD2 B:ASP170 1.8 36.1 1.0
NE2 B:HIS168 2.0 19.9 1.0
ND1 B:HIS196 2.0 22.1 1.0
NE2 B:HIS183 2.0 21.3 1.0
CG B:ASP170 2.9 27.5 1.0
CE1 B:HIS183 2.9 19.0 1.0
CE1 B:HIS196 2.9 15.3 1.0
CE1 B:HIS168 3.0 24.2 1.0
CD2 B:HIS168 3.0 18.8 1.0
CG B:HIS196 3.1 23.0 1.0
CD2 B:HIS183 3.1 26.9 1.0
OD1 B:ASP170 3.4 19.8 1.0
CB B:HIS196 3.5 16.3 1.0
ND1 B:HIS168 4.1 10.9 1.0
NE2 B:HIS196 4.1 20.9 1.0
O B:HIS172 4.1 29.0 1.0
ND1 B:HIS183 4.1 30.5 1.0
CG B:HIS168 4.1 21.8 1.0
CD2 B:HIS196 4.2 24.3 1.0
CB B:ASP170 4.2 24.1 1.0
CG B:HIS183 4.2 26.1 1.0
CE1 B:PHE185 4.3 16.8 1.0
CZ B:PHE174 4.5 12.5 1.0
O B:HOH609 4.6 27.5 1.0
CZ B:PHE185 4.6 19.2 1.0
CE2 B:PHE174 4.7 17.0 1.0
CB B:HIS172 4.9 30.4 1.0
CA B:HIS196 4.9 15.6 1.0

Zinc binding site 5 out of 8 in 5i2z

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Zinc binding site 5 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:33.0
occ:1.00
 O20 C:V24301 1.9 40.4 0.9
NE2 C:HIS222 2.0 20.5 1.0
NE2 C:HIS218 2.1 24.9 1.0
NE2 C:HIS228 2.3 37.0 1.0
C18 C:V24301 2.6 38.2 0.9
O19 C:V24301 2.7 44.3 0.9
CE1 C:HIS222 2.9 22.5 1.0
CE1 C:HIS218 3.0 27.7 1.0
CD2 C:HIS222 3.0 18.5 1.0
CD2 C:HIS218 3.0 23.8 1.0
CD2 C:HIS228 3.2 33.6 1.0
CE1 C:HIS228 3.2 32.7 1.0
C17 C:V24301 4.0 43.8 0.9
ND1 C:HIS222 4.0 25.7 1.0
ND1 C:HIS218 4.1 30.8 1.0
CG C:HIS222 4.1 26.6 1.0
CG C:HIS218 4.1 27.4 1.0
ND1 C:HIS228 4.3 26.4 1.0
NE2 C:GLN219 4.3 31.0 1.0
CG C:HIS228 4.3 31.1 1.0
N16 C:V24301 4.7 53.2 0.9
CE C:MET236 4.7 28.4 1.0
C24 C:V24301 4.8 48.5 0.9
C23 C:V24301 4.9 18.4 0.9
C11 C:V24301 4.9 46.1 0.9
C21 C:V24301 5.0 27.6 0.9

Zinc binding site 6 out of 8 in 5i2z

Go back to Zinc Binding Sites List in 5i2z
Zinc binding site 6 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:17.0
occ:1.00
 NE2 C:HIS168 1.9 7.8 1.0
OD2 C:ASP170 2.0 19.2 1.0
NE2 C:HIS183 2.0 14.3 1.0
ND1 C:HIS196 2.2 22.6 1.0
CE1 C:HIS168 2.8 15.9 1.0
CE1 C:HIS183 2.9 15.0 1.0
CG C:ASP170 2.9 18.1 1.0
CD2 C:HIS168 3.0 7.8 1.0
CD2 C:HIS183 3.0 15.2 1.0
CG C:HIS196 3.1 14.7 1.0
CE1 C:HIS196 3.2 6.5 1.0
OD1 C:ASP170 3.2 17.3 1.0
CB C:HIS196 3.3 17.9 1.0
ND1 C:HIS168 3.9 11.0 1.0
ND1 C:HIS183 4.0 11.4 1.0
O C:HIS172 4.1 19.8 1.0
CG C:HIS168 4.1 16.0 1.0
CG C:HIS183 4.1 7.7 1.0
CD2 C:HIS196 4.2 17.0 1.0
NE2 C:HIS196 4.2 17.0 1.0
CB C:ASP170 4.3 15.2 1.0
CZ C:PHE174 4.4 13.2 1.0
CE1 C:PHE185 4.4 23.8 1.0
O C:HOH429 4.7 19.0 1.0
CE2 C:PHE174 4.8 11.3 1.0
CB C:HIS172 4.8 24.4 1.0
CZ C:PHE185 4.8 26.8 1.0
CA C:HIS196 4.8 10.7 1.0
CE1 C:PHE174 4.9 20.4 1.0

Zinc binding site 7 out of 8 in 5i2z

Go back to Zinc Binding Sites List in 5i2z
Zinc binding site 7 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:29.3
occ:1.00
 O20 D:V24301 2.0 14.6 0.7
NE2 D:HIS222 2.2 12.8 1.0
NE2 D:HIS228 2.2 49.0 1.0
NE2 D:HIS218 2.3 14.1 1.0
C18 D:V24301 2.7 21.6 0.7
O19 D:V24301 2.7 33.3 0.7
CD2 D:HIS222 2.9 10.4 1.0
CD2 D:HIS228 3.1 40.4 1.0
CE1 D:HIS228 3.2 38.0 1.0
CD2 D:HIS218 3.2 15.1 1.0
CE1 D:HIS218 3.2 11.9 1.0
CE1 D:HIS222 3.3 21.1 1.0
C17 D:V24301 4.1 20.7 0.7
CG D:HIS222 4.2 14.7 1.0
ND1 D:HIS228 4.3 28.0 1.0
CG D:HIS228 4.3 34.0 1.0
ND1 D:HIS222 4.3 22.9 1.0
ND1 D:HIS218 4.3 18.7 1.0
CG D:HIS218 4.4 22.9 1.0
NE2 D:GLN219 4.5 30.4 1.0
N16 D:V24301 4.7 29.7 0.7
C23 D:V24301 4.8 24.8 0.7
C21 D:V24301 4.8 27.8 0.7
C24 D:V24301 4.9 44.9 0.7
C9 D:V24301 5.0 32.1 0.7

Zinc binding site 8 out of 8 in 5i2z

Go back to Zinc Binding Sites List in 5i2z
Zinc binding site 8 out of 8 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24).


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelating Water-Soluble Inhibitor (DC24). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:19.1
occ:1.00
 OD2 D:ASP170 1.9 14.6 1.0
NE2 D:HIS183 2.1 13.6 1.0
ND1 D:HIS196 2.2 21.9 1.0
NE2 D:HIS168 2.2 12.3 1.0
CG D:ASP170 2.8 13.4 1.0
CE1 D:HIS183 3.0 14.8 1.0
CD2 D:HIS168 3.0 17.2 1.0
CE1 D:HIS196 3.1 23.0 1.0
OD1 D:ASP170 3.1 12.9 1.0
CD2 D:HIS183 3.2 15.7 1.0
CG D:HIS196 3.2 15.7 1.0
CE1 D:HIS168 3.3 25.3 1.0
CB D:HIS196 3.6 15.2 1.0
ND1 D:HIS183 4.2 15.9 1.0
CB D:ASP170 4.2 13.8 1.0
CE1 D:PHE185 4.2 32.0 1.0
CG D:HIS168 4.2 20.3 1.0
NE2 D:HIS196 4.3 19.1 1.0
O D:HIS172 4.3 25.3 1.0
CG D:HIS183 4.3 11.9 1.0
ND1 D:HIS168 4.3 21.1 1.0
CD2 D:HIS196 4.3 22.8 1.0
CZ D:PHE185 4.4 38.6 1.0
CZ D:PHE174 4.6 30.9 1.0
O D:HOH471 4.7 25.2 1.0
CE2 D:PHE174 4.7 25.2 1.0
CB D:HIS172 5.0 20.8 1.0

Reference:

E.Nuti, D.Cuffaro, F.D'andrea, L.Rosalia, L.Tepshi, M.Fabbi, G.Carbotti, S.Ferrini, S.Santamaria, C.Camodeca, L.Ciccone, E.Orlandini, S.Nencetti, E.A.Stura, V.Dive, A.Rossello. Sugar-Based Arylsulfonamide Carboxylates As Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors. Chemmedchem V. 11 1626 2016.
ISSN: ESSN 1860-7187
PubMed: 27356908
DOI: 10.1002/CMDC.201600235
Page generated: Sun Oct 27 17:47:37 2024

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