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Zinc in PDB 5i43: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelator Water-Soluble Inhibitor (DC32).

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelator Water-Soluble Inhibitor (DC32).

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelator Water-Soluble Inhibitor (DC32).:
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 Chelator Water-Soluble Inhibitor (DC32)., PDB code: 5i43 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) 44.56 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.030, 63.660, 79.030, 90.00, 103.03, 90.00
R / Rfree (%) 20 / 23.3

Other elements in 5i43:

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Chelator Water-Soluble Inhibitor (DC32). 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 Chelator Water-Soluble Inhibitor (DC32). (pdb code 5i43). 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 Chelator Water-Soluble Inhibitor (DC32)., PDB code: 5i43:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:17.6
occ:1.00
O20 A:67M306 1.9 21.1 1.0
NE2 A:HIS218 2.1 23.0 1.0
NE2 A:HIS228 2.1 21.8 1.0
NE2 A:HIS222 2.1 15.3 1.0
O19 A:67M306 2.6 24.8 1.0
C18 A:67M306 2.6 23.6 1.0
CE1 A:HIS218 3.0 20.1 1.0
CD2 A:HIS218 3.0 21.6 1.0
CE1 A:HIS222 3.1 18.4 1.0
CD2 A:HIS228 3.1 19.2 1.0
CE1 A:HIS228 3.1 21.5 1.0
CD2 A:HIS222 3.1 14.3 1.0
ND1 A:HIS218 4.1 20.1 1.0
C17 A:67M306 4.1 27.6 1.0
CG A:HIS218 4.1 19.7 1.0
O A:HOH436 4.1 26.0 1.0
ND1 A:HIS222 4.2 17.5 1.0
ND1 A:HIS228 4.2 22.7 1.0
CG A:HIS228 4.2 19.4 1.0
CG A:HIS222 4.2 18.0 1.0
N16 A:67M306 4.7 31.4 1.0
NE2 A:GLN219 4.7 20.8 1.0
C24 A:67M306 4.8 36.8 1.0
C23 A:67M306 4.8 34.3 1.0
C21 A:67M306 4.8 32.0 1.0
CE A:MET236 4.9 18.0 1.0

Zinc binding site 2 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:17.5
occ:1.00
OD2 A:ASP170 1.9 24.0 1.0
ND1 A:HIS196 2.0 17.6 1.0
NE2 A:HIS183 2.1 19.8 1.0
NE2 A:HIS168 2.2 15.9 1.0
CG A:ASP170 2.8 22.8 1.0
CE1 A:HIS196 2.9 18.1 1.0
CD2 A:HIS168 2.9 20.2 1.0
CE1 A:HIS183 3.0 18.1 1.0
CG A:HIS196 3.0 16.4 1.0
CD2 A:HIS183 3.1 20.8 1.0
OD1 A:ASP170 3.1 17.4 1.0
CE1 A:HIS168 3.3 19.4 1.0
CB A:HIS196 3.4 14.7 1.0
O A:HOH445 3.9 7.2 0.6
NE2 A:HIS196 4.0 15.7 1.0
ND1 A:HIS183 4.1 18.2 1.0
CD2 A:HIS196 4.1 15.7 1.0
CB A:ASP170 4.1 21.3 1.0
CG A:HIS168 4.2 19.1 1.0
CG A:HIS183 4.2 15.5 1.0
ND1 A:HIS168 4.3 18.5 1.0
CE1 A:PHE185 4.3 27.4 1.0
O A:HIS172 4.3 20.4 1.0
CZ A:PHE174 4.5 17.3 1.0
CZ A:PHE185 4.6 27.0 1.0
O A:HOH429 4.7 17.8 1.0
CE2 A:PHE174 4.8 16.0 1.0
CA A:HIS196 5.0 15.3 1.0

Zinc binding site 3 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:20.1
occ:1.00
O20 B:67M301 1.9 19.1 1.0
NE2 B:HIS218 2.0 19.6 1.0
NE2 B:HIS222 2.1 16.1 1.0
NE2 B:HIS228 2.2 24.7 1.0
O19 B:67M301 2.6 29.2 1.0
C18 B:67M301 2.6 24.8 1.0
CE1 B:HIS218 3.0 19.3 1.0
CD2 B:HIS222 3.0 16.9 1.0
CE1 B:HIS222 3.1 17.9 1.0
CD2 B:HIS218 3.1 19.6 1.0
CD2 B:HIS228 3.2 23.2 1.0
CE1 B:HIS228 3.2 25.1 1.0
ND1 B:HIS218 4.1 18.8 1.0
C17 B:67M301 4.1 27.6 1.0
ND1 B:HIS222 4.2 17.5 1.0
CG B:HIS218 4.2 16.8 1.0
CG B:HIS222 4.2 18.4 1.0
ND1 B:HIS228 4.3 20.7 1.0
CG B:HIS228 4.3 21.9 1.0
N16 B:67M301 4.6 29.9 1.0
C24 B:67M301 4.7 38.3 1.0
NE2 B:GLN219 4.7 19.8 1.0
C22 B:67M301 4.8 36.0 1.0
C09 B:67M301 4.9 27.7 1.0
C10 B:67M301 4.9 28.3 1.0
C21 B:67M301 4.9 31.6 1.0
C08 B:67M301 5.0 27.4 1.0

Zinc binding site 4 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:18.5
occ:1.00
OD2 B:ASP170 1.9 17.5 1.0
NE2 B:HIS168 2.1 17.3 1.0
NE2 B:HIS183 2.1 18.1 1.0
ND1 B:HIS196 2.1 21.0 1.0
CG B:ASP170 2.8 19.1 1.0
CD2 B:HIS168 2.9 18.4 1.0
CE1 B:HIS196 3.0 22.1 1.0
CE1 B:HIS183 3.0 16.8 1.0
CE1 B:HIS168 3.1 20.7 1.0
CD2 B:HIS183 3.1 17.6 1.0
CG B:HIS196 3.2 22.0 1.0
OD1 B:ASP170 3.2 17.8 1.0
CB B:HIS196 3.6 17.6 1.0
CG B:HIS168 4.1 20.4 1.0
NE2 B:HIS196 4.1 21.7 1.0
CB B:ASP170 4.1 20.3 1.0
ND1 B:HIS183 4.1 14.2 1.0
ND1 B:HIS168 4.2 20.6 1.0
O B:HIS172 4.2 22.1 1.0
CG B:HIS183 4.2 14.9 1.0
CD2 B:HIS196 4.3 20.9 1.0
CE1 B:PHE185 4.4 25.7 1.0
CZ B:PHE174 4.6 20.8 1.0
CZ B:PHE185 4.7 28.1 1.0
CE2 B:PHE174 4.8 19.4 1.0
O B:HOH460 4.8 41.4 1.0
CB B:HIS172 4.9 21.6 1.0
O B:HOH443 4.9 14.3 1.0

Zinc binding site 5 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:16.1
occ:1.00
O20 C:67M301 1.9 19.4 1.0
NE2 C:HIS222 2.1 12.5 1.0
NE2 C:HIS228 2.1 20.5 1.0
NE2 C:HIS218 2.1 23.3 1.0
O19 C:67M301 2.5 24.9 1.0
C18 C:67M301 2.5 21.3 1.0
CE1 C:HIS222 3.0 15.3 1.0
CD2 C:HIS218 3.0 20.2 1.0
CD2 C:HIS222 3.0 13.4 1.0
CD2 C:HIS228 3.1 19.9 1.0
CE1 C:HIS228 3.1 19.5 1.0
CE1 C:HIS218 3.1 20.1 1.0
C17 C:67M301 4.0 22.3 1.0
ND1 C:HIS222 4.1 16.5 1.0
CG C:HIS218 4.2 18.7 1.0
CG C:HIS222 4.2 17.0 1.0
ND1 C:HIS218 4.2 21.9 1.0
ND1 C:HIS228 4.2 16.9 1.0
CG C:HIS228 4.2 18.4 1.0
N16 C:67M301 4.6 24.0 1.0
C24 C:67M301 4.6 30.4 1.0
C23 C:67M301 4.7 22.7 1.0
NE2 C:GLN219 4.7 16.4 1.0
C09 C:67M301 4.8 21.0 1.0
CE C:MET236 4.8 19.4 1.0
O C:HOH519 4.8 15.2 0.4
C10 C:67M301 4.8 22.5 1.0
C21 C:67M301 4.9 22.7 1.0
O C:HOH519 4.9 41.0 0.6
C08 C:67M301 4.9 20.5 1.0

Zinc binding site 6 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:16.3
occ:1.00
OD2 C:ASP170 1.9 18.6 1.0
ND1 C:HIS196 2.1 15.4 1.0
NE2 C:HIS168 2.1 12.6 1.0
NE2 C:HIS183 2.1 15.6 1.0
CG C:ASP170 2.9 15.2 1.0
CE1 C:HIS196 3.0 16.7 1.0
CE1 C:HIS183 3.0 13.8 1.0
CD2 C:HIS168 3.0 12.3 1.0
CE1 C:HIS168 3.1 15.1 1.0
CG C:HIS196 3.2 14.9 1.0
CD2 C:HIS183 3.2 13.2 1.0
OD1 C:ASP170 3.3 16.8 1.0
CB C:HIS196 3.6 14.0 1.0
NE2 C:HIS196 4.1 15.8 1.0
CB C:ASP170 4.1 15.8 1.0
ND1 C:HIS183 4.2 10.6 1.0
ND1 C:HIS168 4.2 15.9 1.0
CG C:HIS168 4.2 14.3 1.0
CD2 C:HIS196 4.2 15.3 1.0
CG C:HIS183 4.3 11.0 1.0
O C:HIS172 4.3 12.7 1.0
CE1 C:PHE185 4.4 25.1 1.0
CZ C:PHE185 4.5 26.0 1.0
O C:HOH452 4.6 33.9 1.0
CZ C:PHE174 4.7 17.6 1.0
O C:HOH419 4.8 9.1 1.0
CE2 C:PHE174 4.8 15.2 1.0
CB C:HIS172 5.0 22.3 1.0

Zinc binding site 7 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:16.4
occ:1.00
O20 D:67M301 1.8 27.2 1.0
NE2 D:HIS222 2.0 14.0 1.0
NE2 D:HIS218 2.1 14.3 1.0
NE2 D:HIS228 2.1 19.4 1.0
O19 D:67M301 2.6 22.1 1.0
C18 D:67M301 2.6 24.3 1.0
CD2 D:HIS218 2.9 13.8 1.0
CD2 D:HIS222 3.0 13.8 1.0
CD2 D:HIS228 3.0 18.2 1.0
CE1 D:HIS222 3.0 17.1 1.0
CE1 D:HIS218 3.1 14.9 1.0
CE1 D:HIS228 3.1 19.4 1.0
O D:HOH428 3.8 14.1 0.6
CG D:HIS218 4.1 12.9 1.0
C17 D:67M301 4.1 25.3 1.0
ND1 D:HIS222 4.1 15.1 1.0
CG D:HIS222 4.1 15.7 1.0
ND1 D:HIS218 4.1 15.7 1.0
CG D:HIS228 4.2 19.1 1.0
ND1 D:HIS228 4.2 18.2 1.0
N16 D:67M301 4.7 27.5 1.0
C24 D:67M301 4.7 29.9 1.0
NE2 D:GLN219 4.8 21.3 1.0
C22 D:67M301 4.8 30.7 1.0
C21 D:67M301 4.9 28.4 1.0
CE D:MET236 4.9 19.5 1.0

Zinc binding site 8 out of 8 in 5i43

Go back to Zinc Binding Sites List in 5i43
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 Chelator Water-Soluble Inhibitor (DC32).


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 Chelator Water-Soluble Inhibitor (DC32). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:17.3
occ:1.00
OD2 D:ASP170 1.8 21.9 1.0
NE2 D:HIS168 2.0 15.1 1.0
NE2 D:HIS183 2.1 16.5 1.0
ND1 D:HIS196 2.1 16.1 1.0
CG D:ASP170 2.8 20.9 1.0
CD2 D:HIS168 2.8 14.7 1.0
CE1 D:HIS183 2.9 16.2 1.0
CE1 D:HIS196 3.0 16.4 1.0
CG D:HIS196 3.1 16.1 1.0
CD2 D:HIS183 3.1 17.0 1.0
CE1 D:HIS168 3.2 17.4 1.0
OD1 D:ASP170 3.2 17.9 1.0
CB D:HIS196 3.5 14.5 1.0
CG D:HIS168 4.1 15.9 1.0
ND1 D:HIS183 4.1 15.8 1.0
CB D:ASP170 4.1 19.9 1.0
NE2 D:HIS196 4.1 15.9 1.0
O D:HIS172 4.2 14.3 1.0
ND1 D:HIS168 4.2 16.4 1.0
CD2 D:HIS196 4.2 16.9 1.0
CG D:HIS183 4.2 14.8 1.0
CE1 D:PHE185 4.4 23.0 1.0
O D:HOH411 4.6 12.6 1.0
CZ D:PHE174 4.6 17.8 1.0
CZ D:PHE185 4.8 21.6 1.0
CE2 D:PHE174 4.8 19.7 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 17:54:06 2024

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