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Zinc in PDB 5i3m: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).:
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31)., PDB code: 5i3m 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) 48.79 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.720, 63.140, 78.920, 90.00, 103.09, 90.00
R / Rfree (%) 20.6 / 25.3

Other elements in 5i3m:

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). 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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). (pdb code 5i3m). 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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31)., PDB code: 5i3m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:33.4
occ:1.00
 O19 A:67F301 1.9 27.4 1.0
NE2 A:HIS222 2.1 26.3 1.0
NE2 A:HIS218 2.1 29.2 1.0
NE2 A:HIS228 2.2 39.5 1.0
C18 A:67F301 2.7 34.5 1.0
CD2 A:HIS222 2.9 28.1 1.0
CD2 A:HIS218 3.0 27.3 1.0
O20 A:67F301 3.0 38.3 1.0
CE1 A:HIS218 3.0 25.8 1.0
CD2 A:HIS228 3.1 42.1 1.0
CE1 A:HIS222 3.1 29.3 1.0
CE1 A:HIS228 3.1 33.9 1.0
C17 A:67F301 4.0 41.5 1.0
ND1 A:HIS218 4.1 28.0 1.0
CG A:HIS218 4.1 26.9 1.0
CG A:HIS222 4.1 32.0 1.0
ND1 A:HIS222 4.2 31.8 1.0
ND1 A:HIS228 4.2 37.4 1.0
CG A:HIS228 4.3 40.5 1.0
NE2 A:GLN219 4.7 32.5 1.0
N16 A:67F301 4.8 53.8 1.0
CE A:MET236 4.8 31.0 1.0
C09 A:67F301 4.9 49.5 1.0
C10 A:67F301 4.9 49.6 1.0
C25 A:67F301 4.9 78.5 1.0
O A:HOH455 5.0 39.7 1.0
C22 A:67F301 5.0 40.6 1.0
CA A:PRO238 5.0 34.1 1.0

Zinc binding site 2 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:26.4
occ:1.00
 OD2 A:ASP170 1.9 24.0 1.0
ND1 A:HIS196 2.0 23.7 1.0
NE2 A:HIS168 2.1 21.3 1.0
NE2 A:HIS183 2.3 14.4 1.0
CE1 A:HIS196 2.8 25.5 1.0
CD2 A:HIS168 2.9 24.3 1.0
CG A:ASP170 2.9 25.1 1.0
CE1 A:HIS183 3.2 15.4 1.0
CG A:HIS196 3.2 25.6 1.0
CE1 A:HIS168 3.2 22.1 1.0
CD2 A:HIS183 3.3 14.9 1.0
OD1 A:ASP170 3.4 22.0 1.0
CB A:HIS196 3.7 24.1 1.0
NE2 A:HIS196 4.0 26.6 1.0
CG A:HIS168 4.1 25.2 1.0
CB A:ASP170 4.2 23.6 1.0
CD2 A:HIS196 4.2 28.3 1.0
ND1 A:HIS168 4.2 25.2 1.0
CE1 A:PHE185 4.3 28.7 1.0
ND1 A:HIS183 4.3 15.4 1.0
O A:HIS172 4.3 21.5 1.0
CG A:HIS183 4.4 14.3 1.0
CZ A:PHE174 4.6 27.7 1.0
CZ A:PHE185 4.6 30.5 1.0
CE2 A:PHE174 4.7 27.7 1.0
O A:HOH418 4.9 13.9 1.0
CB A:HIS172 4.9 33.8 1.0

Zinc binding site 3 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:35.6
occ:1.00
 O19 B:67F301 1.9 37.7 1.0
NE2 B:HIS218 2.0 30.7 1.0
NE2 B:HIS222 2.1 32.1 1.0
NE2 B:HIS228 2.2 49.4 1.0
CE1 B:HIS222 2.9 34.2 1.0
C18 B:67F301 2.9 49.3 1.0
CE1 B:HIS218 2.9 31.8 1.0
CD2 B:HIS228 3.0 48.4 1.0
CD2 B:HIS218 3.0 29.4 1.0
O20 B:67F301 3.2 60.7 1.0
CD2 B:HIS222 3.2 30.8 1.0
CE1 B:HIS228 3.4 45.8 1.0
O37 B:67F301 3.8 0.4 1.0
ND1 B:HIS218 4.0 32.8 1.0
ND1 B:HIS222 4.1 34.7 1.0
CG B:HIS218 4.1 30.8 1.0
C17 B:67F301 4.2 55.6 1.0
CG B:HIS228 4.2 49.9 1.0
CG B:HIS222 4.2 32.7 1.0
ND1 B:HIS228 4.3 50.8 1.0
NE2 B:GLN219 4.6 33.9 1.0
N16 B:67F301 4.7 58.0 1.0
C24 B:67F301 4.8 63.8 1.0
CE B:MET236 4.8 27.9 1.0
CA B:PRO238 5.0 39.1 1.0
C10 B:67F301 5.0 53.0 1.0
C11 B:67F301 5.0 46.5 1.0

Zinc binding site 4 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:24.1
occ:1.00
 OD2 B:ASP170 1.8 40.2 1.0
NE2 B:HIS183 2.0 24.8 1.0
ND1 B:HIS196 2.1 29.0 1.0
NE2 B:HIS168 2.2 25.3 1.0
CG B:ASP170 2.8 31.4 1.0
CE1 B:HIS183 2.9 24.9 1.0
CE1 B:HIS196 3.0 27.1 1.0
CD2 B:HIS168 3.0 27.4 1.0
CD2 B:HIS183 3.0 29.4 1.0
CG B:HIS196 3.1 24.9 1.0
OD1 B:ASP170 3.3 24.4 1.0
CE1 B:HIS168 3.3 30.5 1.0
CB B:HIS196 3.5 24.4 1.0
ND1 B:HIS183 4.0 24.8 1.0
NE2 B:HIS196 4.1 28.3 1.0
CB B:ASP170 4.1 31.3 1.0
CG B:HIS183 4.1 25.0 1.0
O B:HIS172 4.1 37.8 1.0
CD2 B:HIS196 4.2 27.1 1.0
CE1 B:PHE185 4.2 37.1 1.0
CG B:HIS168 4.2 26.3 1.0
ND1 B:HIS168 4.4 28.6 1.0
CZ B:PHE174 4.4 25.7 1.0
O B:HOH408 4.4 43.5 1.0
CZ B:PHE185 4.4 35.9 1.0
CE2 B:PHE174 4.8 25.1 1.0
CB B:HIS172 4.9 34.3 1.0
CE1 B:PHE174 4.9 27.4 1.0

Zinc binding site 5 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:38.1
occ:1.00
 O19 C:67F301 1.8 48.8 1.0
NE2 C:HIS222 2.1 30.2 1.0
NE2 C:HIS218 2.2 35.3 1.0
NE2 C:HIS228 2.3 46.9 1.0
C18 C:67F301 2.6 46.4 1.0
O20 C:67F301 2.6 47.9 1.0
CD2 C:HIS222 2.8 28.9 1.0
CD2 C:HIS218 3.1 32.4 1.0
CE1 C:HIS218 3.1 34.1 1.0
CD2 C:HIS228 3.1 45.4 1.0
CE1 C:HIS222 3.2 31.9 1.0
CE1 C:HIS228 3.3 46.6 1.0
C17 C:67F301 4.0 51.4 1.0
CG C:HIS222 4.1 30.9 1.0
ND1 C:HIS218 4.2 35.4 1.0
CG C:HIS218 4.2 35.5 1.0
ND1 C:HIS222 4.2 34.7 1.0
CG C:HIS228 4.3 45.0 1.0
ND1 C:HIS228 4.4 48.6 1.0
C23 C:67F301 4.5 47.8 1.0
NE2 C:GLN219 4.6 36.3 1.0
CE C:MET236 4.8 34.5 1.0
C21 C:67F301 4.8 47.5 1.0
N16 C:67F301 4.9 58.0 1.0
C10 C:67F301 5.0 52.8 1.0

Zinc binding site 6 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:26.3
occ:1.00
 OD2 C:ASP170 1.7 37.5 1.0
NE2 C:HIS183 2.0 21.3 1.0
NE2 C:HIS168 2.0 27.0 1.0
ND1 C:HIS196 2.1 30.5 1.0
CG C:ASP170 2.8 34.6 1.0
CE1 C:HIS183 2.8 21.1 1.0
CD2 C:HIS168 2.8 29.1 1.0
CE1 C:HIS196 2.9 33.5 1.0
OD1 C:ASP170 3.2 27.1 1.0
CD2 C:HIS183 3.2 22.6 1.0
CE1 C:HIS168 3.2 30.5 1.0
CG C:HIS196 3.2 29.7 1.0
CB C:HIS196 3.6 27.4 1.0
ND1 C:HIS183 4.0 20.5 1.0
CG C:HIS168 4.0 29.5 1.0
CB C:ASP170 4.1 33.5 1.0
CE1 C:PHE185 4.1 37.5 1.0
NE2 C:HIS196 4.1 30.4 1.0
ND1 C:HIS168 4.2 28.8 1.0
CG C:HIS183 4.2 20.8 1.0
CD2 C:HIS196 4.2 29.0 1.0
O C:HIS172 4.3 31.5 1.0
CZ C:PHE174 4.4 27.3 1.0
CZ C:PHE185 4.4 37.2 1.0
O C:HOH440 4.7 29.3 1.0
CE2 C:PHE174 4.7 26.2 1.0
CB C:HIS172 4.8 34.8 1.0
CE1 C:PHE174 4.9 30.0 1.0

Zinc binding site 7 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:38.0
occ:1.00
 O19 D:67F301 1.7 33.2 1.0
NE2 D:HIS222 2.2 26.4 1.0
NE2 D:HIS228 2.2 44.8 1.0
NE2 D:HIS218 2.2 39.3 1.0
C18 D:67F301 2.7 41.4 1.0
CD2 D:HIS222 3.0 29.2 1.0
CD2 D:HIS228 3.0 42.9 1.0
CE1 D:HIS218 3.1 33.6 1.0
O20 D:67F301 3.1 51.8 1.0
CD2 D:HIS218 3.2 32.9 1.0
CE1 D:HIS222 3.2 29.9 1.0
CE1 D:HIS228 3.2 40.6 1.0
C17 D:67F301 3.9 43.7 1.0
CG D:HIS222 4.2 30.9 1.0
ND1 D:HIS218 4.2 35.1 1.0
CG D:HIS228 4.2 42.0 1.0
ND1 D:HIS222 4.3 31.8 1.0
CG D:HIS218 4.3 31.6 1.0
ND1 D:HIS228 4.3 39.2 1.0
N16 D:67F301 4.7 58.4 1.0
NE2 D:GLN219 4.7 36.1 1.0
C22 D:67F301 4.8 44.9 1.0
O D:HOH484 5.0 46.1 1.0
C21 D:67F301 5.0 46.4 1.0
CA D:PRO238 5.0 43.9 1.0

Zinc binding site 8 out of 8 in 5i3m

Go back to Zinc Binding Sites List in 5i3m
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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31).


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 Thiourea-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC31). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:29.6
occ:1.00
 OD2 D:ASP170 1.9 32.2 1.0
ND1 D:HIS196 2.0 33.5 1.0
CE1 D:HIS183 2.2 19.3 1.0
NE2 D:HIS168 2.2 27.8 1.0
NE2 D:HIS183 2.8 20.2 1.0
CG D:ASP170 2.9 32.0 1.0
CE1 D:HIS196 2.9 30.7 1.0
CD2 D:HIS168 3.0 29.3 1.0
CG D:HIS196 3.1 31.1 1.0
OD1 D:ASP170 3.3 26.5 1.0
CE1 D:HIS168 3.3 27.7 1.0
ND1 D:HIS183 3.3 23.7 1.0
CB D:HIS196 3.5 32.4 1.0
NE2 D:HIS196 4.1 29.9 1.0
CD2 D:HIS183 4.1 18.5 1.0
CD2 D:HIS196 4.2 34.7 1.0
CG D:HIS168 4.2 30.3 1.0
CB D:ASP170 4.2 30.5 1.0
O D:HIS172 4.3 31.2 1.0
ND1 D:HIS168 4.3 31.2 1.0
CG D:HIS183 4.3 19.2 1.0
CE1 D:PHE185 4.4 42.3 1.0
CE2 D:PHE174 4.7 26.4 1.0
CZ D:PHE174 4.7 25.4 1.0
CZ D:PHE185 4.8 48.9 1.0
O D:HOH432 4.9 22.6 1.0
CA D:HIS196 5.0 29.3 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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