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Zinc in PDB 5i4o: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC28).

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC28).

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC28).:
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 Zinc-Chelator Water-Soluble Inhibitor (DC28)., PDB code: 5i4o 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) 32.87 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 63.980, 63.510, 78.640, 90.00, 102.31, 90.00
R / Rfree (%) 21 / 24.9

Other elements in 5i4o:

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Selective Sugar-Conjugated Triazole-Linked Carboxylate Zinc-Chelator Water-Soluble Inhibitor (DC28). 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 Zinc-Chelator Water-Soluble Inhibitor (DC28). (pdb code 5i4o). 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 Zinc-Chelator Water-Soluble Inhibitor (DC28)., PDB code: 5i4o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.9
occ:1.00
 O19 A:V28301 1.9 14.9 1.0
NE2 A:HIS222 2.0 8.3 1.0
NE2 A:HIS218 2.1 10.6 1.0
NE2 A:HIS228 2.1 15.3 1.0
C18 A:V28301 2.7 14.7 1.0
O20 A:V28301 2.8 22.2 1.0
CD2 A:HIS218 3.0 9.8 1.0
CD2 A:HIS228 3.0 14.8 1.0
CD2 A:HIS222 3.0 8.2 1.0
CE1 A:HIS222 3.1 9.3 1.0
CE1 A:HIS228 3.2 15.9 1.0
CE1 A:HIS218 3.2 9.7 1.0
CG A:HIS218 4.2 10.0 1.0
CG A:HIS222 4.2 9.8 1.0
CG A:HIS228 4.2 15.5 1.0
ND1 A:HIS222 4.2 8.9 1.0
C17 A:V28301 4.2 14.9 1.0
ND1 A:HIS218 4.2 10.2 1.0
ND1 A:HIS228 4.2 14.9 1.0
CE A:MET236 4.7 8.1 1.0
N16 A:V28301 4.8 22.6 1.0
C24 A:V28301 4.8 36.9 1.0
C23 A:V28301 4.8 23.7 1.0
C21 A:V28301 4.9 25.6 1.0
NE2 A:GLN219 4.9 14.2 1.0

Zinc binding site 2 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:9.1
occ:1.00
 OD2 A:ASP170 1.9 11.4 1.0
NE2 A:HIS168 2.0 7.1 1.0
ND1 A:HIS196 2.0 7.1 1.0
NE2 A:HIS183 2.2 6.9 1.0
CG A:ASP170 2.8 12.3 1.0
CD2 A:HIS168 2.9 8.4 1.0
CE1 A:HIS196 2.9 7.3 1.0
CE1 A:HIS168 3.0 7.6 1.0
CE1 A:HIS183 3.1 6.8 1.0
CG A:HIS196 3.1 8.0 1.0
OD1 A:ASP170 3.2 11.4 1.0
CD2 A:HIS183 3.2 6.9 1.0
CB A:HIS196 3.6 7.0 1.0
CG A:HIS168 4.1 8.6 1.0
ND1 A:HIS168 4.1 8.1 1.0
NE2 A:HIS196 4.1 7.1 1.0
O A:HIS172 4.1 12.0 1.0
CB A:ASP170 4.2 12.3 1.0
CD2 A:HIS196 4.2 7.5 1.0
ND1 A:HIS183 4.2 6.3 1.0
CE1 A:PHE185 4.3 16.0 1.0
CG A:HIS183 4.3 7.1 1.0
CZ A:PHE174 4.5 9.0 1.0
CZ A:PHE185 4.6 18.3 1.0
CE2 A:PHE174 4.7 8.0 1.0
O A:HOH645 4.8 6.4 1.0

Zinc binding site 3 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:38.6
occ:1.00
 O20 B:V28301 2.0 68.5 1.0
NE2 B:HIS228 2.0 44.5 1.0
NE2 B:HIS218 2.1 33.6 1.0
NE2 B:HIS222 2.2 36.7 1.0
C18 B:V28301 2.7 68.7 1.0
O19 B:V28301 2.8 68.4 1.0
CE1 B:HIS218 2.8 33.5 1.0
CD2 B:HIS228 2.9 42.2 1.0
CE1 B:HIS228 3.1 44.1 1.0
CE1 B:HIS222 3.2 37.8 1.0
CD2 B:HIS222 3.2 35.1 1.0
CD2 B:HIS218 3.2 36.4 1.0
ND1 B:HIS218 4.0 29.1 1.0
C17 B:V28301 4.1 65.5 1.0
CG B:HIS228 4.1 45.7 1.0
ND1 B:HIS228 4.1 43.9 1.0
CG B:HIS218 4.2 31.1 1.0
ND1 B:HIS222 4.3 37.3 1.0
CG B:HIS222 4.3 38.6 1.0
C24 B:V28301 4.4 65.5 1.0
N16 B:V28301 4.5 70.1 1.0
NE2 B:GLN219 4.6 31.5 1.0
C11 B:V28301 4.7 59.7 1.0
C10 B:V28301 4.9 68.6 1.0
C12 B:V28301 4.9 53.4 1.0
CA B:PRO238 4.9 42.1 1.0
C21 B:V28301 4.9 61.8 1.0

Zinc binding site 4 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:33.6
occ:1.00
 NE2 B:HIS183 1.9 39.5 1.0
OD2 B:ASP170 2.0 28.1 1.0
ND1 B:HIS196 2.0 34.1 1.0
O B:HOH603 2.2 33.1 1.0
NE2 B:HIS168 2.3 31.4 1.0
CE1 B:HIS183 2.9 34.1 1.0
CD2 B:HIS183 2.9 36.0 1.0
CE1 B:HIS196 3.0 37.2 1.0
CG B:ASP170 3.0 31.8 1.0
CG B:HIS196 3.0 30.1 1.0
CD2 B:HIS168 3.1 23.6 1.0
CB B:HIS196 3.4 33.7 1.0
CE1 B:HIS168 3.4 37.2 1.0
OD1 B:ASP170 3.4 27.0 1.0
ND1 B:HIS183 3.9 34.2 1.0
CG B:HIS183 4.0 28.4 1.0
NE2 B:HIS196 4.1 29.7 1.0
CD2 B:HIS196 4.2 28.6 1.0
O B:HIS172 4.3 52.2 1.0
CE1 B:PHE185 4.3 43.7 1.0
CG B:HIS168 4.3 29.4 1.0
CB B:ASP170 4.3 30.6 1.0
CZ B:PHE174 4.4 34.9 1.0
ND1 B:HIS168 4.4 27.2 1.0
CZ B:PHE185 4.6 37.0 1.0
CA B:HIS196 4.8 29.1 1.0
CE1 B:PHE174 4.9 31.2 1.0
CE2 B:PHE174 4.9 34.1 1.0
CB B:HIS172 5.0 40.6 1.0

Zinc binding site 5 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:13.0
occ:1.00
 O20 C:V28301 1.9 22.1 1.0
NE2 C:HIS228 2.0 11.7 1.0
NE2 C:HIS218 2.0 7.3 1.0
NE2 C:HIS222 2.0 7.2 1.0
C18 C:V28301 2.7 25.5 1.0
O19 C:V28301 2.8 25.0 1.0
CD2 C:HIS222 3.0 7.5 1.0
CD2 C:HIS218 3.0 7.3 1.0
CE1 C:HIS228 3.0 14.0 1.0
CD2 C:HIS228 3.0 12.1 1.0
CE1 C:HIS218 3.0 7.2 1.0
CE1 C:HIS222 3.1 9.3 1.0
ND1 C:HIS228 4.1 14.3 1.0
ND1 C:HIS218 4.1 7.6 1.0
CG C:HIS228 4.1 14.0 1.0
CG C:HIS218 4.1 7.9 1.0
CG C:HIS222 4.1 9.0 1.0
C17 C:V28301 4.2 20.8 1.0
ND1 C:HIS222 4.2 8.9 1.0
CE C:MET236 4.7 9.0 1.0
C23 C:V28301 4.7 21.0 1.0
C24 C:V28301 4.8 22.8 1.0
N16 C:V28301 4.8 19.4 1.0
C21 C:V28301 4.9 21.4 1.0
NE2 C:GLN219 4.9 10.6 1.0
CA C:PRO238 5.0 16.8 1.0

Zinc binding site 6 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:8.1
occ:1.00
 OD2 C:ASP170 1.8 12.0 1.0
NE2 C:HIS168 2.0 6.7 1.0
ND1 C:HIS196 2.0 9.4 1.0
NE2 C:HIS183 2.1 10.9 1.0
CD2 C:HIS168 2.8 8.4 1.0
CG C:ASP170 2.8 10.7 1.0
CE1 C:HIS196 2.9 10.5 1.0
CE1 C:HIS183 2.9 9.1 1.0
CE1 C:HIS168 3.0 8.8 1.0
CD2 C:HIS183 3.1 9.6 1.0
CG C:HIS196 3.2 8.6 1.0
OD1 C:ASP170 3.2 9.6 1.0
CB C:HIS196 3.6 7.3 1.0
NE2 C:HIS196 4.0 9.1 1.0
CG C:HIS168 4.0 9.2 1.0
ND1 C:HIS183 4.1 10.5 1.0
ND1 C:HIS168 4.1 9.8 1.0
O C:HIS172 4.2 12.2 1.0
CB C:ASP170 4.2 11.2 1.0
CE1 C:PHE185 4.2 16.8 1.0
CD2 C:HIS196 4.2 8.5 1.0
CG C:HIS183 4.2 10.3 1.0
CZ C:PHE174 4.5 8.3 1.0
CZ C:PHE185 4.6 19.0 1.0
CE2 C:PHE174 4.7 8.4 1.0
O C:HOH640 4.8 8.6 1.0

Zinc binding site 7 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:38.6
occ:1.00
 O20 D:V28301 1.9 37.1 1.0
NE2 D:HIS218 2.2 46.1 1.0
NE2 D:HIS228 2.2 40.2 1.0
NE2 D:HIS222 2.2 37.2 1.0
C18 D:V28301 2.5 36.0 1.0
O19 D:V28301 2.6 38.0 1.0
CD2 D:HIS222 3.0 40.7 1.0
CD2 D:HIS228 3.0 39.4 1.0
CD2 D:HIS218 3.1 39.5 1.0
CE1 D:HIS218 3.2 42.0 1.0
CE1 D:HIS228 3.3 40.4 1.0
CE1 D:HIS222 3.4 45.8 1.0
C17 D:V28301 4.0 45.7 1.0
CG D:HIS222 4.2 40.3 1.0
CG D:HIS228 4.3 37.0 1.0
ND1 D:HIS218 4.3 38.3 1.0
CG D:HIS218 4.3 36.3 1.0
ND1 D:HIS228 4.3 36.2 1.0
ND1 D:HIS222 4.4 44.2 1.0
N16 D:V28301 4.5 61.0 1.0
O D:HOH671 4.6 28.2 1.0
C24 D:V28301 4.6 64.6 1.0
NE2 D:GLN219 4.7 46.8 1.0
C09 D:V28301 4.7 49.1 1.0
C23 D:V28301 4.7 54.2 1.0
C21 D:V28301 4.8 49.2 1.0
C08 D:V28301 4.8 39.5 1.0
C10 D:V28301 4.9 46.7 1.0

Zinc binding site 8 out of 8 in 5i4o

Go back to Zinc Binding Sites List in 5i4o
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 Zinc-Chelator Water-Soluble Inhibitor (DC28).


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 Zinc-Chelator Water-Soluble Inhibitor (DC28). within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn303

b:35.9
occ:1.00
 OD2 D:ASP170 2.0 32.5 1.0
NE2 D:HIS183 2.0 26.8 1.0
ND1 D:HIS196 2.1 27.5 1.0
NE2 D:HIS168 2.2 38.7 1.0
CE1 D:HIS183 3.0 27.1 1.0
CG D:ASP170 3.0 30.7 1.0
CE1 D:HIS196 3.0 33.4 1.0
CD2 D:HIS183 3.0 27.2 1.0
CE1 D:HIS168 3.1 39.2 1.0
CG D:HIS196 3.2 30.0 1.0
CD2 D:HIS168 3.2 40.4 1.0
OD1 D:ASP170 3.4 24.4 1.0
CB D:HIS196 3.6 33.9 1.0
ND1 D:HIS183 4.1 22.6 1.0
CG D:HIS183 4.2 24.4 1.0
NE2 D:HIS196 4.2 28.0 1.0
ND1 D:HIS168 4.3 37.2 1.0
CD2 D:HIS196 4.3 28.6 1.0
CB D:ASP170 4.3 31.7 1.0
O D:HIS172 4.3 37.6 1.0
CG D:HIS168 4.3 39.8 1.0
CZ D:PHE174 4.4 39.1 1.0
CE1 D:PHE185 4.5 51.1 1.0
CE2 D:PHE174 4.6 40.4 1.0
CZ D:PHE185 4.7 53.4 1.0
CB D:HIS172 4.9 37.9 1.0
O D:HOH616 5.0 33.4 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 17:54:57 2024

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