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Zinc in PDB 4wzv: Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain

Enzymatic activity of Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain

All present enzymatic activity of Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4wzv was solved by E.A.Stura, L.Vera, E.Cassar-Lajeunesse, E.Nuti, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.13 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 39.950, 97.390, 45.670, 90.00, 112.72, 90.00
R / Rfree (%) 17.6 / 23

Other elements in 4wzv:

The structure of Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain also contains other interesting chemical elements:

Calcium (Ca) 6 atoms
Sodium (Na) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain (pdb code 4wzv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4wzv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4wzv

Go back to Zinc Binding Sites List in 4wzv
Zinc binding site 1 out of 4 in the Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain


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 A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.7
occ:1.00
 NE2 A:HIS226 2.1 15.9 1.0
NE2 A:HIS236 2.1 14.2 1.0
O2 A:E40301 2.1 13.3 1.0
O7 A:E40301 2.1 14.8 1.0
NE2 A:HIS230 2.2 9.3 1.0
C11 A:E40301 2.8 12.8 0.7
N2 A:E40301 2.9 14.3 1.0
CD2 A:HIS236 3.0 12.9 1.0
CD2 A:HIS226 3.0 12.3 1.0
CE1 A:HIS236 3.1 11.7 1.0
CD2 A:HIS230 3.1 10.4 1.0
CE1 A:HIS226 3.1 11.9 1.0
CE1 A:HIS230 3.2 13.0 1.0
CG A:HIS236 4.2 14.2 1.0
ND1 A:HIS236 4.2 15.5 1.0
CG A:HIS226 4.2 7.3 1.0
ND1 A:HIS226 4.2 10.7 1.0
CG A:HIS230 4.3 12.8 1.0
ND1 A:HIS230 4.3 15.2 1.0
C31 A:E40301 4.3 11.9 1.0
OE2 A:GLU227 4.4 14.8 1.0
C52 A:E40301 4.4 16.4 1.0
C51 A:E40301 4.4 17.1 0.8
N48 A:E40301 4.5 16.1 1.0
C29 A:E40301 4.5 12.9 0.8
C50 A:E40301 4.5 14.6 1.0
C49 A:E40301 4.5 17.4 1.0
C15 A:E40301 4.5 11.3 0.9
O15 A:E40301 4.6 15.3 1.0
C28 A:E40301 4.7 15.3 1.0
O54 A:E40301 4.8 16.9 1.0
CE A:MET244 4.8 13.7 1.0
C16 A:E40301 4.8 10.9 1.0
C32 A:E40301 4.9 15.0 1.0
N12 A:E40301 5.0 15.4 1.0

Zinc binding site 2 out of 4 in 4wzv

Go back to Zinc Binding Sites List in 4wzv
Zinc binding site 2 out of 4 in the Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain


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 A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:19.6
occ:1.00
 OD2 A:ASP177 1.9 22.4 1.0
ND1 A:HIS203 2.0 10.8 1.0
NE2 A:HIS190 2.1 14.4 1.0
NE2 A:HIS175 2.1 24.2 1.0
CG A:ASP177 2.9 22.7 1.0
CE1 A:HIS203 2.9 17.2 1.0
CE1 A:HIS190 3.0 16.2 1.0
CG A:HIS203 3.0 15.1 1.0
CD2 A:HIS175 3.0 23.7 1.0
CE1 A:HIS175 3.1 18.4 1.0
CD2 A:HIS190 3.1 18.8 1.0
OD1 A:ASP177 3.2 23.0 1.0
CB A:HIS203 3.4 13.6 1.0
NE2 A:HIS203 4.0 17.7 1.0
O A:TYR179 4.1 20.4 1.0
ND1 A:HIS190 4.1 16.8 1.0
CD2 A:HIS203 4.1 18.2 1.0
CG A:HIS175 4.2 18.9 1.0
ND1 A:HIS175 4.2 17.0 1.0
CB A:ASP177 4.2 22.2 1.0
CG A:HIS190 4.2 14.7 1.0
CE1 A:PHE192 4.5 23.4 1.0
CZ A:PHE181 4.5 13.1 1.0
CZ A:PHE192 4.7 16.0 1.0
CE2 A:PHE181 4.7 19.6 1.0
O A:HOH708 4.8 22.4 1.0
CA A:HIS203 4.9 13.6 1.0
CB A:TYR179 5.0 22.3 1.0

Zinc binding site 3 out of 4 in 4wzv

Go back to Zinc Binding Sites List in 4wzv
Zinc binding site 3 out of 4 in the Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain


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 A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:12.4
occ:1.00
 O2 B:E40301 2.0 8.1 1.0
NE2 B:HIS226 2.0 13.9 1.0
NE2 B:HIS230 2.1 10.6 1.0
NE2 B:HIS236 2.1 13.3 1.0
O7 B:E40301 2.1 12.9 1.0
C11 B:E40301 2.8 14.1 1.0
N2 B:E40301 2.9 11.6 1.0
CD2 B:HIS226 3.0 12.3 1.0
CD2 B:HIS230 3.0 12.4 1.0
CD2 B:HIS236 3.1 13.3 1.0
CE1 B:HIS226 3.1 14.0 1.0
CE1 B:HIS236 3.1 15.6 1.0
CE1 B:HIS230 3.2 13.5 1.0
CG B:HIS226 4.1 8.5 1.0
ND1 B:HIS226 4.2 10.9 1.0
CG B:HIS230 4.2 12.9 1.0
ND1 B:HIS236 4.2 15.9 1.0
CG B:HIS236 4.2 16.9 1.0
ND1 B:HIS230 4.3 13.8 1.0
C31 B:E40301 4.3 14.2 0.8
C52 B:E40301 4.4 13.9 1.0
C29 B:E40301 4.4 14.1 1.0
OE2 B:GLU227 4.4 14.8 1.0
C15 B:E40301 4.5 14.1 1.0
N48 B:E40301 4.5 16.6 0.8
C51 B:E40301 4.5 16.1 1.0
C50 B:E40301 4.6 15.6 1.0
C49 B:E40301 4.6 13.7 1.0
C28 B:E40301 4.6 15.1 0.9
O54 B:E40301 4.7 11.1 0.7
O15 B:E40301 4.7 13.0 0.7
C16 B:E40301 4.8 13.3 1.0
C32 B:E40301 4.9 17.9 1.0
C14 B:E40301 4.9 11.7 0.8
N12 B:E40301 5.0 8.9 0.8

Zinc binding site 4 out of 4 in 4wzv

Go back to Zinc Binding Sites List in 4wzv
Zinc binding site 4 out of 4 in the Crystal Structure of A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain


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 A Hydroxamate Based Inhibitor EN140 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:18.1
occ:1.00
 OD2 B:ASP177 2.0 18.2 1.0
NE2 B:HIS175 2.0 18.4 1.0
ND1 B:HIS203 2.0 15.9 1.0
NE2 B:HIS190 2.1 16.3 1.0
CG B:ASP177 2.9 28.6 1.0
CE1 B:HIS203 2.9 19.4 1.0
CD2 B:HIS175 2.9 19.9 1.0
CE1 B:HIS190 3.0 19.3 1.0
CE1 B:HIS175 3.0 23.6 1.0
CG B:HIS203 3.1 13.4 1.0
OD1 B:ASP177 3.2 30.5 1.0
CD2 B:HIS190 3.2 15.7 1.0
CB B:HIS203 3.5 17.0 1.0
O B:TYR179 4.0 31.3 1.0
NE2 B:HIS203 4.1 18.6 1.0
ND1 B:HIS175 4.1 23.2 1.0
CG B:HIS175 4.1 20.5 1.0
CD2 B:HIS203 4.2 17.4 1.0
ND1 B:HIS190 4.2 15.7 1.0
CB B:ASP177 4.2 23.4 1.0
CG B:HIS190 4.3 15.0 1.0
CE1 B:PHE192 4.3 18.1 1.0
CZ B:PHE192 4.5 23.8 1.0
CZ B:PHE181 4.6 17.5 1.0
O B:HOH754 4.7 30.4 1.0
CE2 B:PHE181 4.8 15.1 1.0
CB B:TYR179 4.8 33.5 1.0
CA B:HIS203 5.0 16.0 1.0
C B:TYR179 5.0 29.7 1.0
O B:HOH651 5.0 24.9 0.5

Reference:

E.Nuti, A.R.Cantelmo, C.Gallo, A.Bruno, B.Bassani, C.Camodeca, T.Tuccinardi, L.Vera, E.Orlandini, S.Nencetti, E.A.Stura, A.Martinelli, V.Dive, A.Albini, A.Rossello. N-O-Isopropyl Sulfonamido-Based Hydroxamates As Matrix Metalloproteinase Inhibitors: Hit Selection and in Vivo Antiangiogenic Activity. J.Med.Chem. V. 58 7224 2015.
ISSN: ISSN 0022-2623
PubMed: 26263024
DOI: 10.1021/ACS.JMEDCHEM.5B00367
Page generated: Sun Oct 27 10:10:15 2024

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