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Calcium 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:

Zinc (Zn) 4 atoms
Sodium (Na) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4wzv

Go back to Calcium Binding Sites List in 4wzv
Calcium binding site 1 out of 6 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 Calcium with other atoms in the Ca 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:Ca304

b:14.8
occ:1.00
 O A:ASP165 2.2 10.2 1.0
OD1 A:ASP201 2.3 14.8 1.0
O A:HOH703 2.3 13.7 1.0
O A:GLY197 2.4 17.7 1.0
O A:GLN199 2.4 14.4 1.0
O A:HOH699 2.5 16.2 1.0
CG A:ASP201 3.3 14.0 1.0
C A:ASP165 3.4 12.0 1.0
C A:GLY197 3.5 19.2 1.0
C A:GLN199 3.5 11.0 1.0
OD2 A:ASP201 3.9 15.7 1.0
N A:ASP201 4.0 11.7 1.0
O A:ALA164 4.1 17.3 1.0
O A:HOH705 4.1 15.7 1.0
O A:HOH660 4.1 19.5 1.0
C A:ILE198 4.2 22.0 1.0
C A:GLY200 4.2 10.9 1.0
CA A:GLY200 4.2 11.3 1.0
N A:GLY197 4.2 13.2 1.0
CA A:ASP165 4.3 15.0 1.0
N A:GLN199 4.3 14.8 1.0
O A:ILE198 4.3 14.2 1.0
N A:GLY200 4.3 17.5 1.0
CA A:GLY197 4.3 11.4 1.0
O A:GLY195 4.4 15.8 1.0
N A:ILE166 4.4 10.7 1.0
CB A:ASP201 4.5 14.4 1.0
N A:ILE198 4.5 17.6 1.0
CA A:GLN199 4.5 18.3 1.0
CA A:ASP201 4.6 13.9 1.0
CA A:ILE166 4.6 8.8 1.0
CA A:ILE198 4.6 14.8 1.0
N A:VAL167 4.6 11.8 1.0
O A:HOH704 4.7 14.4 1.0
C A:PRO196 4.8 16.6 1.0
CH2 A:TRP116 4.8 12.0 1.0
O A:GLY200 4.8 15.3 1.0
CG2 A:VAL167 4.9 14.6 1.0
C A:ALA164 5.0 11.0 1.0

Calcium binding site 2 out of 6 in 4wzv

Go back to Calcium Binding Sites List in 4wzv
Calcium binding site 2 out of 6 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 Calcium with other atoms in the Ca 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:Ca305

b:34.9
occ:1.00
 O A:GLU208 2.3 25.6 1.0
O A:HOH804 2.4 30.0 1.0
OD2 A:ASP131 2.4 21.2 1.0
O A:ASP206 2.4 24.0 1.0
OD1 A:ASP206 2.4 20.3 1.0
CG A:ASP131 3.2 25.8 1.0
C A:ASP206 3.2 23.9 1.0
OD1 A:ASP131 3.4 28.8 1.0
CG A:ASP206 3.4 29.3 1.0
C A:GLU208 3.4 17.6 1.0
CA A:ASP206 3.7 20.2 1.0
C2 A:EDO307 4.0 39.3 1.0
CD1 A:TRP210 4.1 17.6 1.0
OG A:SER129 4.1 17.8 1.0
CB A:ASP206 4.1 20.3 1.0
N A:GLU208 4.1 21.1 1.0
OD2 A:ASP206 4.2 24.6 1.0
CA A:LEU209 4.3 18.5 1.0
N A:LEU209 4.3 18.5 1.0
N A:ASP207 4.3 17.5 1.0
C A:ASP207 4.4 22.9 1.0
CA A:GLU208 4.4 21.2 1.0
O2 A:EDO307 4.5 38.0 1.0
N A:TRP210 4.5 18.3 1.0
CA A:ASP207 4.6 16.7 1.0
CB A:ASP131 4.6 21.5 1.0
NE1 A:TRP210 4.7 18.6 1.0
O A:HOH744 4.8 23.5 1.0
C A:LEU209 4.9 26.8 1.0
O A:ASP205 4.9 16.8 1.0
O1 A:EDO307 4.9 31.7 1.0
C1 A:EDO307 5.0 41.8 1.0

Calcium binding site 3 out of 6 in 4wzv

Go back to Calcium Binding Sites List in 4wzv
Calcium binding site 3 out of 6 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 Calcium with other atoms in the Ca 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
A:Ca306

b:16.6
occ:1.00
 OD2 A:ASP205 2.2 16.6 1.0
O A:GLY183 2.3 21.2 1.0
OE2 A:GLU208 2.3 32.2 1.0
O A:LEU187 2.3 22.5 1.0
O A:ASP185 2.3 18.7 1.0
OD1 A:ASP182 2.4 19.4 1.0
CG A:ASP205 3.4 17.2 1.0
C A:LEU187 3.4 18.1 1.0
C A:ASP185 3.5 22.1 1.0
C A:GLY183 3.5 26.9 1.0
CD A:GLU208 3.5 24.6 1.0
CG A:ASP182 3.6 20.8 1.0
N A:LEU187 3.7 17.6 1.0
N A:ASP185 3.9 20.3 1.0
CA A:LEU187 4.0 21.7 1.0
N A:GLY183 4.1 23.8 1.0
C A:GLY186 4.1 21.3 1.0
OD2 A:ASP182 4.2 21.0 1.0
C A:LYS184 4.2 35.0 1.0
CG A:GLU208 4.2 22.9 1.0
CB A:ASP205 4.2 13.6 1.0
C A:ASP182 4.2 21.6 1.0
CA A:ASP185 4.2 26.1 1.0
N A:ASP182 4.3 21.8 1.0
OD1 A:ASP205 4.3 19.9 1.0
CB A:LEU187 4.3 18.8 1.0
CA A:GLY183 4.4 28.5 1.0
N A:LYS184 4.4 22.3 1.0
CA A:LYS184 4.4 23.5 1.0
N A:GLY186 4.5 27.1 1.0
OE1 A:GLU208 4.5 21.3 1.0
CA A:GLY186 4.6 20.7 1.0
N A:LEU188 4.6 17.4 1.0
CA A:ASP182 4.6 27.0 1.0
O A:ASP182 4.6 23.2 1.0
CB A:ASP182 4.7 18.8 1.0
O A:GLY186 4.7 22.5 1.0
O A:HOH760 4.7 32.1 1.0
O A:LYS184 4.8 28.3 1.0
CA A:LEU188 5.0 13.8 1.0

Calcium binding site 4 out of 6 in 4wzv

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Calcium binding site 4 out of 6 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 Calcium with other atoms in the Ca 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:Ca304

b:15.0
occ:1.00
 O B:ASP165 2.3 13.4 1.0
OD1 B:ASP201 2.3 14.2 1.0
O B:HOH742 2.4 16.3 1.0
O B:HOH740 2.4 13.5 1.0
O B:GLN199 2.4 13.0 1.0
O B:GLY197 2.4 12.4 1.0
CG B:ASP201 3.3 10.8 1.0
C B:ASP165 3.4 13.3 1.0
C B:GLN199 3.6 12.6 1.0
C B:GLY197 3.6 14.3 1.0
OD2 B:ASP201 3.9 13.0 1.0
O B:ALA164 4.0 17.2 1.0
N B:ASP201 4.0 11.2 1.0
O B:HOH743 4.1 16.7 1.0
O B:HOH663 4.2 14.7 1.0
C B:GLY200 4.2 13.7 1.0
CA B:GLY200 4.2 15.8 1.0
CA B:ASP165 4.2 11.6 1.0
C B:ILE198 4.3 15.7 1.0
N B:GLY197 4.3 14.0 1.0
N B:GLN199 4.3 17.0 1.0
N B:GLY200 4.4 16.4 1.0
O B:GLY195 4.4 19.7 1.0
N B:ILE166 4.4 13.4 1.0
O B:ILE198 4.4 12.6 1.0
CA B:GLY197 4.4 16.7 1.0
CB B:ASP201 4.5 11.8 1.0
N B:VAL167 4.6 12.4 1.0
CA B:ILE166 4.6 13.9 1.0
CA B:ASP201 4.6 10.1 1.0
CA B:GLN199 4.6 16.0 1.0
N B:ILE198 4.6 11.5 1.0
CH2 B:TRP116 4.6 13.6 1.0
O B:HOH741 4.6 18.4 1.0
CA B:ILE198 4.8 14.3 1.0
O B:GLY200 4.8 13.3 1.0
C B:PRO196 4.8 14.8 1.0
CG2 B:VAL167 4.9 13.7 1.0
C B:ALA164 5.0 13.7 1.0

Calcium binding site 5 out of 6 in 4wzv

Go back to Calcium Binding Sites List in 4wzv
Calcium binding site 5 out of 6 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 Calcium with other atoms in the Ca binding site number 5 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:Ca305

b:22.8
occ:1.00
 O B:GLU208 2.3 16.6 1.0
O B:ASP206 2.3 17.5 1.0
OD2 B:ASP131 2.4 15.2 1.0
OD1 B:ASP206 2.4 19.6 1.0
O B:HOH656 2.4 26.5 1.0
C B:ASP206 3.2 14.7 1.0
CG B:ASP131 3.2 20.5 1.0
OD1 B:ASP131 3.3 18.4 1.0
CG B:ASP206 3.4 16.5 1.0
C B:GLU208 3.4 17.4 1.0
CA B:ASP206 3.7 15.3 1.0
CB B:ASP206 4.1 15.4 1.0
OG B:SER129 4.1 16.9 1.0
CD1 B:TRP210 4.1 10.9 1.0
OD2 B:ASP206 4.2 18.4 1.0
CA B:LEU209 4.2 16.1 1.0
N B:LEU209 4.2 13.7 1.0
N B:GLU208 4.2 18.6 1.0
N B:ASP207 4.2 15.8 1.0
C B:ASP207 4.4 17.1 1.0
CA B:GLU208 4.5 13.6 1.0
CA B:ASP207 4.5 14.2 1.0
CB B:ASP131 4.6 16.5 1.0
N B:TRP210 4.6 11.9 1.0
O B:HOH757 4.6 24.4 1.0
NE1 B:TRP210 4.7 15.9 1.0
O B:HOH624 4.7 29.4 1.0
C B:LEU209 4.9 15.0 1.0
O B:ASP205 4.9 11.3 1.0
O B:HOH655 5.0 29.3 1.0
O B:ASP207 5.0 18.6 1.0

Calcium binding site 6 out of 6 in 4wzv

Go back to Calcium Binding Sites List in 4wzv
Calcium binding site 6 out of 6 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 Calcium with other atoms in the Ca binding site number 6 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:Ca306

b:16.1
occ:1.00
 OE2 B:GLU208 2.3 20.1 1.0
O B:GLY183 2.3 21.5 1.0
O B:ASP185 2.3 21.6 1.0
O B:LEU187 2.3 21.1 1.0
OD2 B:ASP205 2.3 16.5 1.0
OD1 B:ASP182 2.4 22.7 1.0
CD B:GLU208 3.4 19.8 1.0
C B:LEU187 3.4 22.4 1.0
CG B:ASP205 3.5 15.3 1.0
C B:ASP185 3.5 25.2 1.0
C B:GLY183 3.5 23.0 1.0
CG B:ASP182 3.6 22.6 1.0
N B:LEU187 3.8 25.8 1.0
N B:ASP185 3.9 15.9 1.0
CG B:GLU208 4.0 21.9 1.0
CA B:LEU187 4.1 24.7 1.0
C B:GLY186 4.1 21.2 1.0
N B:GLY183 4.1 18.8 1.0
OD2 B:ASP182 4.2 21.0 1.0
C B:LYS184 4.2 20.3 1.0
CB B:ASP205 4.2 13.8 1.0
CA B:ASP185 4.3 24.7 1.0
C B:ASP182 4.3 15.7 1.0
OD1 B:ASP205 4.3 14.7 1.0
N B:ASP182 4.4 19.7 1.0
CA B:GLY183 4.4 21.7 1.0
N B:LYS184 4.4 16.8 1.0
CA B:LYS184 4.4 17.0 1.0
OE1 B:GLU208 4.4 17.6 1.0
N B:GLY186 4.4 23.8 1.0
CB B:LEU187 4.5 20.6 1.0
O B:HOH604 4.5 32.1 1.0
CA B:GLY186 4.5 22.1 1.0
N B:LEU188 4.6 17.1 1.0
O B:GLY186 4.6 19.8 1.0
CA B:ASP182 4.7 21.1 1.0
O B:ASP182 4.7 20.0 1.0
O B:LYS184 4.7 25.5 1.0
CB B:ASP182 4.7 16.5 1.0
CA B:LEU188 4.9 18.6 1.0

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 Jul 14 14:25:59 2024

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