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Sodium 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
Zinc (Zn) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium 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 Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 4wzv

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Sodium binding site 1 out of 7 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 Sodium with other atoms in the Na 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
B:Na309

b:39.9
occ:1.00
 O B:HOH627 3.2 34.9 1.0
O B:HOH822 3.5 47.2 1.0
O B:HOH697 4.4 34.0 1.0

Sodium binding site 2 out of 7 in 4wzv

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Sodium binding site 2 out of 7 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 Sodium with other atoms in the Na 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
B:Na310

b:24.7
occ:1.00
 O1 B:PEG317 3.6 51.3 1.0
O B:HOH871 3.8 40.6 1.0
C1 B:PEG317 4.0 31.8 1.0
O B:HOH916 4.8 46.2 1.0

Sodium binding site 3 out of 7 in 4wzv

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Sodium binding site 3 out of 7 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 Sodium with other atoms in the Na 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:Na311

b:40.9
occ:1.00
 O A:HOH786 2.4 33.0 1.0
O B:HOH856 2.5 49.3 1.0
O B:HOH859 2.5 37.9 1.0
O B:HOH880 3.4 31.4 1.0
O A:HOH741 3.9 31.7 1.0
O A:HOH845 4.7 47.4 1.0
O B:HOH756 4.8 33.9 1.0
O B:HIS236 4.9 15.5 1.0

Sodium binding site 4 out of 7 in 4wzv

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Sodium binding site 4 out of 7 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 Sodium with other atoms in the Na 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:Na312

b:33.5
occ:1.00
 O B:HOH744 2.4 22.8 1.0
O B:HOH766 2.5 36.0 1.0
O B:HOH839 2.8 38.2 1.0
NH1 B:ARG158 3.0 18.2 1.0
CD B:ARG158 3.4 19.6 1.0
O B:HOH834 3.8 30.4 1.0
CZ B:ARG158 4.0 20.2 1.0
NE B:ARG158 4.1 19.9 1.0
O4 B:PEG317 4.1 45.4 1.0
O B:HOH704 4.3 40.0 1.0
OH B:TYR160 4.3 22.1 1.0
O B:HOH727 4.4 14.3 1.0
O B:HOH827 4.4 23.4 1.0
O B:HOH764 4.5 22.6 1.0
O B:HOH613 4.5 19.1 0.4
O B:HOH724 4.6 22.5 1.0
CG B:ARG158 4.6 17.4 1.0
CB B:ARG158 4.7 16.1 1.0
O B:HOH870 4.7 33.5 1.0
C4 B:PEG317 4.8 18.3 1.0
OD2 B:ASP138 4.9 16.2 1.0
CB B:ASP138 5.0 15.3 1.0
C3 B:PEG317 5.0 45.5 1.0

Sodium binding site 5 out of 7 in 4wzv

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Sodium binding site 5 out of 7 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 Sodium with other atoms in the Na 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:Na313

b:44.0
occ:1.00
 OG B:SER238 2.4 22.8 1.0
O B:HOH835 2.5 26.3 1.0
O B:HOH879 3.1 37.8 1.0
O B:HOH788 3.4 39.0 1.0
O B:HOH903 3.6 43.1 1.0
O B:HOH830 3.7 28.8 1.0
CB B:SER238 3.8 26.3 1.0
CG2 B:VAL239 4.6 14.8 1.0
O B:HOH924 4.7 56.7 1.0
CA B:SER238 4.7 17.9 1.0
O B:HOH796 4.8 34.5 1.0
N B:SER238 4.8 20.9 1.0
C B:SER238 4.9 15.7 1.0
O B:HOH863 5.0 48.8 1.0

Sodium binding site 6 out of 7 in 4wzv

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Sodium binding site 6 out of 7 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 Sodium with other atoms in the Na 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:Na314

b:34.2
occ:1.00
 OXT B:GLY269 2.4 27.4 1.0
O B:GLY269 2.8 28.7 1.0
C B:GLY269 3.0 27.8 1.0
CA B:GLY269 4.5 18.4 1.0

Sodium binding site 7 out of 7 in 4wzv

Go back to Sodium Binding Sites List in 4wzv
Sodium binding site 7 out of 7 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 Sodium with other atoms in the Na binding site number 7 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:Na315

b:44.5
occ:1.00
 O B:HOH753 2.5 34.1 1.0
O B:HOH653 3.5 41.8 1.0
O1 B:PEG317 4.8 51.3 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: Mon Oct 7 18:57:06 2024

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