Zinc in PDB 5cuh: Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4

Enzymatic activity of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4

All present enzymatic activity of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4, PDB code: 5cuh was solved by L.Tepshi, L.Vera, E.Nuti, L.Rosalia, A.Rossello, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.91 / 1.83
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.680, 97.790, 43.490, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 21.4

Other elements in 5cuh:

The structure of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4 also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4 (pdb code 5cuh). 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 Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4, PDB code: 5cuh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5cuh

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Zinc binding site 1 out of 4 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:12.1
occ:1.00
 NE2 A:HIS226 1.9 7.8 1.0
O24 A:LTQ306 2.1 19.9 1.0
NE2 A:HIS236 2.1 8.4 1.0
NE2 A:HIS230 2.1 7.3 1.0
O26 A:LTQ306 2.4 24.2 1.0
CE1 A:HIS226 2.9 8.0 1.0
CD2 A:HIS226 2.9 7.6 1.0
CE1 A:HIS236 3.0 8.6 1.0
C23 A:LTQ306 3.0 23.8 1.0
CD2 A:HIS230 3.1 7.7 1.0
CD2 A:HIS236 3.1 8.1 1.0
CE1 A:HIS230 3.1 8.8 1.0
N25 A:LTQ306 3.2 22.6 1.0
ND1 A:HIS226 4.0 8.3 1.0
CG A:HIS226 4.0 7.7 1.0
O A:HOH419 4.1 17.3 1.0
ND1 A:HIS236 4.1 8.4 1.0
CG A:HIS236 4.2 8.9 1.0
CG A:HIS230 4.2 7.5 1.0
ND1 A:HIS230 4.2 7.5 1.0
O A:HOH546 4.3 38.9 1.0
C19 A:LTQ306 4.4 23.9 1.0
C11 A:LTQ306 4.5 19.8 1.0
OE2 A:GLU227 4.7 15.2 1.0
OE1 A:GLU227 4.7 15.1 1.0
CE A:MET244 4.9 9.4 1.0
N18 A:LTQ306 5.0 22.1 1.0

Zinc binding site 2 out of 4 in 5cuh

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Zinc binding site 2 out of 4 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:17.2
occ:1.00
 OD2 A:ASP177 2.0 22.2 1.0
NE2 A:HIS175 2.1 18.9 1.0
NE2 A:HIS190 2.1 14.6 1.0
ND1 A:HIS203 2.1 13.3 1.0
CD2 A:HIS175 3.0 19.2 1.0
CG A:ASP177 3.0 24.4 1.0
CD2 A:HIS190 3.1 12.3 1.0
CE1 A:HIS203 3.1 14.2 1.0
CE1 A:HIS175 3.1 20.7 1.0
CE1 A:HIS190 3.1 13.9 1.0
CG A:HIS203 3.1 12.5 1.0
OD1 A:ASP177 3.2 24.2 1.0
CB A:HIS203 3.4 11.1 1.0
O A:TYR179 4.1 30.3 1.0
CG A:HIS175 4.1 19.2 1.0
ND1 A:HIS175 4.2 21.4 1.0
NE2 A:HIS203 4.2 14.5 1.0
ND1 A:HIS190 4.2 13.4 1.0
CG A:HIS190 4.2 12.9 1.0
CD2 A:HIS203 4.3 14.0 1.0
CB A:ASP177 4.3 25.2 1.0
CZ A:PHE181 4.4 17.6 1.0
CE1 A:PHE192 4.5 16.0 1.0
CE2 A:PHE181 4.6 18.3 1.0
O A:HOH425 4.7 33.7 1.0
CZ A:PHE192 4.7 16.5 1.0
O A:HOH450 4.8 19.9 1.0
CA A:HIS203 4.9 10.0 1.0

Zinc binding site 3 out of 4 in 5cuh

Go back to Zinc Binding Sites List in 5cuh
Zinc binding site 3 out of 4 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:10.1
occ:1.00
 O24 B:LTQ306 2.0 16.4 1.0
NE2 B:HIS230 2.0 7.5 1.0
NE2 B:HIS236 2.1 10.4 1.0
NE2 B:HIS226 2.1 7.5 1.0
O26 B:LTQ306 2.2 19.3 1.0
C23 B:LTQ306 2.8 19.1 1.0
CE1 B:HIS230 2.9 7.9 1.0
CD2 B:HIS226 3.0 8.2 1.0
N25 B:LTQ306 3.0 18.4 1.0
CD2 B:HIS236 3.0 11.4 1.0
CE1 B:HIS236 3.1 12.1 1.0
CD2 B:HIS230 3.1 7.3 1.0
CE1 B:HIS226 3.1 7.7 1.0
O B:HOH462 4.1 11.1 1.0
ND1 B:HIS230 4.1 7.1 1.0
CG B:HIS226 4.2 8.0 1.0
ND1 B:HIS236 4.2 12.5 1.0
CG B:HIS236 4.2 11.8 1.0
CG B:HIS230 4.2 7.0 1.0
ND1 B:HIS226 4.2 8.6 1.0
C19 B:LTQ306 4.3 18.7 1.0
O B:HOH570 4.3 49.1 1.0
OE2 B:GLU227 4.5 15.9 1.0
OE1 B:GLU227 4.7 15.2 1.0
C11 B:LTQ306 4.7 15.8 1.0
C20 B:LTQ306 4.9 20.5 1.0
N18 B:LTQ306 4.9 18.0 1.0
CD B:GLU227 4.9 12.9 1.0

Zinc binding site 4 out of 4 in 5cuh

Go back to Zinc Binding Sites List in 5cuh
Zinc binding site 4 out of 4 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:11.0
occ:1.00
 OD2 B:ASP177 2.0 11.9 1.0
NE2 B:HIS190 2.0 9.1 1.0
NE2 B:HIS175 2.0 9.3 1.0
ND1 B:HIS203 2.0 11.6 1.0
CG B:ASP177 2.9 13.6 1.0
CE1 B:HIS203 2.9 12.2 1.0
CE1 B:HIS190 3.0 8.9 1.0
CD2 B:HIS175 3.0 10.3 1.0
CE1 B:HIS175 3.0 9.9 1.0
CD2 B:HIS190 3.0 8.6 1.0
CG B:HIS203 3.1 10.4 1.0
OD1 B:ASP177 3.2 13.0 1.0
CB B:HIS203 3.5 9.0 1.0
NE2 B:HIS203 4.1 13.0 1.0
ND1 B:HIS190 4.1 9.1 1.0
ND1 B:HIS175 4.1 9.5 1.0
CG B:HIS175 4.1 10.5 1.0
CG B:HIS190 4.1 8.7 1.0
CD2 B:HIS203 4.2 10.8 1.0
O B:TYR179 4.2 15.0 1.0
CB B:ASP177 4.3 14.1 1.0
CE1 B:PHE192 4.3 15.1 1.0
CZ B:PHE181 4.5 12.3 1.0
CZ B:PHE192 4.6 15.9 1.0
O B:HOH418 4.8 27.0 1.0
CE2 B:PHE181 4.8 12.2 1.0
O B:HOH472 4.8 12.7 1.0
CE1 B:PHE181 5.0 13.1 1.0

Reference:

C.Camodeca, E.Nuti, L.Tepshi, S.Boero, T.Tuccinardi, E.A.Stura, A.Poggi, M.R.Zocchi, A.Rossello. Discovery of A New Selective Inhibitor of A Disintegrin and Metalloprotease 10 (Adam-10) Able to Reduce the Shedding of NKG2D Ligands in Hodgkin'S Lymphoma Cell Models. Eur.J.Med.Chem. V. 111 193 2016.
ISSN: ISSN 0223-5234
PubMed: 26871660
DOI: 10.1016/J.EJMECH.2016.01.053
Page generated: Wed Dec 16 06:07:23 2020

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