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Calcium 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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4, PDB code: 5cuh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5cuh

Go back to Calcium Binding Sites List in 5cuh
Calcium binding site 1 out of 6 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca303

b:10.5
occ:1.00
 O A:GLN199 2.3 9.5 1.0
O A:HOH441 2.3 8.2 1.0
O A:ASP165 2.3 9.2 1.0
O A:GLY197 2.4 12.3 1.0
O A:HOH439 2.4 10.9 1.0
OD1 A:ASP201 2.4 9.9 1.0
CG A:ASP201 3.5 11.6 1.0
C A:ASP165 3.5 8.2 1.0
C A:GLN199 3.5 10.9 1.0
C A:GLY197 3.6 11.4 1.0
OD2 A:ASP201 4.0 10.8 1.0
O A:HOH459 4.1 10.9 1.0
C A:ILE198 4.1 12.7 1.0
N A:ASP201 4.1 10.2 1.0
O A:ALA164 4.1 11.8 1.0
O A:ILE198 4.2 11.8 1.0
O A:HOH514 4.2 14.1 1.0
N A:GLY197 4.2 10.1 1.0
CA A:ASP165 4.3 8.9 1.0
C A:GLY200 4.3 10.6 1.0
N A:GLN199 4.3 11.5 1.0
O A:GLY195 4.3 10.3 1.0
CA A:GLY200 4.4 9.7 1.0
N A:GLY200 4.4 10.4 1.0
CA A:GLY197 4.4 11.1 1.0
N A:ILE166 4.4 7.9 1.0
CA A:GLN199 4.5 12.6 1.0
N A:ILE198 4.5 12.7 1.0
CA A:ILE198 4.6 13.1 1.0
N A:VAL167 4.6 8.2 1.0
CA A:ILE166 4.6 7.9 1.0
CB A:ASP201 4.6 10.6 1.0
O A:HOH458 4.6 12.2 1.0
CA A:ASP201 4.7 10.3 1.0
C A:PRO196 4.7 10.9 1.0
CH2 A:TRP116 4.7 8.7 1.0
O A:GLY200 4.9 10.5 1.0

Calcium binding site 2 out of 6 in 5cuh

Go back to Calcium Binding Sites List in 5cuh
Calcium binding site 2 out of 6 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca304

b:29.2
occ:1.00
 O A:GLU208 2.3 20.8 1.0
O A:HOH512 2.4 30.2 1.0
O A:ASP206 2.4 20.0 1.0
OD1 A:ASP206 2.5 18.9 1.0
OD2 A:ASP131 2.6 23.5 1.0
O A:HOH533 2.9 30.7 1.0
OD1 A:ASP131 2.9 36.0 1.0
O A:HOH482 2.9 31.1 1.0
CG A:ASP131 3.1 27.9 1.0
C A:ASP206 3.4 19.3 1.0
CG A:ASP206 3.5 20.3 1.0
C A:GLU208 3.6 22.0 1.0
CA A:ASP206 4.0 17.8 1.0
OG A:SER129 4.1 20.2 1.0
CB A:ASP206 4.2 18.4 1.0
N A:GLU208 4.3 20.5 1.0
OD2 A:ASP206 4.3 21.6 1.0
CA A:LEU209 4.4 23.8 1.0
C A:ASP207 4.4 24.7 1.0
CD1 A:TRP210 4.4 14.5 1.0
N A:LEU209 4.4 20.3 1.0
N A:ASP207 4.4 18.8 1.0
O A:HOH430 4.4 22.9 1.0
O A:HOH524 4.5 46.0 1.0
CA A:GLU208 4.6 21.1 1.0
CB A:ASP131 4.6 24.1 1.0
CA A:ASP207 4.6 21.9 1.0
N A:TRP210 4.7 22.8 1.0
O A:ASP207 4.9 26.7 1.0
NE1 A:TRP210 5.0 13.9 1.0

Calcium binding site 3 out of 6 in 5cuh

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Calcium binding site 3 out of 6 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca305

b:20.2
occ:1.00
 OE2 A:GLU208 2.2 24.7 1.0
OD1 A:ASP182 2.3 28.3 1.0
O A:ASP185 2.3 29.4 1.0
O A:GLY183 2.3 25.5 1.0
O A:LEU187 2.3 19.6 1.0
OD2 A:ASP205 2.4 16.2 1.0
CG A:ASP205 3.4 16.4 1.0
CD A:GLU208 3.4 22.7 1.0
C A:ASP185 3.5 31.1 1.0
C A:LEU187 3.5 20.3 1.0
CG A:ASP182 3.5 34.5 1.0
C A:GLY183 3.5 31.1 1.0
N A:LEU187 3.9 22.8 1.0
CB A:ASP205 4.0 14.5 1.0
C A:GLY186 4.1 24.3 1.0
N A:ASP185 4.1 36.0 1.0
OD2 A:ASP182 4.2 37.1 1.0
CA A:LEU187 4.2 21.2 1.0
C A:LYS184 4.2 34.9 1.0
OE1 A:GLU208 4.3 22.4 1.0
CG A:GLU208 4.3 20.9 1.0
N A:GLY183 4.3 27.6 1.0
CA A:ASP185 4.3 31.1 1.0
OD1 A:ASP205 4.4 14.8 1.0
N A:ASP182 4.4 26.5 1.0
C A:ASP182 4.4 28.0 1.0
N A:GLY186 4.4 27.6 1.0
CA A:GLY186 4.4 22.8 1.0
N A:LYS184 4.4 30.6 1.0
O A:GLY186 4.5 22.0 1.0
CA A:GLY183 4.5 26.7 1.0
N A:LEU188 4.5 16.5 1.0
O A:LYS184 4.5 37.1 1.0
CA A:LYS184 4.5 34.3 1.0
CA A:LEU188 4.6 14.6 1.0
CB A:LEU187 4.6 21.5 1.0
CB A:ASP182 4.7 31.8 1.0
CA A:ASP182 4.7 28.8 1.0
O A:ASP182 4.8 28.4 1.0
CD2 A:LEU188 5.0 16.4 1.0

Calcium binding site 4 out of 6 in 5cuh

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Calcium binding site 4 out of 6 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca303

b:8.6
occ:1.00
 O B:HOH436 2.3 6.8 1.0
O B:GLN199 2.3 7.8 0.7
O B:GLN199 2.3 8.1 0.3
O B:ASP165 2.3 8.3 1.0
OD1 B:ASP201 2.3 8.0 1.0
O B:HOH429 2.4 8.5 1.0
O B:GLY197 2.4 10.1 1.0
CG B:ASP201 3.4 9.2 1.0
C B:ASP165 3.4 7.7 1.0
C B:GLN199 3.5 8.6 0.3
C B:GLN199 3.5 8.8 0.7
C B:GLY197 3.6 9.9 1.0
OD2 B:ASP201 3.9 9.8 1.0
O B:HOH426 4.0 10.7 1.0
O B:ALA164 4.1 9.5 1.0
C B:ILE198 4.1 10.4 1.0
N B:ASP201 4.1 7.7 1.0
O B:HOH530 4.2 11.2 1.0
N B:GLN199 4.2 9.7 0.3
N B:GLY197 4.2 8.5 1.0
CA B:ASP165 4.2 8.8 1.0
N B:GLN199 4.2 10.1 0.7
C B:GLY200 4.3 7.6 1.0
CA B:GLY200 4.3 7.9 1.0
O B:GLY195 4.3 8.2 1.0
O B:ILE198 4.3 9.8 1.0
N B:GLY200 4.4 8.1 1.0
CA B:GLY197 4.4 9.4 1.0
N B:ILE166 4.5 7.2 1.0
CA B:GLN199 4.5 9.1 0.3
CA B:GLN199 4.5 9.8 0.7
N B:ILE198 4.5 10.8 1.0
CA B:ILE198 4.6 11.4 1.0
CB B:ASP201 4.6 8.0 1.0
N B:VAL167 4.6 7.1 1.0
CA B:ILE166 4.6 7.1 1.0
O B:HOH453 4.7 13.6 1.0
C B:PRO196 4.7 9.2 1.0
CA B:ASP201 4.7 7.8 1.0
CH2 B:TRP116 4.7 7.8 1.0
O B:GLY200 4.9 7.1 1.0

Calcium binding site 5 out of 6 in 5cuh

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Calcium binding site 5 out of 6 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 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:Ca304

b:21.2
occ:1.00
 O B:HOH528 2.3 23.3 1.0
O B:GLU208 2.4 11.3 1.0
OD2 B:ASP131 2.4 16.6 1.0
O B:ASP206 2.5 11.3 1.0
OD1 B:ASP206 2.5 12.3 1.0
O B:HOH553 2.7 31.0 1.0
OD1 B:ASP131 3.0 17.5 1.0
CG B:ASP131 3.1 16.4 1.0
C B:ASP206 3.4 11.3 1.0
CG B:ASP206 3.5 12.3 1.0
C B:GLU208 3.6 11.2 1.0
OG B:SER129 3.9 14.6 1.0
CA B:ASP206 3.9 10.5 1.0
CB B:ASP206 4.2 12.1 1.0
OD2 B:ASP206 4.2 13.8 1.0
CD1 B:TRP210 4.3 8.8 1.0
CA B:LEU209 4.3 11.2 1.0
N B:LEU209 4.4 10.5 1.0
N B:GLU208 4.4 11.3 1.0
N B:ASP207 4.5 12.3 1.0
CB B:ASP131 4.5 14.7 1.0
O B:HOH428 4.5 20.0 1.0
C B:ASP207 4.5 12.1 1.0
N B:TRP210 4.6 9.7 1.0
CA B:GLU208 4.6 11.8 1.0
CA B:ASP207 4.8 12.0 1.0
NE1 B:TRP210 4.9 9.0 1.0
C B:LEU209 5.0 10.9 1.0

Calcium binding site 6 out of 6 in 5cuh

Go back to Calcium Binding Sites List in 5cuh
Calcium binding site 6 out of 6 in the Crystal Structure Mmp-9 Complexes with A Constrained Hydroxamate Based Inhibitor LT4


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 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:Ca305

b:13.1
occ:1.00
 OE2 B:GLU208 2.2 15.5 1.0
O B:GLY183 2.3 15.2 1.0
OD2 B:ASP205 2.3 9.7 1.0
O B:LEU187 2.3 10.8 1.0
OD1 B:ASP182 2.4 14.5 1.0
O B:ASP185 2.5 13.8 1.0
CG B:ASP205 3.4 8.7 1.0
CD B:GLU208 3.4 13.5 1.0
C B:LEU187 3.5 11.2 1.0
C B:GLY183 3.5 15.8 1.0
C B:ASP185 3.6 13.9 1.0
CG B:ASP182 3.6 17.2 1.0
N B:ASP185 3.9 14.0 1.0
N B:LEU187 3.9 13.1 1.0
CB B:ASP205 4.0 8.1 1.0
C B:LYS184 4.0 14.8 0.9
C B:LYS184 4.1 14.2 0.1
N B:GLY183 4.1 15.5 1.0
CA B:LEU187 4.2 12.3 1.0
OD2 B:ASP182 4.2 18.0 1.0
OE1 B:GLU208 4.2 14.6 1.0
N B:ASP182 4.3 17.4 1.0
CA B:ASP185 4.3 13.5 1.0
CG B:GLU208 4.3 13.2 1.0
C B:GLY186 4.3 12.8 1.0
C B:ASP182 4.3 17.6 1.0
OD1 B:ASP205 4.4 8.1 1.0
N B:LYS184 4.4 14.7 0.1
N B:LYS184 4.4 13.5 0.9
CA B:LYS184 4.4 14.8 0.9
CA B:LYS184 4.4 14.4 0.1
N B:LEU188 4.4 9.8 1.0
O B:LYS184 4.5 15.1 0.9
CA B:GLY183 4.5 15.5 1.0
O B:LYS184 4.6 14.4 0.1
CB B:LEU187 4.6 12.7 1.0
CA B:LEU188 4.6 9.6 1.0
N B:GLY186 4.6 14.8 1.0
O B:ASP182 4.7 18.8 1.0
CA B:GLY186 4.7 14.9 1.0
CA B:ASP182 4.7 17.3 1.0
CB B:ASP182 4.8 16.6 1.0
O B:GLY186 4.8 12.9 1.0
CD2 B:LEU188 5.0 9.1 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: Sun Jul 14 17:18:27 2024

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