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Calcium in PDB 6enm: Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.

Enzymatic activity of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.

All present enzymatic activity of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168., PDB code: 6enm was solved by L.Vera, E.Nuti, A.Rossello, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.91 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.410, 67.090, 68.440, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.2

Other elements in 6enm:

The structure of Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168. (pdb code 6enm). 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 MMP12 in Complex with Hydroxamate Inhibitor LP168., PDB code: 6enm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 6enm

Go back to Calcium Binding Sites List in 6enm
Calcium binding site 1 out of 6 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


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 MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:25.2
occ:1.00
 O A:GLY192 2.2 16.4 1.0
OD1 A:ASP194 2.3 15.2 1.0
O A:HOH484 2.4 20.0 1.0
O A:HOH413 2.4 24.8 1.0
O A:ASP158 2.4 13.6 1.0
O A:GLY190 2.5 19.5 1.0
O A:HOH401 3.0 13.5 1.0
CG A:ASP194 3.2 15.2 1.0
C A:GLY192 3.4 12.6 1.0
C A:ASP158 3.4 12.9 1.0
C A:GLY190 3.7 19.5 1.0
OD2 A:ASP194 3.7 16.8 1.0
C A:ILE191 3.9 14.2 0.6
C A:ILE191 3.9 14.9 0.4
O A:HOH431 4.0 33.6 1.0
N A:GLY192 4.0 14.1 1.0
O A:ILE191 4.1 14.2 0.4
O A:ALA157 4.1 15.7 1.0
N A:ASP194 4.1 12.1 1.0
O A:ILE191 4.2 14.0 0.6
N A:GLY193 4.2 13.9 1.0
N A:ILE159 4.2 12.2 1.0
CA A:GLY192 4.2 12.8 1.0
CA A:ILE191 4.4 16.3 0.6
CA A:ILE191 4.4 17.2 0.4
N A:LEU160 4.4 11.0 1.0
CA A:ILE159 4.4 12.4 1.0
CA A:ASP158 4.4 14.7 1.0
CA A:GLY193 4.4 13.7 1.0
O A:GLY188 4.4 17.6 1.0
C A:GLY193 4.4 12.8 1.0
N A:ILE191 4.5 17.3 0.4
N A:ILE191 4.5 16.1 0.6
CB A:ASP194 4.5 14.9 1.0
CA A:ASP194 4.6 12.8 1.0
N A:GLY190 4.7 19.1 1.0
CA A:GLY190 4.7 21.5 1.0
O A:HOH426 4.8 25.5 1.0
C A:ILE159 4.8 12.2 1.0
O A:HOH549 4.8 17.7 1.0

Calcium binding site 2 out of 6 in 6enm

Go back to Calcium Binding Sites List in 6enm
Calcium binding site 2 out of 6 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


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 MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:12.3
occ:1.00
 O A:HOH527 2.3 19.3 1.0
O A:GLU199 2.3 10.8 1.0
O A:GLU201 2.4 12.1 1.0
OE2 A:GLU199 2.4 14.5 1.0
O A:HOH531 2.4 15.2 1.0
OD2 A:ASP124 2.4 13.0 1.0
OD1 A:ASP124 2.6 13.7 1.0
CG A:ASP124 2.9 14.9 1.0
CD A:GLU199 3.5 13.6 1.0
C A:GLU199 3.5 10.4 1.0
C A:GLU201 3.6 13.1 1.0
CG A:GLU199 3.9 13.3 1.0
CA A:GLU199 4.1 11.1 1.0
CA A:PHE202 4.2 13.5 1.0
OG1 A:THR122 4.2 12.4 1.0
CD1 A:TRP203 4.3 8.4 1.0
N A:PHE202 4.3 13.3 1.0
CB A:ASP124 4.4 14.9 1.0
N A:GLU201 4.4 11.5 1.0
O A:HOH583 4.4 30.7 1.0
O A:HOH443 4.5 27.3 1.0
C A:ASP200 4.5 14.2 1.0
N A:ASP200 4.5 10.6 1.0
OE1 A:GLU199 4.6 12.5 1.0
O A:HOH422 4.6 24.2 1.0
CA A:GLU201 4.6 11.9 1.0
CB A:GLU199 4.6 11.6 1.0
O A:HOH433 4.7 20.0 1.0
N A:TRP203 4.7 12.2 1.0
CA A:ASP200 4.7 11.8 1.0
O A:HOH536 4.7 30.9 1.0
CD1 A:PHE202 4.8 15.8 1.0
NE1 A:TRP203 4.8 10.3 1.0
O A:ASP200 4.9 14.6 1.0

Calcium binding site 3 out of 6 in 6enm

Go back to Calcium Binding Sites List in 6enm
Calcium binding site 3 out of 6 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


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 MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:11.3
occ:1.00
 O A:ILE180 2.3 12.8 1.0
O A:GLY176 2.3 11.4 1.0
OE2 A:GLU201 2.3 18.0 1.0
OD1 A:ASP175 2.3 10.6 1.0
OD2 A:ASP198 2.3 11.0 1.0
O A:GLY178 2.3 14.1 1.0
CG A:ASP198 3.4 11.5 1.0
C A:ILE180 3.4 13.1 1.0
CG A:ASP175 3.5 12.3 1.0
C A:GLY176 3.5 12.2 1.0
CD A:GLU201 3.5 17.6 1.0
C A:GLY178 3.5 14.7 1.0
N A:ILE180 3.8 12.7 1.0
N A:GLY178 4.0 16.9 1.0
N A:GLY176 4.0 12.9 1.0
CB A:ASP198 4.1 9.6 1.0
OD2 A:ASP175 4.1 13.9 1.0
C A:GLY179 4.1 13.8 1.0
CA A:ILE180 4.1 12.9 1.0
OE1 A:GLU201 4.2 17.7 1.0
C A:ASP175 4.2 13.7 1.0
N A:ASP175 4.2 13.3 1.0
C A:LYS177 4.3 15.3 1.0
OD1 A:ASP198 4.3 9.6 1.0
CA A:GLY178 4.3 16.4 1.0
CA A:GLY176 4.3 11.5 1.0
N A:LYS177 4.4 14.7 1.0
N A:LEU181 4.5 13.1 1.0
N A:GLY179 4.5 14.7 1.0
CA A:LYS177 4.5 15.1 1.0
CA A:GLY179 4.5 14.1 1.0
CG A:GLU201 4.5 16.6 1.0
O A:GLY179 4.6 15.8 1.0
CA A:ASP175 4.6 13.5 1.0
CB A:ILE180 4.6 12.6 1.0
CB A:ASP175 4.7 13.2 1.0
O A:ASP175 4.7 16.1 1.0
CA A:LEU181 4.7 11.4 1.0
O A:LYS177 4.8 17.2 1.0

Calcium binding site 4 out of 6 in 6enm

Go back to Calcium Binding Sites List in 6enm
Calcium binding site 4 out of 6 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


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 MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:16.8
occ:1.00
 O B:HOH447 2.2 22.6 1.0
O B:GLY192 2.2 12.5 1.0
O B:ASP158 2.4 12.1 1.0
O B:GLY190 2.4 16.3 1.0
OD1 B:ASP194 2.4 17.0 1.0
O B:HOH418 2.4 22.6 1.0
CG B:ASP194 3.4 11.5 1.0
C B:GLY192 3.4 10.6 1.0
C B:ASP158 3.5 12.3 1.0
C B:GLY190 3.6 16.3 1.0
OD2 B:ASP194 3.7 13.7 1.0
O B:HOH414 3.8 42.5 1.0
C B:ILE191 3.9 13.1 1.0
N B:GLY192 4.0 11.0 1.0
O B:ILE191 4.2 11.7 1.0
O B:ALA157 4.2 16.0 1.0
N B:ASP194 4.2 12.3 1.0
O B:GLY188 4.3 13.7 1.0
CA B:ILE191 4.3 16.1 1.0
CA B:GLY192 4.3 12.4 1.0
N B:GLY193 4.3 12.3 1.0
CA B:ASP158 4.4 13.6 1.0
N B:ILE159 4.4 13.2 1.0
N B:ILE191 4.4 15.7 1.0
CA B:GLY193 4.4 11.2 1.0
CA B:ILE159 4.5 12.8 1.0
O B:HOH540 4.6 18.5 1.0
N B:LEU160 4.6 12.1 1.0
C B:GLY193 4.6 11.2 1.0
CB B:ASP194 4.6 12.3 1.0
CA B:GLY190 4.6 17.6 1.0
N B:GLY190 4.6 16.9 1.0
O B:HOH475 4.8 33.8 1.0
CA B:ASP194 4.8 10.9 1.0
O B:HOH539 4.8 49.1 1.0
C B:SER189 4.9 15.8 1.0
C B:ILE159 4.9 14.0 1.0

Calcium binding site 5 out of 6 in 6enm

Go back to Calcium Binding Sites List in 6enm
Calcium binding site 5 out of 6 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


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 MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:15.8
occ:1.00
 O B:HOH509 2.3 22.0 1.0
O B:GLU199 2.4 15.2 1.0
OD2 B:ASP124 2.4 19.7 1.0
O B:HOH545 2.4 20.6 1.0
OE2 B:GLU199 2.5 14.2 1.0
O B:GLU201 2.5 15.0 1.0
OD1 B:ASP124 2.6 19.5 1.0
CG B:ASP124 2.8 20.2 1.0
CD B:GLU199 3.5 16.3 1.0
C B:GLU199 3.5 15.7 1.0
C B:GLU201 3.6 17.3 1.0
CG B:GLU199 3.9 17.6 1.0
OG1 B:THR122 4.1 16.6 1.0
CA B:GLU199 4.1 14.0 1.0
CA B:PHE202 4.2 19.1 1.0
CB B:ASP124 4.3 19.7 1.0
CD1 B:TRP203 4.3 14.8 1.0
O B:HOH570 4.4 36.7 1.0
N B:PHE202 4.4 16.0 1.0
O B:HOH426 4.4 27.6 1.0
C B:ASP200 4.4 16.3 1.0
N B:GLU201 4.4 14.9 1.0
N B:ASP200 4.6 13.9 1.0
O B:HOH402 4.6 29.2 1.0
O B:HOH421 4.6 28.9 1.0
OE1 B:GLU199 4.6 17.9 1.0
CB B:GLU199 4.6 15.5 1.0
CA B:GLU201 4.7 14.6 1.0
CA B:ASP200 4.8 16.6 1.0
N B:TRP203 4.8 15.8 1.0
O B:ASP200 4.8 17.7 1.0
CD1 B:PHE202 4.8 23.2 1.0
NE1 B:TRP203 4.9 13.6 1.0
O B:HOH522 4.9 30.8 1.0

Calcium binding site 6 out of 6 in 6enm

Go back to Calcium Binding Sites List in 6enm
Calcium binding site 6 out of 6 in the Crystal Structure of MMP12 in Complex with Hydroxamate Inhibitor LP168.


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 MMP12 in Complex with Hydroxamate Inhibitor LP168. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:12.2
occ:1.00
 O B:GLY176 2.2 15.6 1.0
OD2 B:ASP198 2.3 14.3 1.0
OD1 B:ASP175 2.3 14.8 1.0
OE2 B:GLU201 2.3 25.7 1.0
O B:ILE180 2.3 14.1 1.0
O B:GLY178 2.3 17.4 1.0
CG B:ASP198 3.4 12.7 1.0
C B:ILE180 3.4 12.4 1.0
C B:GLY176 3.5 16.0 1.0
CG B:ASP175 3.5 14.1 1.0
CD B:GLU201 3.5 24.1 1.0
C B:GLY178 3.5 19.1 1.0
N B:ILE180 3.8 14.9 1.0
N B:GLY178 3.9 17.5 1.0
OD2 B:ASP175 4.0 14.2 1.0
CB B:ASP198 4.1 11.9 1.0
N B:GLY176 4.1 15.5 1.0
C B:GLY179 4.1 15.3 1.0
CA B:ILE180 4.1 13.8 1.0
C B:LYS177 4.2 17.9 1.0
OE1 B:GLU201 4.2 21.2 1.0
C B:ASP175 4.3 14.9 1.0
N B:ASP175 4.3 12.9 1.0
CA B:GLY176 4.3 16.7 1.0
OD1 B:ASP198 4.3 12.0 1.0
CA B:GLY178 4.3 19.9 1.0
N B:LYS177 4.4 15.9 1.0
CA B:LYS177 4.4 17.7 1.0
CG B:GLU201 4.4 17.1 1.0
N B:LEU181 4.5 11.3 1.0
N B:GLY179 4.5 17.9 1.0
O B:HOH519 4.5 36.8 1.0
CA B:GLY179 4.6 15.5 1.0
CA B:ASP175 4.6 13.4 1.0
CB B:ILE180 4.6 17.6 1.0
CB B:ASP175 4.6 13.3 1.0
O B:GLY179 4.6 17.2 1.0
O B:ASP175 4.7 14.8 1.0
CA B:LEU181 4.7 12.8 1.0
O B:LYS177 4.8 22.0 1.0

Reference:

E.Nuti, D.Cuffaro, E.Bernardini, C.Camodeca, L.Panelli, S.Chaves, L.Ciccone, L.Tepshi, L.Vera, E.Orlandini, S.Nencetti, E.A.Stura, M.A.Santos, V.Dive, A.Rossello. Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, uc(Nmr), and Crystallographic Studies. J. Med. Chem. V. 61 4421 2018.
ISSN: ISSN 1520-4804
PubMed: 29727184
DOI: 10.1021/ACS.JMEDCHEM.8B00096
Page generated: Mon Jul 15 18:26:39 2024

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