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Calcium in PDB 4h3x: Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain

Enzymatic activity of Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain

All present enzymatic activity of Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain:
3.4.24.35;

Protein crystallography data

The structure of Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4h3x 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) 42.81 / 1.76
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.110, 97.940, 46.080, 90.00, 111.73, 90.00
R / Rfree (%) 19.6 / 25.4

Other elements in 4h3x:

The structure of Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain (pdb code 4h3x). 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 An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain, PDB code: 4h3x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4h3x

Go back to Calcium Binding Sites List in 4h3x
Calcium binding site 1 out of 6 in the Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 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 An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:17.1
occ:1.00
 OD2 A:ASP205 2.2 13.0 1.0
OE2 A:GLU208 2.2 18.9 1.0
O A:GLY183 2.3 20.8 1.0
OD1 A:ASP182 2.3 18.9 1.0
O A:LEU187 2.3 18.1 1.0
O A:ASP185 2.3 18.7 1.0
CG A:ASP205 3.4 13.1 1.0
CD A:GLU208 3.4 18.1 1.0
C A:LEU187 3.4 18.9 1.0
C A:GLY183 3.5 29.1 1.0
CG A:ASP182 3.5 26.9 1.0
C A:ASP185 3.5 26.7 1.0
N A:LEU187 3.8 20.0 1.0
N A:ASP185 3.9 20.6 1.0
C A:LYS184 4.0 17.4 1.0
OD2 A:ASP182 4.1 22.9 1.0
CA A:LEU187 4.1 16.4 1.0
N A:GLY183 4.1 17.7 1.0
CG A:GLU208 4.1 19.1 1.0
CB A:ASP205 4.1 16.7 1.0
C A:GLY186 4.1 22.1 1.0
C A:ASP182 4.3 19.2 1.0
OD1 A:ASP205 4.3 16.5 1.0
CA A:ASP185 4.3 23.8 1.0
N A:ASP182 4.3 18.6 1.0
CA A:LYS184 4.4 18.2 1.0
N A:LYS184 4.4 16.1 1.0
CA A:GLY183 4.4 21.9 1.0
OE1 A:GLU208 4.4 20.3 1.0
O A:LYS184 4.4 22.2 1.0
N A:GLY186 4.5 18.9 1.0
CB A:LEU187 4.5 17.8 1.0
N A:LEU188 4.5 9.8 1.0
CA A:GLY186 4.6 34.2 1.0
CA A:ASP182 4.6 23.7 1.0
O A:GLY186 4.6 22.2 1.0
CB A:ASP182 4.6 19.0 1.0
O A:ASP182 4.7 20.1 1.0
O A:HOH593 4.7 36.7 1.0
CA A:LEU188 4.8 10.3 1.0

Calcium binding site 2 out of 6 in 4h3x

Go back to Calcium Binding Sites List in 4h3x
Calcium binding site 2 out of 6 in the Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 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 An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:20.2
occ:1.00
 O A:ASP206 2.3 16.0 1.0
OD2 A:ASP131 2.3 11.3 1.0
O A:GLU208 2.3 19.3 1.0
O A:HOH453 2.4 19.9 1.0
OD1 A:ASP206 2.4 17.7 1.0
O A:HOH452 2.5 19.5 1.0
OD1 A:ASP131 2.9 25.5 1.0
CG A:ASP131 3.0 20.9 1.0
C A:ASP206 3.2 11.5 1.0
CG A:ASP206 3.4 18.9 1.0
C A:GLU208 3.5 13.4 1.0
CA A:ASP206 3.8 15.9 1.0
OG A:SER129 4.1 14.9 1.0
CB A:ASP206 4.2 12.8 1.0
CD1 A:TRP210 4.2 13.7 1.0
N A:GLU208 4.2 13.7 1.0
CA A:LEU209 4.3 13.3 1.0
OD2 A:ASP206 4.3 18.0 1.0
N A:ASP207 4.3 21.0 1.0
N A:LEU209 4.3 15.0 1.0
O A:HOH511 4.4 33.1 1.0
C A:ASP207 4.4 18.4 1.0
CB A:ASP131 4.4 12.7 1.0
O A:HOH509 4.5 25.0 1.0
CA A:GLU208 4.5 11.8 1.0
CA A:ASP207 4.6 16.3 1.0
N A:TRP210 4.7 13.3 1.0
NE1 A:TRP210 4.8 15.7 1.0
O A:ASP207 4.9 16.8 1.0
O A:HOH494 4.9 24.2 1.0

Calcium binding site 3 out of 6 in 4h3x

Go back to Calcium Binding Sites List in 4h3x
Calcium binding site 3 out of 6 in the Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 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 An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:11.0
occ:1.00
 O A:ASP165 2.3 9.1 1.0
O A:GLY197 2.3 10.1 1.0
O A:HOH411 2.3 7.2 1.0
O A:GLN199 2.3 10.9 1.0
OD1 A:ASP201 2.3 9.6 1.0
O A:HOH406 2.4 11.5 1.0
CG A:ASP201 3.4 13.5 1.0
C A:ASP165 3.5 13.0 1.0
C A:GLN199 3.5 8.4 1.0
C A:GLY197 3.5 18.7 1.0
OD2 A:ASP201 3.9 10.5 1.0
O A:HOH409 4.0 16.0 1.0
O A:ALA164 4.1 11.4 1.0
N A:ASP201 4.1 10.4 1.0
C A:ILE198 4.2 15.3 0.6
C A:ILE198 4.2 15.3 0.4
O A:HOH407 4.2 20.3 1.0
N A:GLN199 4.2 12.4 1.0
CA A:ASP165 4.3 13.6 1.0
N A:GLY197 4.3 14.9 1.0
C A:GLY200 4.3 10.0 1.0
O A:GLY195 4.3 10.3 1.0
CA A:GLY197 4.3 15.3 1.0
O A:ILE198 4.3 14.2 0.4
O A:ILE198 4.4 14.2 0.6
CA A:GLY200 4.4 13.3 1.0
N A:GLY200 4.4 9.9 1.0
CA A:GLN199 4.5 12.6 1.0
N A:ILE166 4.5 7.5 1.0
N A:ILE198 4.5 12.2 0.6
N A:ILE198 4.5 12.3 0.4
CB A:ASP201 4.6 12.1 1.0
CA A:ILE198 4.6 14.3 0.6
N A:VAL167 4.6 8.5 1.0
CA A:ILE198 4.6 14.3 0.4
CA A:ILE166 4.7 12.6 1.0
CA A:ASP201 4.7 10.1 1.0
C A:PRO196 4.7 15.8 1.0
O A:HOH412 4.8 16.2 1.0
CH2 A:TRP116 4.8 11.9 1.0
O A:GLY200 4.9 13.1 1.0

Calcium binding site 4 out of 6 in 4h3x

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Calcium binding site 4 out of 6 in the Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 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 An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:19.4
occ:1.00
 OE2 B:GLU208 2.2 22.5 1.0
O B:LEU187 2.3 22.6 1.0
OD2 B:ASP205 2.3 15.7 1.0
O B:GLY183 2.3 24.6 1.0
OD1 B:ASP182 2.4 21.9 1.0
O B:ASP185 2.4 22.2 1.0
CG B:ASP205 3.4 21.6 1.0
CD B:GLU208 3.4 24.2 1.0
C B:LEU187 3.4 23.0 1.0
C B:ASP185 3.5 30.5 1.0
CG B:ASP182 3.5 27.7 1.0
C B:GLY183 3.5 28.6 1.0
N B:LEU187 3.8 22.0 1.0
N B:ASP185 3.8 32.5 1.0
OD2 B:ASP182 4.0 25.0 1.0
CA B:LEU187 4.1 18.4 1.0
C B:LYS184 4.1 30.1 1.0
CB B:ASP205 4.1 18.5 1.0
N B:GLY183 4.1 24.0 1.0
CA B:ASP185 4.1 29.5 1.0
CG B:GLU208 4.1 19.8 1.0
N B:ASP182 4.2 19.5 1.0
C B:ASP182 4.2 20.6 1.0
C B:GLY186 4.2 24.7 1.0
OD1 B:ASP205 4.3 17.0 1.0
OE1 B:GLU208 4.4 23.1 1.0
CB B:LEU187 4.4 20.9 1.0
CA B:GLY183 4.4 20.2 1.0
N B:LYS184 4.5 25.4 1.0
O B:LYS184 4.5 30.7 1.0
CA B:LYS184 4.5 23.8 1.0
N B:GLY186 4.5 26.1 1.0
N B:LEU188 4.5 11.6 1.0
O B:ASP182 4.6 25.1 1.0
CA B:ASP182 4.6 27.0 1.0
CB B:ASP182 4.7 18.5 1.0
CA B:GLY186 4.7 14.8 1.0
O B:GLY186 4.8 20.2 1.0
CA B:LEU188 4.8 14.8 1.0

Calcium binding site 5 out of 6 in 4h3x

Go back to Calcium Binding Sites List in 4h3x
Calcium binding site 5 out of 6 in the Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 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 An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:33.7
occ:1.00
 OD2 B:ASP131 2.4 20.0 1.0
O B:GLU208 2.4 21.1 1.0
O B:ASP206 2.4 21.8 1.0
OD1 B:ASP206 2.5 18.4 1.0
O B:HOH468 2.5 28.5 1.0
O B:HOH529 2.5 38.2 1.0
OD1 B:ASP131 2.9 28.7 1.0
CG B:ASP131 3.0 28.6 1.0
C B:ASP206 3.4 18.4 1.0
CG B:ASP206 3.5 18.1 1.0
C B:GLU208 3.5 27.5 1.0
CA B:ASP206 3.9 14.6 1.0
OG B:SER129 4.0 19.4 1.0
CA B:LEU209 4.2 26.2 1.0
N B:LEU209 4.2 18.1 1.0
CB B:ASP206 4.3 12.6 1.0
OD2 B:ASP206 4.3 22.6 1.0
N B:GLU208 4.3 20.6 1.0
CD1 B:TRP210 4.3 14.5 1.0
N B:ASP207 4.4 23.9 1.0
CB B:ASP131 4.4 14.7 1.0
C B:ASP207 4.5 28.0 1.0
CA B:GLU208 4.5 18.7 1.0
N B:TRP210 4.6 15.5 1.0
O B:HOH459 4.6 31.1 1.0
CA B:ASP207 4.7 22.0 1.0
O B:HOH414 4.7 23.4 1.0
NE1 B:TRP210 4.9 15.3 1.0
C B:LEU209 4.9 18.1 1.0

Calcium binding site 6 out of 6 in 4h3x

Go back to Calcium Binding Sites List in 4h3x
Calcium binding site 6 out of 6 in the Crystal Structure of An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 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 An Mmp Broad Spectrum Hydroxamate Based Inhibitor CC27 in Complex with the Mmp-9 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:11.9
occ:1.00
 O B:HOH401 2.3 11.1 1.0
O B:ASP165 2.3 14.6 1.0
O B:HOH405 2.4 11.9 1.0
OD1 B:ASP201 2.4 11.9 1.0
O B:GLN199 2.4 14.7 1.0
O B:GLY197 2.5 9.9 1.0
CG B:ASP201 3.5 13.9 1.0
C B:ASP165 3.5 11.4 1.0
C B:GLN199 3.6 18.5 1.0
C B:GLY197 3.6 13.6 1.0
OD2 B:ASP201 4.0 14.3 1.0
O B:HOH406 4.0 18.9 1.0
O B:HOH404 4.0 16.9 1.0
N B:ASP201 4.1 11.2 1.0
O B:ALA164 4.1 15.1 1.0
C B:ILE198 4.2 16.3 1.0
O B:ILE198 4.3 15.7 1.0
C B:GLY200 4.3 12.6 1.0
CA B:ASP165 4.3 11.9 1.0
N B:GLN199 4.3 13.7 1.0
N B:GLY197 4.3 8.7 1.0
O B:GLY195 4.3 13.3 1.0
CA B:GLY200 4.3 10.3 1.0
N B:GLY200 4.4 14.2 1.0
CA B:GLY197 4.4 14.8 1.0
N B:ILE166 4.5 9.6 1.0
CA B:GLN199 4.5 11.2 1.0
N B:VAL167 4.6 10.6 1.0
CB B:ASP201 4.6 8.3 1.0
N B:ILE198 4.6 14.4 1.0
CA B:ILE166 4.6 13.6 1.0
CA B:ASP201 4.7 12.7 1.0
CA B:ILE198 4.7 12.8 1.0
O B:HOH402 4.7 12.9 1.0
C B:PRO196 4.8 13.6 1.0
CH2 B:TRP116 4.9 18.1 1.0
O B:GLY200 4.9 11.2 1.0
CG2 B:VAL167 5.0 17.3 1.0

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sat Dec 12 04:49:45 2020

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