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Zinc 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:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4h3x

Go back to Zinc Binding Sites List in 4h3x
Zinc binding site 1 out of 4 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 Zinc with other atoms in the Zn 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:Zn301

b:10.9
occ:1.00
 NE2 A:HIS226 2.0 8.0 1.0
O7 A:10B306 2.0 23.3 1.0
NE2 A:HIS230 2.1 7.5 1.0
NE2 A:HIS236 2.2 11.1 1.0
O2 A:10B306 2.4 27.1 1.0
N2 A:10B306 2.8 19.2 1.0
CD2 A:HIS230 2.9 5.5 1.0
CD2 A:HIS226 2.9 6.2 1.0
C11 A:10B306 2.9 17.1 1.0
CE1 A:HIS226 3.0 9.5 1.0
CD2 A:HIS236 3.1 4.5 1.0
CE1 A:HIS236 3.2 8.9 1.0
CE1 A:HIS230 3.3 13.3 1.0
O A:HOH415 4.0 12.3 1.0
CG A:HIS226 4.1 6.7 1.0
ND1 A:HIS226 4.1 6.5 1.0
CG A:HIS230 4.1 14.3 1.0
ND1 A:HIS230 4.3 9.4 1.0
ND1 A:HIS236 4.3 13.2 1.0
CG A:HIS236 4.3 20.8 1.0
OE2 A:GLU227 4.3 14.1 1.0
C31 A:10B306 4.3 32.5 1.0
C14 A:10B306 4.6 12.7 1.0
C17 A:10B306 4.6 11.6 1.0
N12 A:10B306 4.7 27.5 1.0
C28 A:10B306 4.8 13.1 1.0
OE1 A:GLU227 4.9 12.3 1.0
C16 A:10B306 5.0 11.2 1.0
CD A:GLU227 5.0 12.4 1.0
CE A:MET244 5.0 5.5 1.0

Zinc binding site 2 out of 4 in 4h3x

Go back to Zinc Binding Sites List in 4h3x
Zinc binding site 2 out of 4 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 Zinc with other atoms in the Zn 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:Zn302

b:15.8
occ:1.00
 NE2 A:HIS190 1.9 12.0 1.0
ND1 A:HIS203 2.0 12.8 1.0
OD1 A:ASP177 2.0 23.0 1.0
NE2 A:HIS175 2.2 11.4 1.0
CE1 A:HIS190 2.8 20.6 1.0
CG A:ASP177 2.9 27.8 1.0
CE1 A:HIS203 2.9 20.5 1.0
CD2 A:HIS175 3.1 11.3 1.0
CD2 A:HIS190 3.1 10.9 1.0
CG A:HIS203 3.1 15.1 1.0
OD2 A:ASP177 3.1 26.1 1.0
CE1 A:HIS175 3.2 19.2 1.0
CB A:HIS203 3.5 11.0 1.0
ND1 A:HIS190 4.0 18.9 1.0
NE2 A:HIS203 4.1 13.5 1.0
O A:TYR179 4.1 24.4 1.0
CG A:HIS190 4.1 8.9 1.0
CD2 A:HIS203 4.2 13.3 1.0
CG A:HIS175 4.2 14.9 1.0
CB A:ASP177 4.3 22.2 1.0
ND1 A:HIS175 4.3 18.6 1.0
CE1 A:PHE192 4.3 21.1 1.0
CZ A:PHE192 4.4 15.9 1.0
CZ A:PHE181 4.5 10.4 1.0
CE2 A:PHE181 4.7 17.6 1.0
O A:HOH445 4.9 17.9 1.0
CA A:HIS203 5.0 16.0 1.0

Zinc binding site 3 out of 4 in 4h3x

Go back to Zinc Binding Sites List in 4h3x
Zinc binding site 3 out of 4 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 Zinc with other atoms in the Zn 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
B:Zn301

b:11.3
occ:1.00
 NE2 B:HIS236 2.1 13.6 1.0
NE2 B:HIS230 2.1 18.9 1.0
NE2 B:HIS226 2.1 12.2 1.0
O2 B:10B306 2.2 21.1 1.0
O7 B:10B306 2.3 24.2 1.0
CD2 B:HIS230 3.0 6.5 1.0
C11 B:10B306 3.0 18.9 1.0
N2 B:10B306 3.0 21.0 1.0
CD2 B:HIS236 3.0 8.8 1.0
CD2 B:HIS226 3.1 11.7 1.0
CE1 B:HIS236 3.1 17.8 1.0
CE1 B:HIS230 3.1 22.5 1.0
CE1 B:HIS226 3.2 10.5 1.0
O B:HOH444 4.1 15.8 1.0
CG B:HIS230 4.2 13.4 1.0
ND1 B:HIS236 4.2 17.5 1.0
CG B:HIS236 4.2 16.4 1.0
ND1 B:HIS230 4.2 14.6 1.0
CG B:HIS226 4.2 10.1 1.0
ND1 B:HIS226 4.2 9.1 1.0
OE2 B:GLU227 4.3 18.7 1.0
C31 B:10B306 4.4 21.4 1.0
C14 B:10B306 4.6 15.0 1.0
N12 B:10B306 4.7 34.2 1.0
C17 B:10B306 4.8 15.1 1.0
C28 B:10B306 5.0 13.8 1.0

Zinc binding site 4 out of 4 in 4h3x

Go back to Zinc Binding Sites List in 4h3x
Zinc binding site 4 out of 4 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 Zinc with other atoms in the Zn 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:Zn302

b:16.7
occ:1.00
 OD1 B:ASP177 2.0 17.6 1.0
ND1 B:HIS203 2.0 14.2 1.0
NE2 B:HIS190 2.1 15.9 1.0
NE2 B:HIS175 2.1 16.4 1.0
CD2 B:HIS175 2.8 18.4 1.0
CG B:ASP177 2.9 28.6 1.0
CE1 B:HIS203 2.9 18.9 1.0
CE1 B:HIS190 3.0 20.2 1.0
CG B:HIS203 3.1 13.5 1.0
CD2 B:HIS190 3.2 17.7 1.0
OD2 B:ASP177 3.2 27.5 1.0
CE1 B:HIS175 3.3 22.6 1.0
CB B:HIS203 3.5 16.9 1.0
CG B:HIS175 4.1 23.2 1.0
NE2 B:HIS203 4.1 17.5 1.0
ND1 B:HIS190 4.1 17.3 1.0
CD2 B:HIS203 4.2 9.9 1.0
O B:TYR179 4.2 26.1 1.0
CB B:ASP177 4.2 30.8 1.0
ND1 B:HIS175 4.2 23.1 1.0
CG B:HIS190 4.3 22.7 1.0
CE1 B:PHE192 4.4 28.7 1.0
CZ B:PHE192 4.4 15.5 1.0
CZ B:PHE181 4.6 24.5 1.0
O B:HOH447 4.7 24.8 1.0
CE2 B:PHE181 4.8 16.1 1.0
CB B:TYR179 5.0 27.6 1.0
CA B:HIS203 5.0 16.0 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 Oct 26 23:52:47 2024

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