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Zinc in PDB 4h76: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor, PDB code: 4h76 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) 46.76 / 1.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.920, 62.890, 37.700, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.8

Other elements in 4h76:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor (pdb code 4h76). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor, PDB code: 4h76:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4h76

Go back to Zinc Binding Sites List in 4h76
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor


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 the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.7
occ:1.00
 NE2 A:HIS228 2.0 9.7 1.0
NE2 A:HIS218 2.0 9.4 1.0
NE2 A:HIS222 2.0 7.0 1.0
O2 A:10B306 2.1 16.3 0.8
O7 A:10B306 2.3 9.4 0.8
C11 A:10B306 2.9 19.8 0.8
CE1 A:HIS228 3.0 15.4 1.0
CE1 A:HIS218 3.0 12.4 1.0
CD2 A:HIS222 3.0 10.2 1.0
CD2 A:HIS218 3.0 8.2 1.0
CE1 A:HIS222 3.1 8.0 1.0
CD2 A:HIS228 3.1 8.4 1.0
N2 A:10B306 3.1 12.6 0.8
ND1 A:HIS218 4.1 8.9 1.0
ND1 A:HIS228 4.1 16.3 1.0
O A:HOH458 4.2 11.5 1.0
ND1 A:HIS222 4.2 10.0 1.0
CG A:HIS218 4.2 6.1 1.0
CG A:HIS222 4.2 8.4 1.0
CG A:HIS228 4.2 9.5 1.0
C31 A:10B306 4.4 20.7 0.8
OE2 A:GLU219 4.4 11.5 1.0
N12 A:10B306 4.7 37.8 0.8
O15 A:10B306 4.7 37.3 0.8
O A:HOH581 4.8 26.6 1.0
C29 A:10B306 4.9 12.4 0.8
CE A:MET236 5.0 9.2 1.0

Zinc binding site 2 out of 2 in 4h76

Go back to Zinc Binding Sites List in 4h76
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor


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 the Catalytic Domain of Human MMP12 in Complex with A Broad Spectrum Hydroxamate Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:9.4
occ:1.00
 OD2 A:ASP170 2.0 12.6 1.0
NE2 A:HIS168 2.0 7.6 1.0
NE2 A:HIS183 2.0 8.4 1.0
ND1 A:HIS196 2.1 10.2 1.0
CG A:ASP170 2.9 15.3 1.0
CE1 A:HIS183 2.9 11.1 1.0
CE1 A:HIS196 3.0 11.1 1.0
CD2 A:HIS168 3.0 8.4 1.0
CE1 A:HIS168 3.0 7.6 1.0
CD2 A:HIS183 3.1 7.8 1.0
CG A:HIS196 3.1 8.8 1.0
OD1 A:ASP170 3.2 12.4 1.0
CB A:HIS196 3.5 9.0 1.0
ND1 A:HIS168 4.1 9.1 1.0
ND1 A:HIS183 4.1 8.6 1.0
CG A:HIS168 4.1 8.9 1.0
NE2 A:HIS196 4.1 9.6 1.0
CG A:HIS183 4.2 9.4 1.0
CD2 A:HIS196 4.2 9.9 1.0
CE2 A:PHE185 4.2 14.4 1.0
O A:HIS172 4.3 13.0 1.0
CB A:ASP170 4.3 14.8 1.0
CZ A:PHE185 4.7 15.5 1.0
CZ A:PHE174 4.7 10.2 1.0
CE2 A:PHE174 4.8 9.0 1.0
O A:HOH476 4.9 12.0 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 23:54:32 2024

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