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Zinc in PDB 3lk8: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate, PDB code: 3lk8 was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.81 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.708, 60.251, 54.144, 90.00, 115.16, 90.00
R / Rfree (%) 16.8 / 20

Other elements in 3lk8:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate 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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate (pdb code 3lk8). 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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate, PDB code: 3lk8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3lk8

Go back to Zinc Binding Sites List in 3lk8
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate


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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:6.5
occ:1.00
 NE2 A:HIS218 2.0 2.7 1.0
NE2 A:HIS228 2.1 6.5 1.0
O4 A:Z790 2.1 10.2 1.0
NE2 A:HIS222 2.1 2.9 1.0
O5 A:Z790 2.3 5.3 1.0
C8 A:Z790 2.9 10.7 1.0
N2 A:Z790 3.0 8.2 1.0
CD2 A:HIS218 3.0 3.4 1.0
CE1 A:HIS228 3.1 6.7 1.0
CD2 A:HIS222 3.1 2.0 1.0
CE1 A:HIS218 3.1 2.8 1.0
CD2 A:HIS228 3.1 6.9 1.0
CE1 A:HIS222 3.2 4.6 1.0
O A:HOH9 4.0 7.1 1.0
OE1 A:GLU219 4.1 6.3 1.0
CG A:HIS218 4.1 3.5 1.0
ND1 A:HIS218 4.2 4.4 1.0
ND1 A:HIS228 4.2 6.0 1.0
CG A:HIS222 4.2 3.8 1.0
CG A:HIS228 4.3 6.7 1.0
ND1 A:HIS222 4.3 3.5 1.0
C7 A:Z790 4.3 10.7 1.0
O A:HOH57 4.7 21.6 1.0
C6 A:Z790 4.8 14.2 1.0
CE A:MET236 4.9 4.8 1.0
N1 A:Z790 4.9 11.6 1.0
CD A:GLU219 4.9 3.9 1.0
O A:HOH317 4.9 27.0 1.0
O A:HOH319 4.9 15.0 1.0
OE2 A:GLU219 5.0 5.9 1.0

Zinc binding site 2 out of 2 in 3lk8

Go back to Zinc Binding Sites List in 3lk8
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate


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 Complexed with the Inhibitor Paramethoxy-Sulfonyl-Glycine Hydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:9.0
occ:1.00
 OD1 A:ASP170 1.9 5.7 0.7
NE2 A:HIS183 1.9 10.2 1.0
ND1 A:HIS196 2.1 4.3 1.0
NE2 A:HIS168 2.1 6.7 1.0
CE1 A:HIS183 2.8 13.9 1.0
CG A:ASP170 2.9 11.8 0.7
CD2 A:HIS168 2.9 7.7 1.0
CE1 A:HIS196 3.0 4.0 1.0
CD2 A:HIS183 3.0 11.6 1.0
CG A:HIS196 3.1 5.2 1.0
OD2 A:ASP170 3.1 7.6 0.7
CE1 A:HIS168 3.2 9.2 1.0
CB A:HIS196 3.5 5.5 1.0
ND1 A:HIS183 4.0 13.9 1.0
CG A:HIS183 4.1 7.3 1.0
CG A:HIS168 4.1 9.2 1.0
NE2 A:HIS196 4.1 5.2 1.0
CD2 A:HIS196 4.2 4.4 1.0
ND1 A:HIS168 4.2 7.5 1.0
O A:HIS172 4.2 15.0 1.0
CB A:ASP170 4.3 13.6 0.7
CE2 A:PHE185 4.4 14.6 1.0
CB A:HIS172 4.5 16.8 1.0
CZ A:PHE185 4.5 13.5 1.0
CZ A:PHE174 4.6 5.5 1.0
CE1 A:PHE174 4.6 6.0 1.0
O A:HOH38 4.9 8.5 1.0
C A:HIS172 4.9 14.7 1.0
CA A:HIS196 5.0 5.2 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, A.Giachetti, M.Loconte, C.Luchinat, M.Maletta, C.Nativi, K.J.Yeo. Exploring the Subtleties of Drug-Receptor Interactions: the Case of Matrix Metalloproteinases J.Am.Chem.Soc. V. 129 2466 2007.
ISSN: ISSN 0002-7863
PubMed: 17269766
Page generated: Sat Oct 26 08:41:04 2024

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