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Zinc in PDB 3ljg: Human MMP12 in Complex with Non-Zinc Chelating Inhibitor

Enzymatic activity of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor

All present enzymatic activity of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor:
3.4.24.65;

Protein crystallography data

The structure of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor, PDB code: 3ljg was solved by E.A.Stura, V.Dive, L.Devel, L.Vera, F.Beau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.59 / 1.31
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.090, 62.820, 37.550, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.5

Other elements in 3ljg:

The structure of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor (pdb code 3ljg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor, PDB code: 3ljg:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3ljg

Go back to Zinc Binding Sites List in 3ljg
Zinc binding site 1 out of 2 in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:7.0
occ:1.00
NE2 A:HIS218 2.1 6.2 1.0
O A:HAE301 2.1 6.7 0.7
NE2 A:HIS222 2.1 6.3 1.0
NE2 A:HIS228 2.1 7.3 1.0
O2 A:HAE301 2.2 10.3 0.7
O A:HAE301 2.3 15.1 0.3
O2 A:HAE301 2.4 8.8 0.3
N A:HAE301 2.5 9.9 0.3
C2 A:HAE301 2.7 8.7 0.3
C2 A:HAE301 2.9 9.8 0.7
N A:HAE301 2.9 7.8 0.7
CD2 A:HIS222 3.0 7.4 1.0
CD2 A:HIS218 3.1 7.7 1.0
CE1 A:HIS228 3.1 11.0 1.0
CE1 A:HIS218 3.1 7.9 1.0
CD2 A:HIS228 3.1 8.3 1.0
CE1 A:HIS222 3.1 8.4 1.0
C1 A:HAE301 3.8 11.1 0.3
C1 A:EEF302 4.0 12.9 1.0
O A:HOH1 4.0 9.6 1.0
O A:HOH340 4.2 20.5 1.0
ND1 A:HIS218 4.2 7.2 1.0
ND1 A:HIS228 4.2 11.8 1.0
CG A:HIS218 4.2 7.1 1.0
CG A:HIS222 4.2 8.2 1.0
OE1 A:GLU219 4.2 6.7 1.0
ND1 A:HIS222 4.2 8.3 1.0
CG A:HIS228 4.2 9.6 1.0
C1 A:HAE301 4.4 11.8 0.7
O A:HOH91 4.5 31.9 1.0
C14 A:EEF302 4.6 11.1 1.0
OE2 A:GLU219 4.9 8.5 1.0
O A:HOH61 4.9 15.9 1.0
CD A:GLU219 4.9 7.4 1.0
CE A:MET236 4.9 7.6 1.0

Zinc binding site 2 out of 2 in 3ljg

Go back to Zinc Binding Sites List in 3ljg
Zinc binding site 2 out of 2 in the Human MMP12 in Complex with Non-Zinc Chelating Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human MMP12 in Complex with Non-Zinc Chelating Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:8.0
occ:1.00
NE2 A:HIS183 2.0 9.7 1.0
OD1 A:ASP170 2.0 9.3 1.0
NE2 A:HIS168 2.0 7.6 1.0
ND1 A:HIS196 2.1 7.8 1.0
CE1 A:HIS183 2.8 9.6 1.0
CG A:ASP170 2.9 9.3 1.0
CD2 A:HIS168 2.9 7.0 1.0
CE1 A:HIS196 3.0 9.9 1.0
CE1 A:HIS168 3.0 8.1 1.0
CG A:HIS196 3.1 7.2 1.0
CD2 A:HIS183 3.1 12.2 1.0
OD2 A:ASP170 3.1 10.0 1.0
CB A:HIS196 3.5 7.9 1.0
ND1 A:HIS183 4.0 12.3 1.0
CG A:HIS168 4.1 8.0 1.0
ND1 A:HIS168 4.1 8.0 1.0
NE2 A:HIS196 4.1 8.9 1.0
CG A:HIS183 4.2 8.6 1.0
CD2 A:HIS196 4.2 7.9 1.0
O A:HIS172 4.3 12.4 1.0
CB A:ASP170 4.3 10.4 1.0
O A:HOH366 4.5 22.6 1.0
CE2 A:PHE185 4.5 14.6 1.0
CB A:HIS172 4.6 13.7 1.0
CZ A:PHE174 4.7 8.7 1.0
CZ A:PHE185 4.8 13.7 1.0
O A:HOH3 4.9 10.9 1.0
CE1 A:PHE174 5.0 8.4 1.0
CA A:HIS196 5.0 7.3 1.0

Reference:

L.Devel, S.Garcia, B.Czarny, F.Beau, E.Lajeunesse, L.Vera, D.Georgiadis, E.Stura, V.Dive. Insights From Selective Non-Phosphinic Inhibitors of Mmp-12 Tailored to Fit with An S1' Loop Canonical Conformation. J.Biol.Chem. V. 285 35900 2010.
ISSN: ISSN 0021-9258
PubMed: 20817735
DOI: 10.1074/JBC.M110.139634
Page generated: Wed Dec 16 04:32:26 2020

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