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Zinc in PDB 4efs: Human MMP12 in Complex with L-Glutamate Motif Inhibitor

Enzymatic activity of Human MMP12 in Complex with L-Glutamate Motif Inhibitor

All present enzymatic activity of Human MMP12 in Complex with L-Glutamate Motif Inhibitor:
3.4.24.65;

Protein crystallography data

The structure of Human MMP12 in Complex with L-Glutamate Motif Inhibitor, PDB code: 4efs was solved by E.A.Stura, V.Dive, L.Devel, B.Czarny, F.Beau, L.Vera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.59 / 1.63
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.970, 63.190, 37.510, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19

Other elements in 4efs:

The structure of Human MMP12 in Complex with L-Glutamate Motif 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 L-Glutamate Motif Inhibitor (pdb code 4efs). 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 L-Glutamate Motif Inhibitor, PDB code: 4efs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4efs

Go back to Zinc Binding Sites List in 4efs
Zinc binding site 1 out of 2 in the Human MMP12 in Complex with L-Glutamate Motif 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 L-Glutamate Motif Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:13.2
occ:1.00
NE2 A:HIS218 2.0 13.8 1.0
NE2 A:HIS222 2.0 14.1 1.0
NE2 A:HIS228 2.0 14.1 1.0
O4 A:E37306 2.2 16.4 1.0
C10 A:E37306 2.6 19.6 1.0
O4E A:E37306 2.7 19.8 1.0
CE1 A:HIS228 3.0 19.6 1.0
CD2 A:HIS222 3.0 13.1 1.0
CE1 A:HIS218 3.0 12.6 1.0
CD2 A:HIS218 3.0 13.4 1.0
CD2 A:HIS228 3.0 16.4 1.0
CE1 A:HIS222 3.1 13.3 1.0
C9 A:E37306 4.1 14.8 1.0
ND1 A:HIS228 4.1 19.4 1.0
ND1 A:HIS218 4.1 12.6 1.0
CG A:HIS218 4.2 12.0 1.0
CG A:HIS222 4.2 12.0 1.0
ND1 A:HIS222 4.2 14.8 1.0
CG A:HIS228 4.2 17.3 1.0
C28 A:E37306 4.4 17.3 1.0
N2 A:E37306 4.4 17.5 1.0
O1 A:PGR309 4.4 31.3 1.0
O A:HOH438 4.6 16.4 1.0
CE A:MET236 4.6 17.6 1.0
OE2 A:GLU219 4.6 13.7 1.0
C8 A:E37306 4.7 17.6 1.0
C27 A:E37306 4.8 17.2 1.0
O A:HOH517 4.8 38.9 1.0
C2 A:EDO308 4.9 36.8 1.0
C15 A:E37306 5.0 15.3 1.0
C11 A:E37306 5.0 20.5 1.0

Zinc binding site 2 out of 2 in 4efs

Go back to Zinc Binding Sites List in 4efs
Zinc binding site 2 out of 2 in the Human MMP12 in Complex with L-Glutamate Motif 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 L-Glutamate Motif Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:13.5
occ:1.00
OD1 A:ASP170 1.9 13.2 1.0
NE2 A:HIS168 2.1 11.2 1.0
ND1 A:HIS196 2.1 12.3 1.0
NE2 A:HIS183 2.1 14.2 1.0
CG A:ASP170 2.9 21.1 1.0
CD2 A:HIS168 2.9 13.0 1.0
CE1 A:HIS183 3.0 15.2 1.0
CE1 A:HIS196 3.0 12.7 1.0
CE1 A:HIS168 3.1 11.1 1.0
CG A:HIS196 3.1 13.0 1.0
OD2 A:ASP170 3.2 18.0 1.0
CD2 A:HIS183 3.2 12.9 1.0
CB A:HIS196 3.5 12.7 1.0
CG A:HIS168 4.1 13.9 1.0
ND1 A:HIS183 4.2 13.9 1.0
NE2 A:HIS196 4.2 14.9 1.0
ND1 A:HIS168 4.2 11.7 1.0
CD2 A:HIS196 4.2 12.8 1.0
CB A:ASP170 4.2 18.8 1.0
CE2 A:PHE185 4.2 20.5 1.0
CG A:HIS183 4.3 12.5 1.0
O A:HIS172 4.3 15.6 1.0
CZ A:PHE174 4.6 14.4 1.0
CZ A:PHE185 4.7 17.1 1.0
O A:HOH418 4.9 16.1 1.0
CE2 A:PHE174 4.9 12.5 1.0
CE1 A:PHE174 5.0 14.2 1.0

Reference:

L.Devel, F.Beau, M.Amoura, L.Vera, E.Cassar-Lajeunesse, S.Garcia, B.Czarny, E.A.Stura, V.Dive. Simple Pseudo-Dipeptides with A P2' Glutamate: A Novel Inhibitor Family of Matrix Metalloproteases and Other Metzincins. J.Biol.Chem. V. 287 26647 2012.
ISSN: ISSN 0021-9258
PubMed: 22689580
DOI: 10.1074/JBC.M112.380782
Page generated: Wed Dec 16 05:16:00 2020

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