Atomistry » Zinc » PDB 4ggg-4gsk » 4gr3
Atomistry »
  Zinc »
    PDB 4ggg-4gsk »
      4gr3 »

Zinc in PDB 4gr3: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A, PDB code: 4gr3 was solved by E.A.Stura, L.Vera, F.Beau, L.Devel, E.Cassar-Lajeunesse, V.Dive, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.56 / 1.49
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.960, 63.130, 37.310, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.6

Other elements in 4gr3:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A also contains other interesting chemical elements:

Bromine (Br) 1 atom
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 Selective Phosphinic Inhibitor RXP470A (pdb code 4gr3). 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 Selective Phosphinic Inhibitor RXP470A, PDB code: 4gr3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gr3

Go back to Zinc Binding Sites List in 4gr3
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A


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 Selective Phosphinic Inhibitor RXP470A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.3
occ:1.00
O3 A:R45306 1.9 8.5 1.0
NE2 A:HIS228 2.0 10.7 1.0
NE2 A:HIS218 2.0 8.2 1.0
NE2 A:HIS222 2.1 7.8 1.0
CE1 A:HIS228 2.9 17.3 1.0
CE1 A:HIS218 2.9 10.7 1.0
CD2 A:HIS228 3.0 14.1 1.0
CE1 A:HIS222 3.0 10.1 1.0
P1 A:R45306 3.0 10.5 1.0
CD2 A:HIS218 3.0 6.4 1.0
CD2 A:HIS222 3.1 10.0 1.0
O2 A:R45306 3.3 9.9 1.0
ND1 A:HIS228 4.1 12.4 1.0
ND1 A:HIS218 4.1 8.8 1.0
O A:HOH512 4.1 15.1 1.0
CG A:HIS228 4.1 11.7 1.0
ND1 A:HIS222 4.2 8.3 1.0
CG A:HIS218 4.2 7.1 1.0
CG A:HIS222 4.2 7.0 1.0
C19 A:R45306 4.2 15.5 1.0
C18 A:R45306 4.3 10.6 1.0
C20 A:R45306 4.3 20.2 1.0
C17 A:R45306 4.3 9.1 1.0
C16 A:R45306 4.6 10.5 1.0
CE A:MET236 4.7 10.1 1.0
O A:HOH588 4.7 28.4 1.0
O A:HOH401 4.8 10.6 1.0
O A:PRO238 4.9 11.9 1.0
OE1 A:GLU219 4.9 9.9 1.0
C14 A:R45306 4.9 7.5 1.0
C15 A:R45306 5.0 7.2 1.0

Zinc binding site 2 out of 2 in 4gr3

Go back to Zinc Binding Sites List in 4gr3
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470A


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 Selective Phosphinic Inhibitor RXP470A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:8.6
occ:1.00
OD1 A:ASP170 1.9 11.1 1.0
NE2 A:HIS168 2.0 7.8 1.0
NE2 A:HIS183 2.0 9.2 1.0
ND1 A:HIS196 2.0 8.7 1.0
CG A:ASP170 2.8 12.8 1.0
CD2 A:HIS168 2.9 8.3 1.0
CE1 A:HIS183 2.9 8.7 1.0
CE1 A:HIS196 2.9 9.0 1.0
OD2 A:ASP170 3.0 11.5 1.0
CE1 A:HIS168 3.0 8.3 1.0
CG A:HIS196 3.1 7.3 1.0
CD2 A:HIS183 3.1 11.1 1.0
CB A:HIS196 3.5 7.7 1.0
ND1 A:HIS183 4.0 9.6 1.0
CG A:HIS168 4.1 8.5 1.0
ND1 A:HIS168 4.1 10.7 1.0
NE2 A:HIS196 4.1 9.3 1.0
O A:HIS172 4.1 9.7 1.0
CG A:HIS183 4.2 8.4 1.0
CD2 A:HIS196 4.2 7.2 1.0
CB A:ASP170 4.2 12.8 1.0
CE2 A:PHE185 4.6 10.3 1.0
O A:HOH616 4.7 32.3 1.0
CZ A:PHE174 4.8 10.0 1.0
CB A:HIS172 4.8 16.3 1.0
O A:HOH403 4.8 11.4 1.0
CZ A:PHE185 4.9 9.9 1.0
CE1 A:PHE174 5.0 8.8 1.0
C A:HIS172 5.0 13.9 1.0
CA A:HIS196 5.0 6.1 1.0

Reference:

B.Czarny, E.A.Stura, L.Devel, L.Vera, E.Cassar-Lajeunesse, F.Beau, V.Calderone, M.Fragai, C.Luchinat, V.Dive. Molecular Determinants of A Selective Matrix Metalloprotease-12 Inhibitor: Insights From Crystallography and Thermodynamic Studies. J.Med.Chem. V. 56 1149 2013.
ISSN: ISSN 0022-2623
PubMed: 23343195
DOI: 10.1021/JM301574D
Page generated: Sat Oct 26 23:26:17 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy