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Zinc in PDB 4gql: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1:
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 RXP470.1, PDB code: 4gql 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) 32.60 / 1.15
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.580, 63.390, 36.900, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 15.4

Other elements in 4gql:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1 also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Calcium (Ca) 3 atoms
Chlorine (Cl) 2 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 RXP470.1 (pdb code 4gql). 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 RXP470.1, PDB code: 4gql:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gql

Go back to Zinc Binding Sites List in 4gql
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1


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 RXP470.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:8.9
occ:1.00
O2 A:R47306 1.8 8.5 0.4
O2 A:R47306 1.8 8.5 0.6
NE2 A:HIS228 2.0 9.3 1.0
NE2 A:HIS222 2.0 8.8 1.0
NE2 A:HIS218 2.0 8.1 1.0
CE1 A:HIS222 2.9 11.6 1.0
CE1 A:HIS218 3.0 9.2 1.0
CE1 A:HIS228 3.0 10.3 1.0
CD2 A:HIS228 3.0 10.6 1.0
CD2 A:HIS218 3.1 7.9 1.0
CD2 A:HIS222 3.1 8.5 1.0
P1 A:R47306 3.1 7.8 0.4
P1 A:R47306 3.1 8.2 0.6
HE1 A:HIS222 3.1 13.9 1.0
HE1 A:HIS218 3.1 11.0 1.0
HD2 A:HIS228 3.2 12.7 1.0
HE1 A:HIS228 3.2 12.4 1.0
HD2 A:HIS218 3.3 9.5 1.0
HD2 A:HIS222 3.3 10.2 1.0
O3 A:R47306 3.3 7.2 0.4
O3 A:R47306 3.3 7.5 0.6
H16 A:R47306 3.6 17.9 0.6
H10 A:R47306 3.9 16.2 0.4
H10 A:R47306 3.9 16.4 0.6
H16 A:R47306 3.9 17.8 0.4
O A:HOH505 4.0 14.7 1.0
ND1 A:HIS218 4.1 8.6 1.0
ND1 A:HIS222 4.1 11.9 1.0
ND1 A:HIS228 4.1 12.0 1.0
HA A:PRO238 4.1 12.5 1.0
CG A:HIS228 4.1 10.6 1.0
CG A:HIS218 4.2 8.3 1.0
CG A:HIS222 4.2 8.5 1.0
H8 A:R47306 4.2 15.3 0.6
H8 A:R47306 4.2 15.1 0.4
C19 A:R47306 4.2 11.4 0.6
HE3 A:MET236 4.2 12.5 1.0
C24 A:R47306 4.2 14.9 0.6
C19 A:R47306 4.2 11.1 0.4
HE1 A:MET236 4.3 12.5 1.0
C18 A:R47306 4.4 9.7 0.4
C18 A:R47306 4.4 10.4 0.6
C24 A:R47306 4.4 14.8 0.4
C17 A:R47306 4.4 13.5 0.4
C17 A:R47306 4.4 13.7 0.6
H7 A:R47306 4.5 14.5 0.4
H7 A:R47306 4.5 14.8 0.6
OE1 A:GLU219 4.6 8.1 0.7
C16 A:R47306 4.7 12.8 0.6
C16 A:R47306 4.7 12.6 0.4
CE A:MET236 4.7 10.4 1.0
O A:PRO238 4.8 12.7 1.0
H12 A:R47306 4.8 11.7 0.4
H12 A:R47306 4.8 12.4 0.6
HD1 A:HIS218 4.9 10.4 1.0
HD1 A:HIS222 4.9 14.2 1.0
C14 A:R47306 4.9 12.3 0.6
C14 A:R47306 4.9 12.1 0.4
HD1 A:HIS228 4.9 14.4 1.0
O A:HOH401 4.9 10.5 1.0
O A:HOH455 4.9 42.9 1.0

Zinc binding site 2 out of 2 in 4gql

Go back to Zinc Binding Sites List in 4gql
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with Selective Phosphinic Inhibitor RXP470.1


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 RXP470.1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:7.9
occ:1.00
OD1 A:ASP170 2.0 9.7 0.9
NE2 A:HIS183 2.0 6.4 0.7
NE2 A:HIS168 2.0 7.4 1.0
ND1 A:HIS196 2.0 7.4 1.0
NE2 A:HIS183 2.1 11.8 0.3
HE1 A:HIS183 2.7 11.4 0.3
CE1 A:HIS183 2.7 9.6 0.3
CG A:ASP170 2.9 9.3 0.9
CE1 A:HIS183 2.9 6.9 0.7
CD2 A:HIS168 2.9 7.8 1.0
CE1 A:HIS196 3.0 7.9 1.0
HE1 A:HIS183 3.0 8.2 0.7
CE1 A:HIS168 3.1 7.3 1.0
HD2 A:HIS168 3.1 9.3 1.0
OD2 A:ASP170 3.1 11.9 0.9
CD2 A:HIS183 3.1 6.3 0.7
HE1 A:HIS196 3.1 9.4 1.0
CG A:HIS196 3.1 7.1 1.0
HB2 A:HIS196 3.2 9.6 1.0
CD2 A:HIS183 3.3 10.9 0.3
HE1 A:HIS168 3.3 8.8 1.0
HD2 A:HIS183 3.3 7.6 0.7
HB3 A:HIS196 3.4 9.6 1.0
CB A:HIS196 3.5 8.0 1.0
HD2 A:HIS183 3.6 13.0 0.3
HE2 A:PHE185 3.9 18.5 1.0
HB2 A:HIS172 3.9 18.4 1.0
ND1 A:HIS183 4.0 11.7 0.3
ND1 A:HIS183 4.0 6.3 0.7
CG A:HIS168 4.1 6.9 1.0
NE2 A:HIS196 4.1 8.0 1.0
ND1 A:HIS168 4.1 7.8 1.0
CG A:HIS183 4.2 6.1 0.7
CD2 A:HIS196 4.2 7.6 1.0
CG A:HIS183 4.2 10.6 0.3
CB A:ASP170 4.3 12.0 0.9
O A:HIS172 4.3 14.0 1.0
HZ A:PHE185 4.4 18.0 1.0
HB3 A:ASP170 4.4 14.4 0.9
O A:HOH502 4.4 41.1 1.0
CE2 A:PHE185 4.5 15.4 1.0
HZ A:PHE174 4.6 10.7 1.0
HB2 A:ASP170 4.6 14.4 0.9
HD1 A:HIS183 4.7 14.1 0.3
CZ A:PHE174 4.8 8.9 1.0
HD1 A:HIS183 4.8 7.6 0.7
H A:HIS172 4.8 17.1 1.0
CZ A:PHE185 4.8 15.0 1.0
CB A:HIS172 4.9 15.3 1.0
HE2 A:HIS196 4.9 9.6 1.0
O A:HOH403 4.9 10.3 1.0
HD1 A:HIS168 4.9 9.3 1.0
HE1 A:PHE174 5.0 10.6 1.0
CE1 A:PHE174 5.0 8.8 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: Wed Dec 16 05:20:15 2020

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