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Zinc in PDB 4h84: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor., PDB code: 4h84 was solved by E.A.Stura, C.Antoni, L.Vera, E.Cassar-Lajeunesse, E.Nuti, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.03 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.140, 62.790, 113.140, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.6

Other elements in 4h84:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. (pdb code 4h84). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor., PDB code: 4h84:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4h84

Go back to Zinc Binding Sites List in 4h84
Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


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 A Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:8.7
occ:1.00
 O22 A:Y38306 1.9 10.5 1.0
NE2 A:HIS228 2.0 7.4 1.0
NE2 A:HIS218 2.0 7.7 1.0
NE2 A:HIS222 2.0 7.8 1.0
C21 A:Y38306 2.7 13.3 1.0
O23 A:Y38306 2.8 9.2 1.0
CE1 A:HIS228 3.0 10.5 1.0
CD2 A:HIS228 3.0 10.4 1.0
CE1 A:HIS222 3.0 8.2 1.0
CE1 A:HIS218 3.0 9.6 1.0
CD2 A:HIS218 3.0 6.7 1.0
CD2 A:HIS222 3.1 6.2 1.0
ND1 A:HIS228 4.1 14.5 1.0
CG A:HIS228 4.1 8.6 1.0
ND1 A:HIS218 4.1 7.0 1.0
ND1 A:HIS222 4.1 6.8 1.0
C17 A:Y38306 4.2 8.7 1.0
CG A:HIS218 4.2 7.3 1.0
CG A:HIS222 4.2 5.7 1.0
C19 A:Y38306 4.7 15.2 1.0
N16 A:Y38306 4.7 8.8 1.0
CE A:MET236 4.7 10.0 1.0
C24 A:Y38306 4.7 10.8 1.0
C18 A:Y38306 4.7 8.1 1.0
CA A:PRO238 4.9 12.9 1.0

Zinc binding site 2 out of 4 in 4h84

Go back to Zinc Binding Sites List in 4h84
Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


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 A Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:8.7
occ:1.00
 OD2 A:ASP170 1.9 8.3 0.5
NE2 A:HIS183 2.0 6.3 1.0
OD2 A:ASP170 2.0 8.4 0.5
NE2 A:HIS168 2.0 7.0 1.0
ND1 A:HIS196 2.0 8.2 1.0
CE1 A:HIS183 2.9 7.5 1.0
CG A:ASP170 2.9 16.0 0.5
CG A:ASP170 2.9 16.0 0.5
CD2 A:HIS168 2.9 10.3 1.0
CE1 A:HIS196 3.0 6.3 1.0
CE1 A:HIS168 3.0 9.1 1.0
CD2 A:HIS183 3.1 9.8 1.0
CG A:HIS196 3.1 6.6 1.0
OD1 A:ASP170 3.2 12.7 0.5
OD1 A:ASP170 3.2 12.7 0.5
CB A:HIS196 3.4 6.8 1.0
ND1 A:HIS183 4.0 6.8 1.0
CG A:HIS168 4.1 11.0 1.0
NE2 A:HIS196 4.1 7.6 1.0
ND1 A:HIS168 4.1 8.8 1.0
CG A:HIS183 4.2 4.9 1.0
CD2 A:HIS196 4.2 6.8 1.0
CB A:ASP170 4.2 11.5 0.5
CE2 A:PHE185 4.3 11.2 1.0
O A:HIS172 4.3 11.3 1.0
CB A:ASP170 4.3 11.9 0.5
CZ A:PHE174 4.7 9.3 1.0
CZ A:PHE185 4.7 10.6 1.0
CE1 A:PHE174 4.8 6.3 1.0
CB A:HIS172 4.9 15.6 1.0
CA A:HIS196 4.9 6.4 1.0

Zinc binding site 3 out of 4 in 4h84

Go back to Zinc Binding Sites List in 4h84
Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:9.4
occ:1.00
 O22 B:Y38301 1.9 14.5 1.0
NE2 B:HIS222 2.0 7.8 1.0
NE2 B:HIS228 2.0 7.9 1.0
NE2 B:HIS218 2.0 9.6 1.0
C21 B:Y38301 2.7 11.6 1.0
O23 B:Y38301 2.9 8.8 1.0
CE1 B:HIS222 3.0 10.5 1.0
CE1 B:HIS228 3.0 11.1 1.0
CD2 B:HIS218 3.0 6.5 1.0
CE1 B:HIS218 3.0 9.0 1.0
CD2 B:HIS228 3.0 9.0 1.0
CD2 B:HIS222 3.0 5.7 1.0
ND1 B:HIS222 4.1 10.1 1.0
ND1 B:HIS228 4.1 9.9 1.0
ND1 B:HIS218 4.1 8.6 1.0
C17 B:Y38301 4.1 11.4 1.0
CG B:HIS218 4.1 6.5 1.0
CG B:HIS228 4.1 7.9 1.0
CG B:HIS222 4.2 6.3 1.0
O A:HOH485 4.4 39.1 1.0
C24 B:Y38301 4.6 13.9 1.0
N16 B:Y38301 4.6 13.1 1.0
CE B:MET236 4.7 11.1 1.0
C19 B:Y38301 4.7 11.7 1.0
C18 B:Y38301 4.7 9.3 1.0

Zinc binding site 4 out of 4 in 4h84

Go back to Zinc Binding Sites List in 4h84
Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Selective Carboxylate Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:13.6
occ:1.00
 OD2 B:ASP170 2.0 15.6 1.0
NE2 B:HIS183 2.0 10.2 1.0
NE2 B:HIS168 2.0 12.9 1.0
ND1 B:HIS196 2.1 9.0 1.0
CG B:ASP170 2.9 23.7 1.0
CE1 B:HIS183 2.9 14.0 1.0
CD2 B:HIS168 2.9 18.7 1.0
CE1 B:HIS196 3.0 14.0 1.0
CD2 B:HIS183 3.1 12.2 1.0
CG B:HIS196 3.1 10.1 1.0
CE1 B:HIS168 3.1 15.1 1.0
OD1 B:ASP170 3.2 19.9 1.0
CB B:HIS196 3.4 9.6 1.0
ND1 B:HIS183 4.1 11.4 1.0
CG B:HIS168 4.1 18.9 1.0
NE2 B:HIS196 4.1 16.6 1.0
ND1 B:HIS168 4.2 16.8 1.0
CG B:HIS183 4.2 6.5 1.0
CD2 B:HIS196 4.2 11.8 1.0
CB B:ASP170 4.3 22.6 1.0
CE2 B:PHE185 4.4 12.1 1.0
O B:HIS172 4.4 15.7 1.0
CZ B:PHE185 4.6 15.2 1.0
CZ B:PHE174 4.8 10.8 1.0
CE1 B:PHE174 4.8 10.7 1.0
O B:HOH404 4.9 18.8 1.0
CA B:HIS196 5.0 8.5 1.0

Reference:

C.Antoni, L.Vera, L.Devel, M.P.Catalani, B.Czarny, E.Cassar-Lajeunesse, E.Nuti, A.Rossello, V.Dive, E.A.Stura. Crystallization of Bi-Functional Ligand Protein Complexes. J.Struct.Biol. V. 182 246 2013.
ISSN: ISSN 1047-8477
PubMed: 23567804
DOI: 10.1016/J.JSB.2013.03.015
Page generated: Sat Oct 26 23:55:22 2024

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