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Zinc in PDB 4h30: Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor.:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin Inhibitor., PDB code: 4h30 was solved by C.Antoni, E.A.Stura, L.Vera, E.Nuti, L.Carafa, E.Cassar-Lajeunesse, V.Dive, A.Rossello, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.31 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.910, 61.750, 112.560, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.7

Other elements in 4h30:

The structure of Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. (pdb code 4h30). 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 Mmp-12 in Complex with A Twin Inhibitor., PDB code: 4h30:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4h30

Go back to Zinc Binding Sites List in 4h30
Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:10.7
occ:1.00
 O22 B:0ZD306 1.9 14.1 1.0
NE2 A:HIS228 2.0 10.9 1.0
NE2 A:HIS218 2.0 11.0 1.0
NE2 A:HIS222 2.0 11.1 1.0
C21 B:0ZD306 2.8 13.4 1.0
O23 B:0ZD306 2.9 15.8 1.0
CE1 A:HIS222 3.0 12.2 1.0
CD2 A:HIS228 3.0 11.3 1.0
CD2 A:HIS218 3.0 10.5 1.0
CE1 A:HIS228 3.0 12.3 1.0
CE1 A:HIS218 3.0 10.0 1.0
CD2 A:HIS222 3.1 9.7 1.0
ND1 A:HIS218 4.1 10.4 1.0
ND1 A:HIS228 4.1 13.1 1.0
ND1 A:HIS222 4.1 12.6 1.0
CG A:HIS228 4.1 12.4 1.0
CG A:HIS218 4.1 10.0 1.0
C17 B:0ZD306 4.2 12.2 1.0
CG A:HIS222 4.2 10.7 1.0
C24 B:0ZD306 4.5 12.8 1.0
O B:HOH473 4.5 32.6 1.0
C19 B:0ZD306 4.6 19.4 1.0
N16 B:0ZD306 4.6 12.3 1.0
O A:HOH433 4.8 17.5 1.0
OE2 A:GLU219 4.8 12.1 1.0
CE A:MET236 4.8 11.6 1.0
CA A:PRO238 4.9 12.6 1.0
CB A:PRO238 4.9 13.7 1.0
C18 B:0ZD306 4.9 14.7 1.0

Zinc binding site 2 out of 4 in 4h30

Go back to Zinc Binding Sites List in 4h30
Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.3
occ:1.00
 OD2 A:ASP170 1.9 13.6 1.0
NE2 A:HIS183 2.0 9.7 1.0
NE2 A:HIS168 2.0 11.9 1.0
ND1 A:HIS196 2.0 11.6 1.0
CG A:ASP170 2.9 11.4 1.0
CE1 A:HIS183 2.9 16.1 1.0
CD2 A:HIS168 2.9 11.9 1.0
CE1 A:HIS196 2.9 12.1 1.0
CE1 A:HIS168 3.1 11.9 1.0
CD2 A:HIS183 3.1 12.0 1.0
CG A:HIS196 3.1 11.2 1.0
OD1 A:ASP170 3.2 15.5 1.0
CB A:HIS196 3.5 12.0 1.0
ND1 A:HIS183 4.0 15.0 1.0
CG A:HIS168 4.1 11.1 1.0
NE2 A:HIS196 4.1 13.0 1.0
ND1 A:HIS168 4.1 11.8 1.0
CG A:HIS183 4.2 10.8 1.0
CD2 A:HIS196 4.2 12.6 1.0
CB A:ASP170 4.2 17.5 1.0
CE2 A:PHE185 4.3 18.6 1.0
O A:HIS172 4.3 15.7 1.0
CZ A:PHE174 4.6 13.8 1.0
CZ A:PHE185 4.7 23.2 1.0
CE2 A:PHE174 4.7 11.8 1.0
O A:HOH422 4.9 15.5 1.0
CA A:HIS196 5.0 11.6 1.0

Zinc binding site 3 out of 4 in 4h30

Go back to Zinc Binding Sites List in 4h30
Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:11.8
occ:1.00
 O62 B:0ZD306 1.9 13.4 1.0
NE2 B:HIS218 2.0 10.8 1.0
NE2 B:HIS222 2.0 11.4 1.0
NE2 B:HIS228 2.0 12.5 1.0
C60 B:0ZD306 2.8 13.7 1.0
CE1 B:HIS222 2.9 14.1 1.0
O61 B:0ZD306 3.0 16.7 1.0
CD2 B:HIS228 3.0 14.3 1.0
CD2 B:HIS218 3.0 9.4 1.0
CE1 B:HIS218 3.0 10.6 1.0
CE1 B:HIS228 3.0 13.9 1.0
CD2 B:HIS222 3.1 11.1 1.0
ND1 B:HIS222 4.1 14.1 1.0
ND1 B:HIS218 4.1 11.3 1.0
ND1 B:HIS228 4.1 14.3 1.0
CG B:HIS218 4.1 10.4 1.0
CG B:HIS228 4.1 15.8 1.0
CG B:HIS222 4.2 12.1 1.0
C56 B:0ZD306 4.2 12.6 1.0
C39 B:0ZD306 4.5 14.2 1.0
N40 B:0ZD306 4.6 12.8 1.0
O B:HOH551 4.7 36.1 1.0
C58 B:0ZD306 4.7 26.0 1.0
CE B:MET236 4.7 12.9 1.0
O B:HOH438 4.7 19.8 1.0
OE2 B:GLU219 4.7 11.8 1.0
CA B:PRO238 4.9 13.9 1.0
CB B:PRO238 4.9 17.2 1.0
C5A B:0ZD306 4.9 12.7 1.0
C57 B:0ZD306 5.0 18.7 1.0

Zinc binding site 4 out of 4 in 4h30

Go back to Zinc Binding Sites List in 4h30
Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Mmp-12 in Complex with A Twin 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 Mmp-12 in Complex with A Twin Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:12.5
occ:1.00
 OD2 B:ASP170 1.9 13.8 1.0
NE2 B:HIS183 2.0 14.8 1.0
NE2 B:HIS168 2.0 11.8 1.0
NE2 B:HIS183 2.0 15.7 0.0
ND1 B:HIS196 2.0 10.2 1.0
CE1 B:HIS183 2.8 17.4 1.0
CE1 B:HIS183 2.8 16.2 0.0
CG B:ASP170 2.9 15.7 1.0
CD2 B:HIS168 2.9 12.7 1.0
CE1 B:HIS196 3.0 10.7 1.0
CE1 B:HIS168 3.1 12.6 1.0
CG B:HIS196 3.1 10.8 1.0
CD2 B:HIS183 3.1 17.3 1.0
OD1 B:ASP170 3.1 17.1 1.0
CD2 B:HIS183 3.2 17.1 0.0
CB B:HIS196 3.5 10.7 1.0
ND1 B:HIS183 4.0 17.3 1.0
ND1 B:HIS183 4.0 16.6 0.0
CG B:HIS168 4.1 13.4 1.0
NE2 B:HIS196 4.1 11.9 1.0
ND1 B:HIS168 4.1 13.2 1.0
CG B:HIS183 4.2 13.3 1.0
CD2 B:HIS196 4.2 11.7 1.0
CG B:HIS183 4.2 13.5 0.0
CB B:ASP170 4.2 18.0 1.0
O B:HIS172 4.3 20.8 1.0
CE2 B:PHE185 4.5 24.2 1.0
CZ B:PHE174 4.7 12.6 1.0
CZ B:PHE185 4.8 30.9 1.0
CE2 B:PHE174 4.9 12.1 1.0
O B:HOH415 4.9 17.7 1.0
CA B:HIS196 5.0 10.0 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 23:52:47 2024

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