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Zinc in PDB 4h49: 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: 4h49 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) 47.26 / 2.16
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.440, 106.490, 65.880, 90.00, 94.96, 90.00
R / Rfree (%) 16.7 / 24.1

Other elements in 4h49:

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) 12 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 4h49). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 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: 4h49:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4h49

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Zinc binding site 1 out of 8 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:14.2
occ:1.00
NE2 A:HIS228 2.0 13.9 1.0
NE2 A:HIS222 2.1 17.8 1.0
NE2 A:HIS218 2.1 12.4 1.0
O23 B:L29601 2.2 15.2 1.0
O22 B:L29601 2.5 20.9 1.0
CD2 A:HIS218 2.9 12.1 1.0
C21 B:L29601 3.0 15.2 1.0
CD2 A:HIS228 3.0 17.1 1.0
CE1 A:HIS228 3.0 16.3 1.0
CE1 A:HIS222 3.1 13.4 1.0
CD2 A:HIS222 3.1 12.0 1.0
CE1 A:HIS218 3.1 13.0 1.0
N22 B:L29601 3.2 20.0 1.0
ND1 A:HIS228 4.1 11.3 1.0
CG A:HIS218 4.1 11.0 1.0
CG A:HIS228 4.1 15.7 1.0
ND1 A:HIS218 4.2 10.3 1.0
ND1 A:HIS222 4.2 14.9 1.0
CG A:HIS222 4.2 15.9 1.0
O B:HOH729 4.2 14.8 1.0
C17 B:L29601 4.4 13.3 1.0
OE2 A:GLU219 4.5 17.4 1.0
C11 B:L29601 4.7 10.0 1.0
O A:HOH418 4.8 22.7 1.0
C24 B:L29601 4.8 18.3 1.0
CE A:MET236 4.9 8.6 1.0
C12 B:L29601 4.9 13.2 1.0
N16 B:L29601 4.9 18.9 1.0
OE1 A:GLU219 5.0 17.2 1.0
C10 B:L29601 5.0 11.8 1.0

Zinc binding site 2 out of 8 in 4h49

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Zinc binding site 2 out of 8 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:14.4
occ:1.00
NE2 A:HIS183 1.9 15.3 1.0
NE2 A:HIS168 1.9 14.8 1.0
OD2 A:ASP170 2.0 17.6 1.0
ND1 A:HIS196 2.2 12.5 1.0
CE1 A:HIS183 2.8 15.7 1.0
CE1 A:HIS168 2.9 14.9 1.0
CG A:ASP170 2.9 22.2 1.0
CD2 A:HIS168 3.0 16.6 1.0
CD2 A:HIS183 3.0 14.9 1.0
CE1 A:HIS196 3.2 10.3 1.0
OD1 A:ASP170 3.2 18.0 1.0
CG A:HIS196 3.2 14.7 1.0
CB A:HIS196 3.5 12.6 1.0
ND1 A:HIS183 4.0 13.5 1.0
ND1 A:HIS168 4.0 14.4 1.0
CG A:HIS168 4.1 21.4 1.0
CG A:HIS183 4.1 17.6 1.0
O A:HIS172 4.2 18.1 1.0
CB A:ASP170 4.3 22.7 1.0
NE2 A:HIS196 4.3 10.6 1.0
CD2 A:HIS196 4.3 9.2 1.0
CE2 A:PHE185 4.4 25.2 1.0
CZ A:PHE174 4.6 9.2 1.0
CE2 A:PHE174 4.7 9.1 1.0
CZ A:PHE185 4.7 14.1 1.0
CB A:HIS172 5.0 21.1 1.0

Zinc binding site 3 out of 8 in 4h49

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Zinc binding site 3 out of 8 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:Zn602

b:16.2
occ:1.00
NE2 B:HIS228 2.0 17.1 1.0
O62 B:L29601 2.1 18.0 1.0
NE2 B:HIS222 2.1 18.4 1.0
NE2 B:HIS218 2.2 12.4 1.0
O61 B:L29601 2.3 21.9 1.0
C60 B:L29601 2.9 21.9 1.0
CD2 B:HIS228 3.0 17.1 1.0
CD2 B:HIS218 3.0 11.0 1.0
CE1 B:HIS228 3.0 16.5 1.0
N61 B:L29601 3.1 19.7 1.0
CD2 B:HIS222 3.1 9.6 1.0
CE1 B:HIS222 3.1 16.6 1.0
CE1 B:HIS218 3.3 11.3 1.0
ND1 B:HIS228 4.1 15.5 1.0
CG B:HIS228 4.2 17.3 1.0
O B:HOH728 4.2 18.1 1.0
CG B:HIS218 4.2 11.3 1.0
CG B:HIS222 4.2 13.4 1.0
ND1 B:HIS222 4.2 18.2 1.0
ND1 B:HIS218 4.3 15.6 1.0
C56 B:L29601 4.3 22.1 1.0
OE2 B:GLU219 4.6 18.1 1.0
C39 B:L29601 4.7 16.9 1.0
C59 B:L29601 4.8 16.1 1.0
OE1 B:GLU219 4.9 19.1 1.0
C5A B:L29601 4.9 10.6 1.0
CE B:MET236 4.9 14.7 1.0
N40 B:L29601 4.9 16.5 1.0
CB B:PRO238 5.0 17.0 1.0

Zinc binding site 4 out of 8 in 4h49

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Zinc binding site 4 out of 8 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:Zn603

b:26.4
occ:1.00
OD1 B:ASP170 1.9 32.9 1.0
NE2 B:HIS168 2.0 29.8 1.0
NE2 B:HIS183 2.1 25.2 1.0
ND1 B:HIS196 2.1 22.0 1.0
CG B:ASP170 2.8 39.8 1.0
CE1 B:HIS183 2.9 24.1 1.0
CE1 B:HIS168 3.0 32.3 1.0
CD2 B:HIS168 3.0 31.3 1.0
OD2 B:ASP170 3.1 30.7 1.0
CE1 B:HIS196 3.1 21.7 1.0
CG B:HIS196 3.1 20.2 1.0
CD2 B:HIS183 3.2 20.1 1.0
CB B:HIS196 3.4 15.9 1.0
ND1 B:HIS183 4.1 22.6 1.0
ND1 B:HIS168 4.1 32.3 1.0
CG B:HIS168 4.1 39.4 1.0
O B:HIS172 4.2 37.2 1.0
CB B:ASP170 4.2 38.6 1.0
NE2 B:HIS196 4.2 22.5 1.0
CG B:HIS183 4.2 21.3 1.0
CD2 B:HIS196 4.3 18.5 1.0
CE2 B:PHE185 4.4 25.6 1.0
CZ B:PHE174 4.4 19.8 1.0
CZ B:PHE185 4.6 25.1 1.0
CE2 B:PHE174 4.7 20.1 1.0
CA B:HIS196 4.9 18.7 1.0

Zinc binding site 5 out of 8 in 4h49

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Zinc binding site 5 out of 8 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 5 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
C:Zn301

b:16.5
occ:1.00
NE2 C:HIS218 2.1 10.2 1.0
NE2 C:HIS228 2.1 14.7 1.0
NE2 C:HIS222 2.1 15.1 1.0
O23 C:L29306 2.1 21.0 1.0
O22 C:L29306 2.2 23.9 1.0
CD2 C:HIS218 2.9 11.8 1.0
C21 C:L29306 2.9 20.6 1.0
CE1 C:HIS228 3.0 17.0 1.0
N22 C:L29306 3.1 20.5 1.0
CD2 C:HIS222 3.1 12.0 1.0
CD2 C:HIS228 3.1 13.0 1.0
CE1 C:HIS222 3.1 16.8 1.0
CE1 C:HIS218 3.2 11.1 1.0
CG C:HIS218 4.1 12.1 1.0
ND1 C:HIS228 4.2 15.2 1.0
O C:HOH444 4.2 16.7 1.0
CG C:HIS228 4.2 16.6 1.0
ND1 C:HIS218 4.2 12.6 1.0
ND1 C:HIS222 4.2 16.2 1.0
CG C:HIS222 4.2 11.8 1.0
C17 C:L29306 4.4 22.1 1.0
OE2 C:GLU219 4.4 20.1 1.0
CE C:MET236 4.8 16.4 1.0
C11 C:L29306 4.8 12.4 1.0
C24 C:L29306 4.9 15.3 1.0
C19 C:L29306 4.9 20.8 1.0
N16 C:L29306 4.9 16.8 1.0
C12 C:L29306 5.0 13.8 1.0

Zinc binding site 6 out of 8 in 4h49

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Zinc binding site 6 out of 8 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 6 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
C:Zn302

b:22.0
occ:1.00
NE2 C:HIS183 2.0 22.9 1.0
OD1 C:ASP170 2.0 29.3 1.0
NE2 C:HIS168 2.1 17.5 1.0
ND1 C:HIS196 2.2 19.4 1.0
CE1 C:HIS183 2.9 17.5 1.0
CG C:ASP170 2.9 28.7 1.0
CD2 C:HIS183 3.0 18.6 1.0
CE1 C:HIS168 3.1 20.8 1.0
CD2 C:HIS168 3.1 20.6 1.0
CG C:HIS196 3.1 19.3 1.0
CE1 C:HIS196 3.2 21.5 1.0
OD2 C:ASP170 3.2 22.8 1.0
CB C:HIS196 3.4 18.4 1.0
ND1 C:HIS183 4.0 23.4 1.0
CG C:HIS183 4.1 15.2 1.0
ND1 C:HIS168 4.2 21.0 1.0
CE2 C:PHE185 4.2 28.4 1.0
O C:HIS172 4.2 26.9 1.0
CG C:HIS168 4.2 26.0 1.0
CB C:ASP170 4.3 32.9 1.0
NE2 C:HIS196 4.3 22.2 1.0
CD2 C:HIS196 4.3 23.2 1.0
CZ C:PHE185 4.5 26.3 1.0
CZ C:PHE174 4.6 11.5 1.0
CE2 C:PHE174 4.7 19.3 1.0
CB C:HIS172 4.9 28.3 1.0
CA C:HIS196 4.9 16.5 1.0

Zinc binding site 7 out of 8 in 4h49

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Zinc binding site 7 out of 8 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 7 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
D:Zn301

b:17.8
occ:1.00
NE2 D:HIS218 2.0 17.0 1.0
NE2 D:HIS222 2.1 26.4 1.0
O61 C:L29306 2.2 23.7 1.0
NE2 D:HIS228 2.2 15.5 1.0
O62 C:L29306 2.2 24.1 1.0
C60 C:L29306 2.9 18.4 1.0
N61 C:L29306 2.9 20.5 1.0
CD2 D:HIS218 2.9 14.4 1.0
CD2 D:HIS222 3.0 16.8 1.0
CE1 D:HIS218 3.0 15.2 1.0
CD2 D:HIS228 3.2 16.4 1.0
CE1 D:HIS228 3.2 18.4 1.0
CE1 D:HIS222 3.2 23.1 1.0
ND1 D:HIS218 4.1 12.1 1.0
CG D:HIS218 4.1 13.0 1.0
CG D:HIS222 4.2 17.6 1.0
O D:HOH415 4.2 16.5 1.0
ND1 D:HIS222 4.3 19.2 1.0
ND1 D:HIS228 4.3 14.3 1.0
OE2 D:GLU219 4.3 22.4 1.0
CG D:HIS228 4.3 16.7 1.0
C56 C:L29306 4.3 14.4 1.0
O D:HOH428 4.8 27.9 1.0
C5A C:L29306 4.8 15.5 1.0
C39 C:L29306 4.8 21.4 1.0
C58 C:L29306 4.8 22.0 1.0
OE1 D:GLU219 4.9 24.1 1.0
C45 C:L29306 4.9 13.6 1.0
CD D:GLU219 5.0 21.5 1.0
C49 C:L29306 5.0 13.4 1.0

Zinc binding site 8 out of 8 in 4h49

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Zinc binding site 8 out of 8 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 8 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
D:Zn302

b:24.3
occ:1.00
OD1 D:ASP170 1.9 24.4 1.0
NE2 D:HIS183 1.9 15.4 1.0
NE2 D:HIS168 2.1 24.7 1.0
ND1 D:HIS196 2.2 17.2 1.0
CE1 D:HIS183 2.7 21.5 1.0
CG D:ASP170 2.9 30.5 1.0
CD2 D:HIS168 3.1 23.5 1.0
CE1 D:HIS168 3.1 25.5 1.0
CD2 D:HIS183 3.1 21.3 1.0
CE1 D:HIS196 3.2 21.6 1.0
CG D:HIS196 3.2 21.7 1.0
OD2 D:ASP170 3.3 25.0 1.0
CB D:HIS196 3.5 16.8 1.0
ND1 D:HIS183 3.9 22.4 1.0
CG D:HIS183 4.1 17.1 1.0
ND1 D:HIS168 4.2 29.2 1.0
CG D:HIS168 4.2 30.4 1.0
CE2 D:PHE185 4.2 29.7 1.0
CB D:ASP170 4.3 24.6 1.0
NE2 D:HIS196 4.3 16.7 1.0
CD2 D:HIS196 4.3 22.7 1.0
O D:HIS172 4.3 30.1 1.0
CZ D:PHE185 4.4 26.3 1.0
CZ D:PHE174 4.6 18.1 1.0
CE2 D:PHE174 4.7 21.0 1.0
CB D:HIS172 5.0 36.1 1.0
CA D:HIS196 5.0 16.5 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 23:53:37 2024

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