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Zinc in PDB 6ela: Crystal Structure of MMP12 in Complex with Inhibitor BE4.

Enzymatic activity of Crystal Structure of MMP12 in Complex with Inhibitor BE4.

All present enzymatic activity of Crystal Structure of MMP12 in Complex with Inhibitor BE4.:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of MMP12 in Complex with Inhibitor BE4., PDB code: 6ela was solved by L.Ciccone, L.Tepshi, E.Nuti, A.Rossello, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.04 / 1.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.190, 63.320, 78.320, 90.00, 103.73, 90.00
R / Rfree (%) 17.1 / 20.7

Other elements in 6ela:

The structure of Crystal Structure of MMP12 in Complex with Inhibitor BE4. also contains other interesting chemical elements:

Calcium (Ca) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of MMP12 in Complex with Inhibitor BE4. (pdb code 6ela). 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 MMP12 in Complex with Inhibitor BE4., PDB code: 6ela:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6ela

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Zinc binding site 1 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.2
occ:1.00
 O25 A:B9Z306 1.9 10.3 1.0
NE2 A:HIS218 2.0 9.8 1.0
NE2 A:HIS228 2.0 9.9 1.0
NE2 A:HIS222 2.0 9.4 1.0
C23 A:B9Z306 2.7 11.3 1.0
O24 A:B9Z306 2.7 12.6 1.0
CE1 A:HIS218 2.9 10.3 1.0
CE1 A:HIS228 3.0 12.4 1.0
CE1 A:HIS222 3.0 10.0 1.0
CD2 A:HIS218 3.0 8.8 1.0
CD2 A:HIS228 3.1 9.6 1.0
CD2 A:HIS222 3.1 10.8 1.0
O A:HOH449 4.0 14.7 1.0
O A:HOH514 4.0 9.5 0.4
ND1 A:HIS218 4.1 9.6 1.0
ND1 A:HIS228 4.1 12.7 1.0
CG A:HIS218 4.1 8.4 1.0
ND1 A:HIS222 4.1 11.4 1.0
C22 A:B9Z306 4.1 10.2 1.0
CG A:HIS228 4.2 11.8 1.0
CG A:HIS222 4.2 10.5 1.0
C11 A:B9Z306 4.3 14.1 1.0
OE2 A:GLU219 4.6 11.5 1.0
C12 A:B9Z306 4.7 12.6 1.0
C26 A:B9Z306 4.7 11.1 1.0
C10 A:B9Z306 4.7 12.9 1.0
CE A:MET236 4.7 11.8 1.0
O A:HOH514 4.8 5.7 0.6
C21 A:B9Z306 4.8 12.7 1.0
O A:HOH563 5.0 25.8 1.0

Zinc binding site 2 out of 8 in 6ela

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Zinc binding site 2 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:12.5
occ:1.00
 OD2 A:ASP170 2.0 12.6 1.0
NE2 A:HIS168 2.0 10.6 1.0
ND1 A:HIS196 2.0 12.7 1.0
NE2 A:HIS183 2.0 10.2 1.0
CD2 A:HIS168 2.9 11.2 1.0
CG A:ASP170 2.9 12.5 1.0
CE1 A:HIS183 2.9 10.5 1.0
CE1 A:HIS196 2.9 12.9 1.0
CG A:HIS196 3.1 11.5 1.0
CE1 A:HIS168 3.1 10.9 1.0
CD2 A:HIS183 3.1 9.9 1.0
OD1 A:ASP170 3.2 12.8 1.0
CB A:HIS196 3.5 10.3 1.0
O A:HOH406 3.9 22.9 0.5
NE2 A:HIS196 4.1 12.8 1.0
CG A:HIS168 4.1 11.8 1.0
ND1 A:HIS183 4.1 10.8 1.0
ND1 A:HIS168 4.1 10.1 1.0
CD2 A:HIS196 4.2 12.1 1.0
CG A:HIS183 4.2 10.1 1.0
CB A:ASP170 4.2 13.3 1.0
CE1 A:PHE185 4.3 12.7 1.0
O A:HIS172 4.3 13.3 1.0
CZ A:PHE174 4.5 11.9 1.0
CZ A:PHE185 4.6 13.2 1.0
CE2 A:PHE174 4.7 10.2 1.0
O A:HOH448 4.8 13.6 1.0
CA A:HIS196 5.0 10.8 1.0
O A:HOH406 5.0 23.1 0.5

Zinc binding site 3 out of 8 in 6ela

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Zinc binding site 3 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:13.4
occ:1.00
 O25 B:B9Z306 1.9 13.3 1.0
NE2 B:HIS228 2.0 12.2 1.0
NE2 B:HIS218 2.0 12.0 1.0
NE2 B:HIS222 2.1 12.4 1.0
C23 B:B9Z306 2.6 13.9 1.0
O24 B:B9Z306 2.7 13.2 1.0
CE1 B:HIS228 2.9 12.9 1.0
CE1 B:HIS218 2.9 12.7 1.0
CD2 B:HIS228 3.0 11.2 1.0
CD2 B:HIS222 3.1 11.4 1.0
CE1 B:HIS222 3.1 14.3 1.0
CD2 B:HIS218 3.1 11.5 1.0
O B:HOH450 4.0 16.8 1.0
ND1 B:HIS228 4.0 14.2 1.0
ND1 B:HIS218 4.1 12.0 1.0
CG B:HIS228 4.1 12.5 1.0
C22 B:B9Z306 4.1 14.3 1.0
CG B:HIS218 4.2 11.7 1.0
ND1 B:HIS222 4.2 13.3 1.0
CG B:HIS222 4.2 13.3 1.0
C11 B:B9Z306 4.2 14.2 1.0
OE2 B:GLU219 4.7 12.9 1.0
C26 B:B9Z306 4.7 15.9 1.0
C12 B:B9Z306 4.7 13.3 1.0
O B:HOH512 4.7 15.5 1.0
C10 B:B9Z306 4.8 13.6 1.0
C21 B:B9Z306 4.8 14.3 1.0
CE B:MET236 4.9 12.4 1.0
O B:HOH555 4.9 27.5 1.0

Zinc binding site 4 out of 8 in 6ela

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Zinc binding site 4 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:13.4
occ:1.00
 OD2 B:ASP170 1.9 12.8 1.0
NE2 B:HIS183 2.0 12.7 0.3
NE2 B:HIS168 2.0 11.7 1.0
NE2 B:HIS183 2.0 10.5 0.7
ND1 B:HIS196 2.0 13.7 1.0
CE1 B:HIS183 2.5 12.7 0.3
CG B:ASP170 2.9 12.6 1.0
CD2 B:HIS168 2.9 11.8 1.0
CE1 B:HIS183 2.9 10.5 0.7
CE1 B:HIS196 2.9 14.4 1.0
CD2 B:HIS183 3.1 10.5 0.7
CE1 B:HIS168 3.1 12.8 1.0
CG B:HIS196 3.1 13.7 1.0
CD2 B:HIS183 3.2 12.9 0.3
OD1 B:ASP170 3.3 12.9 1.0
CB B:HIS196 3.5 11.7 1.0
ND1 B:HIS183 3.7 10.9 0.3
ND1 B:HIS183 4.1 9.3 0.7
CG B:HIS168 4.1 12.2 1.0
NE2 B:HIS196 4.1 13.4 1.0
CG B:HIS183 4.1 12.2 0.3
ND1 B:HIS168 4.1 12.4 1.0
CG B:HIS183 4.2 10.6 0.7
O B:HIS172 4.2 13.5 1.0
CD2 B:HIS196 4.2 12.8 1.0
CB B:ASP170 4.2 14.5 1.0
CE1 B:PHE185 4.3 14.1 1.0
CZ B:PHE174 4.5 11.9 1.0
CE2 B:PHE174 4.6 11.5 1.0
CZ B:PHE185 4.6 15.1 1.0
O B:HOH449 4.9 13.5 1.0
CA B:HIS196 5.0 12.6 1.0

Zinc binding site 5 out of 8 in 6ela

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Zinc binding site 5 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:12.1
occ:1.00
 O25 C:B9Z307 2.0 11.7 1.0
NE2 C:HIS228 2.0 13.3 1.0
NE2 C:HIS218 2.0 11.3 1.0
NE2 C:HIS222 2.1 10.3 1.0
C23 C:B9Z307 2.7 12.2 1.0
O24 C:B9Z307 2.7 11.8 1.0
CE1 C:HIS228 2.9 14.4 1.0
CE1 C:HIS218 2.9 12.4 1.0
CE1 C:HIS222 3.0 9.2 1.0
CD2 C:HIS228 3.1 11.4 1.0
CD2 C:HIS218 3.1 9.6 1.0
CD2 C:HIS222 3.1 10.9 1.0
O C:HOH455 4.0 14.1 1.0
ND1 C:HIS228 4.1 14.1 1.0
ND1 C:HIS218 4.1 9.9 1.0
ND1 C:HIS222 4.2 10.6 1.0
C22 C:B9Z307 4.2 12.4 1.0
CG C:HIS218 4.2 10.7 1.0
CG C:HIS228 4.2 13.0 1.0
CG C:HIS222 4.2 10.3 1.0
C11 C:B9Z307 4.3 13.7 1.0
OE2 C:GLU219 4.7 11.7 1.0
CE C:MET236 4.7 12.0 1.0
C12 C:B9Z307 4.7 12.4 1.0
C26 C:B9Z307 4.7 11.7 1.0
C10 C:B9Z307 4.7 14.0 1.0
C21 C:B9Z307 4.8 12.6 1.0
O C:HOH502 4.8 7.3 0.7
O C:HOH580 4.9 23.9 0.8

Zinc binding site 6 out of 8 in 6ela

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Zinc binding site 6 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:12.7
occ:1.00
 OD2 C:ASP170 1.9 11.7 1.0
NE2 C:HIS183 2.0 12.1 1.0
NE2 C:HIS168 2.0 11.6 1.0
ND1 C:HIS196 2.0 13.3 1.0
CE1 C:HIS183 2.9 13.1 1.0
CD2 C:HIS168 2.9 11.9 1.0
CG C:ASP170 2.9 12.9 1.0
CE1 C:HIS196 2.9 13.4 1.0
CD2 C:HIS183 3.0 10.5 1.0
CE1 C:HIS168 3.1 11.1 1.0
CG C:HIS196 3.1 12.9 1.0
OD1 C:ASP170 3.3 13.3 1.0
CB C:HIS196 3.5 11.1 1.0
ND1 C:HIS183 4.0 10.5 1.0
CG C:HIS168 4.1 11.9 1.0
NE2 C:HIS196 4.1 12.0 1.0
CG C:HIS183 4.1 8.5 1.0
ND1 C:HIS168 4.1 10.8 1.0
CD2 C:HIS196 4.2 12.4 1.0
CB C:ASP170 4.2 13.9 1.0
CE1 C:PHE185 4.3 13.6 1.0
O C:HIS172 4.3 13.7 1.0
CZ C:PHE174 4.5 11.4 1.0
CZ C:PHE185 4.6 14.5 1.0
CE2 C:PHE174 4.7 10.7 1.0
O C:HOH479 4.9 13.4 1.0

Zinc binding site 7 out of 8 in 6ela

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Zinc binding site 7 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:13.3
occ:1.00
 O25 D:B9Z306 1.9 12.8 1.0
NE2 D:HIS228 2.0 13.0 1.0
NE2 D:HIS218 2.0 10.8 1.0
NE2 D:HIS222 2.1 12.6 1.0
C23 D:B9Z306 2.7 12.2 1.0
O24 D:B9Z306 2.7 11.3 1.0
CE1 D:HIS218 3.0 10.6 1.0
CD2 D:HIS228 3.0 13.1 1.0
CE1 D:HIS228 3.0 12.7 1.0
CD2 D:HIS222 3.0 11.9 1.0
CD2 D:HIS218 3.1 11.3 1.0
CE1 D:HIS222 3.1 12.7 1.0
O D:HOH445 4.0 17.9 1.0
ND1 D:HIS218 4.1 12.1 1.0
ND1 D:HIS228 4.1 14.0 1.0
C22 D:B9Z306 4.1 13.2 1.0
CG D:HIS228 4.1 13.6 1.0
CG D:HIS218 4.2 11.5 1.0
ND1 D:HIS222 4.2 13.6 1.0
CG D:HIS222 4.2 12.6 1.0
C11 D:B9Z306 4.3 14.8 1.0
C26 D:B9Z306 4.7 14.9 1.0
C12 D:B9Z306 4.7 13.5 1.0
OE2 D:GLU219 4.7 13.8 1.0
C10 D:B9Z306 4.8 13.3 1.0
CE D:MET236 4.8 14.0 1.0
O D:HOH519 4.8 15.4 1.0
C21 D:B9Z306 4.8 13.0 1.0
O D:HOH570 4.9 28.8 1.0

Zinc binding site 8 out of 8 in 6ela

Go back to Zinc Binding Sites List in 6ela
Zinc binding site 8 out of 8 in the Crystal Structure of MMP12 in Complex with Inhibitor BE4.


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 MMP12 in Complex with Inhibitor BE4. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:13.4
occ:1.00
 OD2 D:ASP170 1.9 12.0 1.0
NE2 D:HIS183 2.0 13.5 1.0
NE2 D:HIS168 2.0 11.5 1.0
ND1 D:HIS196 2.0 11.6 1.0
CE1 D:HIS183 2.9 11.7 1.0
CG D:ASP170 2.9 13.7 1.0
CD2 D:HIS168 2.9 10.5 1.0
CE1 D:HIS196 2.9 12.5 1.0
CE1 D:HIS168 3.1 12.3 1.0
CD2 D:HIS183 3.1 14.2 1.0
CG D:HIS196 3.1 13.2 1.0
OD1 D:ASP170 3.2 13.4 1.0
CB D:HIS196 3.5 12.6 1.0
O D:HOH470 3.7 31.2 1.0
ND1 D:HIS183 4.0 11.9 1.0
NE2 D:HIS196 4.1 12.1 1.0
CG D:HIS168 4.1 10.9 1.0
ND1 D:HIS168 4.1 11.7 1.0
CG D:HIS183 4.2 12.8 1.0
CD2 D:HIS196 4.2 13.3 1.0
O D:HIS172 4.2 13.2 1.0
CB D:ASP170 4.2 13.5 1.0
CE1 D:PHE185 4.3 13.2 1.0
CZ D:PHE174 4.5 12.2 1.0
CE2 D:PHE174 4.7 11.3 1.0
CZ D:PHE185 4.7 13.6 1.0
O D:HOH461 4.9 14.0 1.0
CA D:HIS196 5.0 11.6 1.0

Reference:

E.Nuti, D.Cuffaro, E.Bernardini, C.Camodeca, L.Panelli, S.Chaves, L.Ciccone, L.Tepshi, L.Vera, E.Orlandini, S.Nencetti, E.A.Stura, M.A.Santos, V.Dive, A.Rossello. Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, uc(Nmr), and Crystallographic Studies. J. Med. Chem. V. 61 4421 2018.
ISSN: ISSN 1520-4804
PubMed: 29727184
DOI: 10.1021/ACS.JMEDCHEM.8B00096
Page generated: Mon Oct 28 20:12:02 2024

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