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Zinc in PDB 5cxa: Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470, PDB code: 5cxa was solved by C.Rouanet-Mehouas, L.Devel, V.Dive, E.A.Stura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.62 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.230, 63.700, 36.620, 90.00, 90.00, 90.00
R / Rfree (%) 14 / 18.1

Other elements in 5cxa:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 3 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 Carboxylate Inhibitor Related to RXP470 (pdb code 5cxa). 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 A Carboxylate Inhibitor Related to RXP470, PDB code: 5cxa:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5cxa

Go back to Zinc Binding Sites List in 5cxa
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470


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 Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:11.7
occ:1.00
 O23 A:55L306 1.9 11.0 0.9
O23 A:55L306 1.9 12.0 0.1
NE2 A:HIS228 2.0 12.5 1.0
NE2 A:HIS222 2.0 11.1 1.0
NE2 A:HIS218 2.1 12.2 1.0
C22 A:55L306 2.7 12.1 0.1
C22 A:55L306 2.7 10.3 0.9
O24 A:55L306 2.8 12.1 0.1
O24 A:55L306 2.9 11.4 0.9
CD2 A:HIS228 3.0 12.9 1.0
CE1 A:HIS222 3.0 12.4 1.0
CE1 A:HIS228 3.0 13.1 1.0
CE1 A:HIS218 3.0 11.5 1.0
CD2 A:HIS222 3.0 10.1 1.0
CD2 A:HIS218 3.1 10.0 1.0
C21 A:55L306 4.0 12.4 0.1
C21 A:55L306 4.0 10.2 0.9
ND1 A:HIS228 4.1 14.6 1.0
ND1 A:HIS222 4.1 12.2 1.0
CG A:HIS228 4.1 13.5 1.0
O A:HOH466 4.1 21.7 1.0
ND1 A:HIS218 4.1 11.1 1.0
CG A:HIS222 4.2 11.1 1.0
CG A:HIS218 4.2 10.3 1.0
O A:HOH535 4.4 13.9 1.0
C19 A:55L306 4.5 10.4 0.9
C19 A:55L306 4.5 12.9 0.1
O A:HOH613 4.5 35.0 1.0
CE A:MET236 4.6 13.0 1.0
O A:HOH664 4.7 36.8 1.0
C71 A:55L306 4.8 11.1 0.9
C71 A:55L306 4.8 12.9 0.1
O A:HOH610 4.8 22.7 1.0

Zinc binding site 2 out of 2 in 5cxa

Go back to Zinc Binding Sites List in 5cxa
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 in Complex with A Carboxylate Inhibitor Related to RXP470


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 Carboxylate Inhibitor Related to RXP470 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:10.1
occ:1.00
 OD2 A:ASP170 2.0 12.4 1.0
NE2 A:HIS183 2.0 13.7 1.0
NE2 A:HIS168 2.0 9.5 1.0
ND1 A:HIS196 2.1 9.1 1.0
CE1 A:HIS183 2.8 16.1 1.0
CG A:ASP170 2.9 10.6 1.0
CD2 A:HIS168 2.9 10.4 1.0
CE1 A:HIS196 3.0 11.4 1.0
CE1 A:HIS168 3.1 8.1 1.0
CG A:HIS196 3.1 8.9 1.0
OD1 A:ASP170 3.1 12.4 1.0
CD2 A:HIS183 3.2 16.8 1.0
CB A:HIS196 3.5 9.0 1.0
ND1 A:HIS183 4.0 15.1 1.0
CG A:HIS168 4.1 10.8 1.0
NE2 A:HIS196 4.1 10.5 1.0
ND1 A:HIS168 4.1 9.7 1.0
CG A:HIS183 4.2 11.4 1.0
CD2 A:HIS196 4.2 10.7 1.0
O A:HIS172 4.3 14.8 1.0
CB A:ASP170 4.3 12.7 1.0
CE1 A:PHE185 4.5 14.9 1.0
CZ A:PHE185 4.7 14.8 1.0
CZ A:PHE174 4.7 9.1 1.0
O A:HOH546 4.7 36.8 1.0
O A:HOH486 4.9 13.7 1.0
CB A:HIS172 4.9 20.8 1.0
CE2 A:PHE174 5.0 9.4 1.0

Reference:

C.Rouanet-Mehouas, B.Czarny, F.Beau, E.Cassar-Lajeunesse, E.A.Stura, V.Dive, L.Devel. Zinc-Metalloproteinase Inhibitors: Evaluation of the Complex Role Played By the Zinc-Binding Group on Potency and Selectivity. J. Med. Chem. V. 60 403 2017.
ISSN: ISSN 1520-4804
PubMed: 27996256
DOI: 10.1021/ACS.JMEDCHEM.6B01420
Page generated: Sun Oct 27 14:29:40 2024

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