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Zinc in PDB 5h8x: Crystal Structure of the Complex Mmp-8/BF471 (Catechol Inhibitor)

Enzymatic activity of Crystal Structure of the Complex Mmp-8/BF471 (Catechol Inhibitor)

All present enzymatic activity of Crystal Structure of the Complex Mmp-8/BF471 (Catechol Inhibitor):
3.4.24.34;

Protein crystallography data

The structure of Crystal Structure of the Complex Mmp-8/BF471 (Catechol Inhibitor), PDB code: 5h8x was solved by G.Pochetti, R.Montanari, D.Capelli, P.Tortorella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 32.910, 68.460, 68.530, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.7

Other elements in 5h8x:

The structure of Crystal Structure of the Complex Mmp-8/BF471 (Catechol Inhibitor) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Complex Mmp-8/BF471 (Catechol Inhibitor) (pdb code 5h8x). 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 Complex Mmp-8/BF471 (Catechol Inhibitor), PDB code: 5h8x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5h8x

Go back to Zinc Binding Sites List in 5h8x
Zinc binding site 1 out of 2 in the Crystal Structure of the Complex Mmp-8/BF471 (Catechol 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 Complex Mmp-8/BF471 (Catechol Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:9.0
occ:1.00
OD2 A:ASP149 2.0 10.6 1.0
NE2 A:HIS162 2.0 8.7 1.0
NE2 A:HIS147 2.0 7.1 1.0
ND1 A:HIS175 2.1 8.7 1.0
CE1 A:HIS162 2.9 9.6 1.0
CG A:ASP149 2.9 11.2 1.0
CD2 A:HIS147 2.9 7.8 1.0
CE1 A:HIS175 3.0 8.4 1.0
CE1 A:HIS147 3.1 6.7 1.0
CD2 A:HIS162 3.1 7.9 1.0
CG A:HIS175 3.1 7.4 1.0
OD1 A:ASP149 3.2 11.2 1.0
CB A:HIS175 3.5 7.9 1.0
ND1 A:HIS162 4.1 8.9 1.0
CG A:HIS147 4.1 7.0 1.0
ND1 A:HIS147 4.1 8.1 1.0
NE2 A:HIS175 4.1 8.5 1.0
CG A:HIS162 4.2 7.9 1.0
CD2 A:HIS175 4.2 8.3 1.0
CB A:ASP149 4.2 12.3 1.0
CE2 A:PHE164 4.3 14.1 1.0
O A:SER151 4.3 11.7 1.0
CZ A:PHE164 4.6 18.0 1.0
CZ A:PHE153 4.6 7.8 1.0
O A:HOH478 4.8 13.8 1.0
CE2 A:PHE153 4.8 8.3 1.0
CA A:HIS175 4.9 6.6 1.0
O A:HOH479 5.0 10.9 1.0

Zinc binding site 2 out of 2 in 5h8x

Go back to Zinc Binding Sites List in 5h8x
Zinc binding site 2 out of 2 in the Crystal Structure of the Complex Mmp-8/BF471 (Catechol 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 Complex Mmp-8/BF471 (Catechol Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:9.8
occ:1.00
OAD A:7FY306 1.8 19.2 0.2
NE2 A:HIS207 2.0 10.2 1.0
NE2 A:HIS197 2.1 9.8 1.0
NE2 A:HIS201 2.1 8.8 1.0
CAW A:7FY306 2.5 19.4 0.2
CAE A:5XT305 2.6 17.9 0.8
CAG A:7FY306 2.7 20.9 0.2
CAF A:5XT305 2.8 18.8 0.8
CD2 A:HIS207 2.9 12.2 1.0
CE1 A:HIS207 3.0 12.3 1.0
CE1 A:HIS197 3.0 10.1 1.0
CD2 A:HIS201 3.0 8.8 1.0
CD2 A:HIS197 3.1 7.3 1.0
CE1 A:HIS201 3.1 10.2 1.0
CAR A:5XT305 3.5 18.1 0.8
CAR A:7FY306 3.8 18.6 0.2
CAS A:5XT305 3.8 23.1 0.8
CAS A:7FY306 4.0 22.6 0.2
CG A:HIS207 4.1 11.9 1.0
ND1 A:HIS207 4.1 11.5 1.0
OAA A:5XT305 4.1 16.0 0.8
ND1 A:HIS197 4.1 9.7 1.0
ND1 A:HIS201 4.2 9.6 1.0
CG A:HIS197 4.2 6.9 1.0
CG A:HIS201 4.2 9.3 1.0
CAW A:5XT305 4.3 18.4 0.8
OAA A:7FY306 4.4 17.6 0.2
CAG A:5XT305 4.4 23.2 0.8
O A:HOH458 4.6 22.7 1.0
CE A:MET215 4.7 10.9 1.0
OE1 A:GLU198 4.7 10.0 1.0
OE2 A:GLU198 4.7 11.2 1.0
NAQ A:5XT305 4.7 25.2 0.8
NAQ A:7FY306 4.8 24.1 0.2
CAE A:7FY306 4.8 19.8 0.2
CAF A:7FY306 4.9 21.3 0.2

Reference:

M.Tauro, A.Laghezza, F.Loiodice, L.Piemontese, A.Caradonna, D.Capelli, R.Montanari, G.Pochetti, A.Di Pizio, M.Agamennone, C.Campestre, P.Tortorella. Catechol-Based Matrix Metalloproteinase Inhibitors with Additional Antioxidative Activity. J Enzyme Inhib Med Chem V. 31 25 2016.
ISSN: ESSN 1475-6374
PubMed: 27556138
DOI: 10.1080/14756366.2016.1217853
Page generated: Wed Dec 16 06:20:09 2020

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