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Zinc in PDB 5n5k: Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide

Enzymatic activity of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide

All present enzymatic activity of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide:
3.4.24.65;

Protein crystallography data

The structure of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide, PDB code: 5n5k was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.62 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 50.790, 60.170, 53.730, 90.00, 114.61, 90.00
R / Rfree (%) 16.7 / 22.7

Other elements in 5n5k:

The structure of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide (pdb code 5n5k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide, PDB code: 5n5k:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5n5k

Go back to Zinc Binding Sites List in 5n5k
Zinc binding site 1 out of 2 in the Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:9.4
occ:1.00
NE2 A:HIS228 2.0 11.0 1.0
O2 A:HAE306 2.1 25.7 1.0
O A:HAE306 2.1 18.5 1.0
NE2 A:HIS222 2.1 9.8 1.0
NE2 A:HIS218 2.1 9.2 1.0
CE1 A:HIS228 2.9 11.6 1.0
C2 A:HAE306 2.9 25.0 1.0
N A:HAE306 3.0 21.7 1.0
CD2 A:HIS222 3.0 9.6 1.0
CD2 A:HIS228 3.1 11.2 1.0
CD2 A:HIS218 3.1 8.8 1.0
CE1 A:HIS218 3.1 9.2 1.0
CE1 A:HIS222 3.1 9.8 1.0
O1 A:8NW307 3.6 41.7 1.0
O A:HOH515 4.0 10.5 1.0
ND1 A:HIS228 4.1 12.0 1.0
CG A:HIS228 4.1 11.8 1.0
OE1 A:GLU219 4.2 10.4 1.0
CG A:HIS222 4.2 9.5 1.0
ND1 A:HIS222 4.2 9.6 1.0
ND1 A:HIS218 4.2 8.6 1.0
CG A:HIS218 4.2 8.7 1.0
C1 A:HAE306 4.4 27.4 1.0
C10 A:8NW307 4.7 34.6 1.0
OE2 A:GLU219 4.9 10.2 1.0
CD A:GLU219 4.9 10.0 1.0
O A:HOH560 4.9 43.5 1.0
CE A:MET236 5.0 10.5 1.0

Zinc binding site 2 out of 2 in 5n5k

Go back to Zinc Binding Sites List in 5n5k
Zinc binding site 2 out of 2 in the Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Catalytic Mmp-12 in Complex with 5-(1,2-Dithiolan-3-Yl)-N-(3- Hydroxypropyl)Pentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:11.5
occ:1.00
OD2 A:ASP170 2.0 16.3 1.0
ND1 A:HIS196 2.0 10.1 1.0
NE2 A:HIS168 2.0 12.0 1.0
NE2 A:HIS183 2.1 15.3 1.0
CE1 A:HIS183 2.7 16.7 1.0
CG A:ASP170 2.9 18.0 1.0
CD2 A:HIS168 2.9 12.3 1.0
CE1 A:HIS196 2.9 10.3 1.0
CG A:HIS196 3.1 9.7 1.0
CE1 A:HIS168 3.1 12.9 1.0
OD1 A:ASP170 3.2 16.1 1.0
CD2 A:HIS183 3.3 16.1 1.0
CB A:HIS196 3.5 9.3 1.0
ND1 A:HIS183 4.0 17.1 1.0
NE2 A:HIS196 4.1 10.2 1.0
CG A:HIS168 4.1 13.1 1.0
O A:HIS172 4.1 17.3 1.0
ND1 A:HIS168 4.2 12.8 1.0
CD2 A:HIS196 4.2 9.7 1.0
CB A:ASP170 4.2 19.5 1.0
CG A:HIS183 4.3 14.1 1.0
CE1 A:PHE185 4.4 16.3 1.0
CB A:HIS172 4.5 26.0 1.0
CZ A:PHE174 4.7 11.2 1.0
CE2 A:PHE174 4.7 11.4 1.0
CZ A:PHE185 4.8 17.1 1.0
C A:HIS172 4.9 19.3 1.0
O A:HOH443 4.9 39.6 1.0
O A:HOH460 5.0 11.7 1.0

Reference:

M.Fragai, G.Comito, L.Di Cesare Mannelli, R.Gualdani, V.Calderone, A.Louka, B.Richichi, O.Francesconi, A.Angeli, A.Nocentini, P.Gratteri, P.Chiarugi, C.Ghelardini, F.Tadini-Buoninsegni, C.T.Supuran, C.Nativi. Lipoyl-Homotaurine Derivative (ADM_12) Reverts Oxaliplatin-Induced Neuropathy and Reduces Cancer Cells Malignancy By Inhibiting Carbonic Anhydrase IX (Caix). J. Med. Chem. V. 60 9003 2017.
ISSN: ISSN 1520-4804
PubMed: 29048889
DOI: 10.1021/ACS.JMEDCHEM.7B01237
Page generated: Wed Dec 16 06:34:29 2020

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