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Calcium 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:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5n5k

Go back to Calcium Binding Sites List in 5n5k
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca303

b:9.9
occ:1.00
 O A:ASP158 2.2 11.3 1.0
O A:GLY192 2.2 11.9 1.0
O A:HOH414 2.3 12.7 1.0
O A:GLY190 2.3 17.5 1.0
O A:HOH434 2.3 10.9 1.0
OD1 A:ASP194 2.4 10.3 1.0
CG A:ASP194 3.3 10.6 1.0
C A:ASP158 3.4 11.9 1.0
C A:GLY192 3.4 11.8 1.0
C A:GLY190 3.5 16.7 1.0
OD2 A:ASP194 3.8 10.7 1.0
C A:ILE191 4.0 14.5 1.0
O A:ALA157 4.0 17.1 1.0
N A:GLY192 4.1 13.8 1.0
O A:ILE191 4.1 13.3 1.0
O A:HOH464 4.2 25.1 1.0
CA A:ASP158 4.2 12.5 1.0
CA A:GLY192 4.3 12.9 1.0
O A:GLY188 4.3 14.5 1.0
N A:ASP194 4.3 10.0 1.0
N A:ILE191 4.3 16.3 1.0
N A:ILE159 4.3 11.2 1.0
CA A:ILE191 4.3 16.0 1.0
N A:GLY193 4.4 11.0 1.0
CA A:GLY190 4.4 17.6 1.0
N A:GLY190 4.5 17.0 1.0
CA A:GLY193 4.5 10.3 1.0
CA A:ILE159 4.5 11.1 1.0
N A:LEU160 4.6 11.3 1.0
CB A:ASP194 4.6 10.2 1.0
C A:GLY193 4.6 9.9 1.0
O A:HOH454 4.7 14.7 1.0
C A:SER189 4.8 17.1 1.0
CA A:ASP194 4.8 9.9 1.0
C A:ALA157 5.0 15.8 1.0

Calcium binding site 2 out of 3 in 5n5k

Go back to Calcium Binding Sites List in 5n5k
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca304

b:9.7
occ:1.00
 O A:GLU201 2.3 9.8 1.0
OD2 A:ASP124 2.3 10.0 1.0
O A:GLU199 2.3 10.4 1.0
O A:HOH507 2.4 12.6 1.0
OE1 A:GLU199 2.4 10.3 1.0
OD1 A:ASP124 2.5 9.9 1.0
CG A:ASP124 2.8 10.5 1.0
C A:GLU199 3.5 10.5 1.0
CD A:GLU199 3.5 10.4 1.0
C A:GLU201 3.6 10.0 1.0
CG A:GLU199 3.9 10.3 1.0
OG1 A:THR122 4.1 9.5 1.0
CA A:GLU199 4.2 10.1 1.0
CA A:PHE202 4.2 10.3 1.0
N A:PHE202 4.3 10.1 1.0
CB A:ASP124 4.3 10.3 1.0
CD1 A:TRP203 4.4 9.1 1.0
N A:GLU201 4.5 10.4 1.0
N A:ASP200 4.5 11.2 1.0
C A:ASP200 4.6 11.0 1.0
CB A:GLU199 4.6 10.2 1.0
OE2 A:GLU199 4.6 10.4 1.0
CA A:GLU201 4.7 10.3 1.0
CA A:ASP200 4.7 11.3 1.0
N A:TRP203 4.8 9.9 1.0
O A:HOH451 4.8 14.8 1.0
NE1 A:TRP203 4.8 9.2 1.0
CD1 A:PHE202 4.8 11.1 1.0
NH2 A:ARG165 4.9 19.6 1.0

Calcium binding site 3 out of 3 in 5n5k

Go back to Calcium Binding Sites List in 5n5k
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca305

b:12.1
occ:1.00
 O A:GLY176 2.2 13.1 1.0
OD2 A:ASP198 2.3 9.4 1.0
O A:GLY178 2.3 14.3 1.0
O A:ILE180 2.3 12.6 1.0
OE1 A:GLU201 2.3 12.3 1.0
OD1 A:ASP175 2.4 13.5 1.0
CG A:ASP198 3.4 9.4 1.0
C A:ILE180 3.4 12.9 1.0
C A:GLY178 3.5 14.4 1.0
C A:GLY176 3.5 13.9 1.0
CG A:ASP175 3.6 14.1 1.0
CD A:GLU201 3.6 11.3 1.0
N A:GLY178 3.9 14.2 1.0
CB A:ASP198 4.0 9.2 1.0
N A:GLY176 4.0 13.8 1.0
N A:ILE180 4.0 14.0 1.0
OD2 A:ASP175 4.1 14.1 1.0
C A:LYS177 4.1 15.0 1.0
CA A:GLY178 4.2 14.6 1.0
OE2 A:GLU201 4.2 11.4 1.0
C A:ASP175 4.2 14.2 1.0
CA A:ILE180 4.2 13.6 1.0
N A:ASP175 4.3 13.7 1.0
OD1 A:ASP198 4.3 9.4 1.0
CA A:GLY176 4.4 13.7 1.0
N A:LYS177 4.4 14.4 1.0
C A:GLY179 4.4 14.0 1.0
N A:LEU181 4.4 11.6 1.0
CA A:LYS177 4.4 15.6 1.0
N A:GLY179 4.5 14.4 1.0
CA A:LEU181 4.6 11.2 1.0
CG A:GLU201 4.6 10.5 1.0
CA A:ASP175 4.6 14.2 1.0
O A:LYS177 4.6 15.1 1.0
O A:ASP175 4.6 14.5 1.0
CB A:ASP175 4.7 14.4 1.0
CB A:ILE180 4.7 13.9 1.0
CA A:GLY179 4.7 14.9 1.0
O A:GLY179 4.9 13.8 1.0
CD2 A:LEU181 4.9 11.8 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: Mon Jul 15 08:47:41 2024

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