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Calcium in PDB 3n2u: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide, PDB code: 3n2u was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.22 / 1.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.394, 60.446, 54.043, 90.00, 114.67, 90.00
R / Rfree (%) 16.1 / 21.9

Other elements in 3n2u:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide (pdb code 3n2u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide, PDB code: 3n2u:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3n2u

Go back to Calcium Binding Sites List in 3n2u
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:16.9
occ:1.00
 O A:GLY190 2.4 11.8 1.0
O A:GLY192 2.4 6.9 1.0
O A:ASP158 2.5 8.2 1.0
O A:HOH320 2.5 24.4 1.0
OD2 A:ASP194 2.6 5.7 1.0
O A:HOH7 2.6 5.2 1.0
CG A:ASP194 3.5 5.8 1.0
C A:ASP158 3.5 8.4 1.0
C A:GLY192 3.6 6.4 1.0
C A:GLY190 3.6 11.8 1.0
OD1 A:ASP194 3.8 6.1 1.0
O A:ALA157 3.8 11.1 1.0
C A:ILE191 3.9 10.0 1.0
N A:GLY192 4.0 8.9 1.0
O A:HOH51 4.1 16.8 1.0
O A:ILE191 4.1 9.9 1.0
CA A:ILE191 4.2 11.5 1.0
CA A:ASP158 4.3 9.3 1.0
N A:ILE191 4.3 10.4 1.0
N A:ASP194 4.4 3.7 1.0
CA A:GLY192 4.4 7.2 1.0
N A:ILE159 4.4 7.2 1.0
O A:GLY188 4.5 11.4 1.0
N A:LEU160 4.6 6.1 1.0
N A:GLY193 4.6 5.8 1.0
CA A:ILE159 4.6 6.2 1.0
CA A:GLY190 4.7 12.4 1.0
N A:GLY190 4.7 11.9 1.0
CB A:ASP194 4.7 4.5 1.0
CA A:GLY193 4.7 5.2 1.0
C A:GLY193 4.8 5.1 1.0
O A:HOH44 4.8 8.3 1.0
C A:ALA157 4.8 11.9 1.0
CA A:ASP194 4.9 5.0 1.0

Calcium binding site 2 out of 3 in 3n2u

Go back to Calcium Binding Sites List in 3n2u
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:7.0
occ:1.00
 O A:GLU199 2.3 5.1 1.0
OD2 A:ASP124 2.4 8.0 1.0
OE2 A:GLU199 2.4 4.7 1.0
O A:HOH15 2.4 6.7 1.0
O A:GLU201 2.4 7.0 1.0
O A:HOH56 2.5 9.2 1.0
OD1 A:ASP124 2.5 4.5 1.0
CG A:ASP124 2.8 5.1 1.0
C A:GLU199 3.5 6.1 1.0
CD A:GLU199 3.5 5.9 1.0
C A:GLU201 3.6 6.5 1.0
CG A:GLU199 3.9 4.0 1.0
OG1 A:THR122 4.1 4.5 1.0
CA A:GLU199 4.1 5.6 1.0
CA A:PHE202 4.3 7.5 1.0
CB A:ASP124 4.3 6.2 1.0
N A:PHE202 4.4 6.7 1.0
CD1 A:TRP203 4.4 4.3 1.0
N A:GLU201 4.4 6.9 1.0
C A:ASP200 4.5 7.8 1.0
N A:ASP200 4.5 6.5 1.0
OE1 A:GLU199 4.6 5.4 1.0
CB A:GLU199 4.6 6.1 1.0
CA A:GLU201 4.7 7.2 1.0
CA A:ASP200 4.7 7.2 1.0
O A:HOH40 4.8 14.9 1.0
NH2 A:ARG165 4.8 15.2 1.0
N A:TRP203 4.9 6.3 1.0
NE1 A:TRP203 4.9 3.7 1.0
CD1 A:PHE202 4.9 8.0 1.0
O A:ASP200 4.9 8.8 1.0

Calcium binding site 3 out of 3 in 3n2u

Go back to Calcium Binding Sites List in 3n2u
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-Hydroxy-2-(4-Methoxy-N(2-(3,4,5-Trihydroxy-6- (Hydroxymethyl)Tetrahydro-2H-Pyran-2-Yloxy)Ethyl)Phenylsulfonamido) Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:11.8
occ:1.00
 O A:GLY176 2.3 12.7 1.0
OD2 A:ASP175 2.3 12.6 1.0
O A:ILE180 2.3 11.2 1.0
OD1 A:ASP198 2.4 7.0 1.0
OE2 A:GLU201 2.4 12.2 1.0
O A:GLY178 2.4 12.1 1.0
CG A:ASP198 3.4 6.2 1.0
C A:GLY176 3.5 12.5 1.0
C A:ILE180 3.5 10.0 1.0
CG A:ASP175 3.5 13.0 1.0
CD A:GLU201 3.6 9.4 1.0
C A:GLY178 3.6 12.5 1.0
N A:GLY178 3.9 13.4 1.0
N A:ILE180 4.0 10.7 1.0
CB A:ASP198 4.1 4.2 1.0
OD1 A:ASP175 4.1 13.8 1.0
C A:LYS177 4.1 14.1 1.0
N A:GLY176 4.2 11.3 1.0
CA A:ILE180 4.3 10.6 1.0
CG A:GLU201 4.3 7.7 1.0
C A:GLY179 4.3 11.3 1.0
C A:ASP175 4.3 10.9 1.0
CA A:GLY178 4.3 13.3 1.0
CA A:LYS177 4.3 14.0 1.0
N A:ASP175 4.3 9.9 1.0
N A:LYS177 4.3 12.3 1.0
OD2 A:ASP198 4.4 6.5 1.0
CA A:GLY176 4.4 11.4 1.0
OE1 A:GLU201 4.5 10.9 1.0
N A:LEU181 4.5 8.1 1.0
N A:GLY179 4.6 12.5 1.0
CA A:LEU181 4.7 7.3 1.0
CA A:ASP175 4.7 10.9 1.0
O A:LYS177 4.7 14.6 1.0
CB A:ASP175 4.7 10.9 1.0
O A:ASP175 4.7 11.2 1.0
CB A:ILE180 4.8 10.6 1.0
CA A:GLY179 4.8 12.2 1.0
O A:GLY179 4.8 11.0 1.0
O A:HOH9 4.9 6.1 1.0

Reference:

E.Attolino, V.Calderone, E.Dragoni, M.Fragai, B.Richichi, C.Luchinat, C.Nativi. Structure-Based Approach to Nanomolar, Water Soluble Matrix Metalloproteinases Inhibitors (Mmpis). Eur.J.Med.Chem. V. 45 5919 2010.
ISSN: ISSN 0223-5234
PubMed: 20965620
DOI: 10.1016/J.EJMECH.2010.09.057
Page generated: Sat Jul 13 14:50:36 2024

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