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Calcium in PDB 3f1a: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide, PDB code: 3f1a was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.69 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.834, 60.282, 54.178, 90.00, 115.17, 90.00
R / Rfree (%) 16.7 / 18.9

Other elements in 3f1a:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide 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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide (pdb code 3f1a). 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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide, PDB code: 3f1a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3f1a

Go back to Calcium Binding Sites List in 3f1a
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide


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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:13.6
occ:1.00
 O A:HOH99 2.3 20.4 1.0
O A:GLY192 2.4 7.6 1.0
O A:GLY190 2.4 13.8 1.0
O A:ASP158 2.4 7.9 1.0
O A:HOH9 2.5 8.8 1.0
OD2 A:ASP194 2.6 8.3 1.0
CG A:ASP194 3.5 7.7 1.0
C A:ASP158 3.5 7.3 1.0
C A:GLY192 3.5 7.7 1.0
C A:GLY190 3.6 12.9 1.0
C A:ILE191 3.8 10.7 1.0
OD1 A:ASP194 3.9 8.6 1.0
O A:ALA157 3.9 9.7 1.0
N A:GLY192 4.0 9.6 1.0
O A:ILE191 4.1 10.1 1.0
CA A:ILE191 4.2 12.1 1.0
O A:HOH41 4.2 16.2 1.0
O A:HOH323 4.3 0.5 1.0
CA A:ASP158 4.3 7.5 1.0
N A:ILE191 4.3 12.3 1.0
N A:ASP194 4.3 6.4 1.0
CA A:GLY192 4.4 8.7 1.0
N A:ILE159 4.4 6.7 1.0
O A:HOH328 4.4 24.9 1.0
N A:GLY193 4.5 7.4 1.0
CA A:ILE159 4.5 6.4 1.0
O A:GLY188 4.6 11.3 1.0
N A:LEU160 4.6 6.4 1.0
CA A:GLY193 4.6 7.0 1.0
CA A:GLY190 4.7 13.4 1.0
CB A:ASP194 4.7 6.7 1.0
N A:GLY190 4.7 13.4 1.0
C A:GLY193 4.7 6.8 1.0
O A:HOH31 4.9 10.5 1.0
C A:ALA157 4.9 9.4 1.0
CA A:ASP194 4.9 6.5 1.0

Calcium binding site 2 out of 3 in 3f1a

Go back to Calcium Binding Sites List in 3f1a
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide


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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:6.6
occ:1.00
 O A:GLU199 2.3 7.3 1.0
O A:HOH16 2.4 9.2 1.0
OE2 A:GLU199 2.4 6.1 1.0
OD2 A:ASP124 2.4 6.5 1.0
O A:HOH7 2.4 8.5 1.0
O A:GLU201 2.4 7.0 1.0
OD1 A:ASP124 2.6 7.2 1.0
CG A:ASP124 2.8 6.2 1.0
C A:GLU199 3.4 7.1 1.0
CD A:GLU199 3.5 6.2 1.0
C A:GLU201 3.6 7.0 1.0
CG A:GLU199 3.9 7.0 1.0
CA A:GLU199 4.1 7.0 1.0
OG1 A:THR122 4.1 6.8 1.0
CA A:PHE202 4.2 7.7 1.0
CB A:ASP124 4.3 6.3 1.0
N A:PHE202 4.4 7.5 1.0
CD1 A:TRP203 4.4 6.0 1.0
N A:GLU201 4.5 7.3 1.0
N A:ASP200 4.5 7.6 1.0
C A:ASP200 4.6 7.9 1.0
OE1 A:GLU199 4.6 7.6 1.0
CB A:GLU199 4.6 6.5 1.0
NH2 A:ARG165 4.7 12.3 1.0
CA A:ASP200 4.7 7.7 1.0
CA A:GLU201 4.7 7.3 1.0
O A:HOH15 4.8 11.2 1.0
CD1 A:PHE202 4.8 9.0 1.0
NE1 A:TRP203 4.9 5.9 1.0
N A:TRP203 4.9 6.9 1.0
O A:HOH23 4.9 12.8 1.0

Calcium binding site 3 out of 3 in 3f1a

Go back to Calcium Binding Sites List in 3f1a
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide


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-(2-Nitroso-2-Oxoethyl) Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:9.9
occ:1.00
 OE2 A:GLU201 2.2 13.3 1.0
O A:GLY176 2.3 10.5 1.0
O A:ILE180 2.3 10.5 1.0
OD2 A:ASP175 2.3 10.5 1.0
OD1 A:ASP198 2.3 8.8 1.0
O A:GLY178 2.4 11.9 1.0
C A:ILE180 3.4 9.9 1.0
CG A:ASP198 3.4 7.1 1.0
CD A:GLU201 3.5 11.2 1.0
C A:GLY176 3.5 10.7 1.0
CG A:ASP175 3.5 11.0 1.0
C A:GLY178 3.5 11.9 1.0
N A:GLY178 3.8 12.0 1.0
N A:ILE180 3.9 11.3 1.0
OD1 A:ASP175 4.0 12.4 1.0
CB A:ASP198 4.1 6.8 1.0
N A:GLY176 4.1 10.5 1.0
C A:LYS177 4.1 11.9 1.0
CA A:ILE180 4.2 10.7 1.0
OE1 A:GLU201 4.2 11.8 1.0
C A:ASP175 4.3 10.6 1.0
N A:ASP175 4.3 10.2 1.0
CA A:GLY178 4.3 11.9 1.0
C A:GLY179 4.3 11.7 1.0
N A:LYS177 4.4 11.0 1.0
CA A:LYS177 4.4 11.8 1.0
OD2 A:ASP198 4.4 7.2 1.0
CA A:GLY176 4.4 10.5 1.0
N A:LEU181 4.4 8.7 1.0
CG A:GLU201 4.4 8.6 1.0
N A:GLY179 4.6 11.9 1.0
CA A:ASP175 4.6 10.5 1.0
CB A:ASP175 4.6 11.2 1.0
CA A:LEU181 4.6 8.2 1.0
CB A:ILE180 4.7 11.2 1.0
O A:LYS177 4.7 12.5 1.0
O A:ASP175 4.7 10.8 1.0
CA A:GLY179 4.7 12.0 1.0
O A:GLY179 4.9 12.3 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, A.Giachetti, M.Loconte, C.Luchinat, M.Maletta, C.Nativi, K.J.Yeo. Exploring the Subtleties of Drug-Receptor Interactions: the Case of Matrix Metalloproteinases. J.Am.Chem.Soc. V. 129 2466 2007.
ISSN: ISSN 0002-7863
PubMed: 17269766
DOI: 10.1021/JA065156Z
Page generated: Tue Jul 8 12:04:28 2025

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