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Calcium in PDB 3f15: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-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 (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide, PDB code: 3f15 was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.45 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.557, 60.472, 53.859, 90.00, 114.55, 90.00
R / Rfree (%) 17.1 / 19

Other elements in 3f15:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-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 (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide (pdb code 3f15). 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 (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide, PDB code: 3f15:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3f15

Go back to Calcium Binding Sites List in 3f15
Calcium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-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 (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:18.0
occ:1.00
 O A:GLY190 2.4 12.1 1.0
O A:GLY192 2.5 6.7 1.0
OD2 A:ASP194 2.6 6.9 1.0
O A:HOH9 2.6 7.0 1.0
O A:ASP158 2.6 9.0 1.0
O A:HOH295 3.3 25.1 1.0
CG A:ASP194 3.5 7.8 1.0
C A:GLY190 3.6 11.4 1.0
C A:ASP158 3.6 8.1 1.0
C A:GLY192 3.7 6.7 1.0
O A:ALA157 3.8 10.7 1.0
OD1 A:ASP194 3.8 7.8 1.0
C A:ILE191 3.8 9.2 1.0
N A:GLY192 4.0 7.7 1.0
CA A:ILE191 4.0 10.7 1.0
O A:HOH56 4.1 17.9 1.0
O A:ILE191 4.1 9.3 1.0
O A:HOH300 4.1 27.0 1.0
N A:ILE191 4.3 10.9 1.0
CA A:ASP158 4.4 8.7 1.0
N A:ASP194 4.4 4.9 1.0
CA A:GLY192 4.4 6.8 1.0
N A:ILE159 4.5 7.5 1.0
N A:LEU160 4.6 6.7 1.0
N A:GLY193 4.6 6.0 1.0
CA A:ILE159 4.6 6.9 1.0
O A:GLY188 4.6 10.4 1.0
CB A:ASP194 4.7 5.5 1.0
CA A:GLY190 4.7 12.0 1.0
C A:ALA157 4.8 11.1 1.0
CA A:GLY193 4.8 5.5 1.0
N A:GLY190 4.8 11.3 1.0
C A:GLY193 4.8 5.5 1.0
CA A:ASP194 4.9 5.5 1.0
O A:HOH74 5.0 10.6 1.0

Calcium binding site 2 out of 3 in 3f15

Go back to Calcium Binding Sites List in 3f15
Calcium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-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 (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:6.0
occ:1.00
 O A:GLU199 2.3 3.4 1.0
OD2 A:ASP124 2.4 5.8 1.0
OE2 A:GLU199 2.4 5.6 1.0
O A:HOH48 2.4 7.0 1.0
O A:GLU201 2.4 5.2 1.0
O A:HOH13 2.4 5.1 1.0
OD1 A:ASP124 2.6 6.4 1.0
CG A:ASP124 2.8 5.0 1.0
CD A:GLU199 3.4 5.9 1.0
C A:GLU199 3.5 5.1 1.0
C A:GLU201 3.7 5.4 1.0
CG A:GLU199 3.9 5.1 1.0
OG1 A:THR122 4.0 4.0 1.0
CA A:GLU199 4.1 4.9 1.0
CA A:PHE202 4.3 5.5 1.0
CB A:ASP124 4.3 5.9 1.0
CD1 A:TRP203 4.4 4.7 1.0
N A:PHE202 4.4 5.1 1.0
N A:GLU201 4.5 6.4 1.0
N A:ASP200 4.5 5.9 1.0
OE1 A:GLU199 4.6 6.6 1.0
C A:ASP200 4.6 6.8 1.0
CB A:GLU199 4.6 5.2 1.0
NH2 A:ARG165 4.7 9.7 1.0
CA A:ASP200 4.7 6.0 1.0
CA A:GLU201 4.7 5.5 1.0
NE1 A:TRP203 4.8 5.1 1.0
O A:HOH12 4.9 7.8 1.0
O A:HOH10 4.9 7.3 1.0
CD1 A:PHE202 4.9 7.0 1.0
N A:TRP203 4.9 5.2 1.0

Calcium binding site 3 out of 3 in 3f15

Go back to Calcium Binding Sites List in 3f15
Calcium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-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 (S)-N-(2,3-Dihydroxypropyl)-4-Methoxy-N-(2- Nitroso-2-Oxoethyl)Benzenesulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:8.4
occ:1.00
 OE2 A:GLU201 2.2 11.8 1.0
O A:GLY176 2.3 9.3 1.0
O A:ILE180 2.3 8.8 1.0
OD1 A:ASP198 2.3 5.9 1.0
OD2 A:ASP175 2.4 10.7 1.0
O A:GLY178 2.4 10.1 1.0
C A:ILE180 3.4 8.2 1.0
CD A:GLU201 3.4 9.1 1.0
CG A:ASP198 3.4 4.9 1.0
C A:GLY176 3.5 9.0 1.0
CG A:ASP175 3.6 11.5 1.0
C A:GLY178 3.6 10.2 1.0
N A:GLY178 3.9 10.6 1.0
N A:ILE180 3.9 8.5 1.0
CB A:ASP198 4.0 4.6 1.0
OE1 A:GLU201 4.1 9.4 1.0
N A:GLY176 4.1 8.2 1.0
C A:LYS177 4.2 10.4 1.0
OD1 A:ASP175 4.2 10.8 1.0
CA A:ILE180 4.2 8.2 1.0
N A:ASP175 4.2 9.4 1.0
C A:ASP175 4.3 8.7 1.0
C A:GLY179 4.3 9.4 1.0
N A:LEU181 4.3 6.8 1.0
CA A:GLY178 4.4 10.7 1.0
OD2 A:ASP198 4.4 4.4 1.0
CA A:GLY176 4.4 8.1 1.0
N A:LYS177 4.4 9.0 1.0
CA A:LYS177 4.4 10.4 1.0
CG A:GLU201 4.5 6.0 1.0
CA A:LEU181 4.5 6.3 1.0
CA A:ASP175 4.6 9.0 1.0
N A:GLY179 4.6 9.8 1.0
CB A:ASP175 4.7 9.4 1.0
CB A:ILE180 4.7 8.5 1.0
O A:ASP175 4.7 8.7 1.0
CA A:GLY179 4.8 9.7 1.0
O A:LYS177 4.8 10.6 1.0
O A:GLY179 4.8 9.3 1.0
CD2 A:LEU181 4.9 7.0 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 12:03:13 2025

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