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Calcium in PDB 3f17: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide:
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) Biphenyl-4-Sulfonamide, PDB code: 3f17 was solved by V.Calderone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.59 / 1.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.636, 60.250, 54.220, 90.00, 115.44, 90.00
R / Rfree (%) 17 / 18.1

Other elements in 3f17:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor N-(2-Nitroso-2-Oxoethyl) Biphenyl-4-Sulfonamide 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) Biphenyl-4-Sulfonamide (pdb code 3f17). 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) Biphenyl-4-Sulfonamide, PDB code: 3f17:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3f17

Go back to Calcium Binding Sites List in 3f17
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) Biphenyl-4-Sulfonamide


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) Biphenyl-4-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca266

b:13.2
occ:1.00
 O A:HOH66 2.3 17.6 1.0
O A:GLY192 2.3 8.2 1.0
O A:GLY190 2.4 14.4 1.0
O A:ASP158 2.5 8.3 1.0
O A:HOH12 2.5 9.1 1.0
OD2 A:ASP194 2.6 9.3 1.0
CG A:ASP194 3.5 8.2 1.0
C A:GLY192 3.5 7.8 1.0
C A:ASP158 3.5 7.3 1.0
C A:GLY190 3.6 13.5 1.0
C A:ILE191 3.9 11.4 1.0
OD1 A:ASP194 3.9 9.0 1.0
O A:ALA157 4.0 9.8 1.0
N A:GLY192 4.0 9.8 1.0
O A:ILE191 4.0 9.9 1.0
O A:HOH44 4.2 16.8 1.0
CA A:ILE191 4.3 13.8 1.0
N A:ASP194 4.3 6.3 1.0
CA A:GLY192 4.3 8.8 1.0
CA A:ASP158 4.3 7.5 1.0
N A:ILE191 4.4 13.3 1.0
O A:HOH412 4.4 25.0 1.0
N A:ILE159 4.4 6.5 1.0
N A:GLY193 4.5 7.2 1.0
O A:GLY188 4.5 11.6 1.0
CA A:ILE159 4.6 6.4 1.0
CA A:GLY193 4.6 6.8 1.0
CA A:GLY190 4.6 13.7 1.0
N A:GLY190 4.7 13.5 1.0
N A:LEU160 4.7 6.5 1.0
C A:GLY193 4.7 6.5 1.0
CB A:ASP194 4.7 7.0 1.0
CA A:ASP194 4.9 6.6 1.0
O A:HOH27 4.9 10.8 1.0
C A:ALA157 4.9 8.9 1.0
C A:SER189 5.0 13.4 1.0

Calcium binding site 2 out of 3 in 3f17

Go back to Calcium Binding Sites List in 3f17
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) Biphenyl-4-Sulfonamide


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) Biphenyl-4-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca267

b:6.7
occ:1.00
 O A:GLU199 2.3 7.1 1.0
O A:HOH6 2.4 8.1 1.0
OD2 A:ASP124 2.4 6.4 1.0
O A:HOH13 2.4 8.3 1.0
OE2 A:GLU199 2.4 6.7 1.0
O A:GLU201 2.4 7.2 1.0
OD1 A:ASP124 2.6 6.8 1.0
CG A:ASP124 2.8 6.1 1.0
C A:GLU199 3.4 7.2 1.0
CD A:GLU199 3.5 6.5 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 6.8 1.0
OG1 A:THR122 4.2 6.3 1.0
CA A:PHE202 4.2 7.4 1.0
CB A:ASP124 4.3 6.1 1.0
N A:PHE202 4.4 7.3 1.0
N A:GLU201 4.4 7.5 1.0
CD1 A:TRP203 4.5 6.2 1.0
N A:ASP200 4.5 7.6 1.0
C A:ASP200 4.5 8.2 1.0
OE1 A:GLU199 4.6 7.4 1.0
CB A:GLU199 4.6 6.8 1.0
CA A:ASP200 4.7 8.2 1.0
CA A:GLU201 4.7 7.4 1.0
O A:HOH23 4.8 11.1 1.0
CD1 A:PHE202 4.8 8.5 1.0
NH2 A:ARG165 4.8 13.2 1.0
N A:TRP203 4.9 6.7 1.0
NE1 A:TRP203 4.9 6.3 1.0

Calcium binding site 3 out of 3 in 3f17

Go back to Calcium Binding Sites List in 3f17
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) Biphenyl-4-Sulfonamide


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) Biphenyl-4-Sulfonamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca268

b:13.2
occ:1.00
 O A:GLY176 2.3 12.7 1.0
OD2 A:ASP175 2.3 12.7 1.0
O A:ILE180 2.3 12.2 1.0
OD1 A:ASP198 2.4 10.6 1.0
OE2 A:GLU201 2.5 16.4 1.0
O A:GLY178 2.5 14.7 1.0
C A:ILE180 3.4 11.8 1.0
CG A:ASP175 3.5 13.9 1.0
CG A:ASP198 3.5 8.3 1.0
C A:GLY176 3.5 12.9 1.0
CD A:GLU201 3.7 13.2 1.0
C A:GLY178 3.7 15.4 1.0
N A:ILE180 3.9 13.6 1.0
N A:GLY176 4.0 12.5 1.0
N A:GLY178 4.1 15.2 1.0
CB A:ASP198 4.1 7.4 1.0
OD1 A:ASP175 4.1 15.8 1.0
N A:ASP175 4.1 12.3 1.0
CA A:ILE180 4.1 13.1 1.0
C A:ASP175 4.2 13.0 1.0
C A:LYS177 4.3 14.7 1.0
CA A:GLY176 4.3 12.6 1.0
C A:GLY179 4.3 14.5 1.0
CG A:GLU201 4.3 9.8 1.0
OD2 A:ASP198 4.4 8.7 1.0
N A:LYS177 4.4 13.3 1.0
N A:LEU181 4.5 10.0 1.0
CA A:LYS177 4.5 14.2 1.0
CA A:ASP175 4.5 12.9 1.0
CA A:GLY178 4.5 15.5 1.0
CB A:ASP175 4.6 13.2 1.0
CB A:ILE180 4.6 13.6 1.0
OE1 A:GLU201 4.6 14.2 1.0
O A:ASP175 4.6 13.4 1.0
N A:GLY179 4.7 15.4 1.0
CA A:LEU181 4.7 9.4 1.0
CA A:GLY179 4.8 15.2 1.0
O A:GLY179 4.8 15.3 1.0
O A:LYS177 4.9 15.5 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: Sat Jul 13 09:39:59 2024

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