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Calcium in PDB 1os9: Binary Enzyme-Product Complexes of Human MMP12

Enzymatic activity of Binary Enzyme-Product Complexes of Human MMP12

All present enzymatic activity of Binary Enzyme-Product Complexes of Human MMP12:
3.4.24.65;

Protein crystallography data

The structure of Binary Enzyme-Product Complexes of Human MMP12, PDB code: 1os9 was solved by I.Bertini, V.Calderone, M.Fragai, C.Luchinat, S.Mangani, B.Terni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 1.85
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 125.445, 125.445, 72.339, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 24.4

Other elements in 1os9:

The structure of Binary Enzyme-Product Complexes of Human MMP12 also contains other interesting chemical elements:

Zinc (Zn) 12 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Binary Enzyme-Product Complexes of Human MMP12 (pdb code 1os9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Binary Enzyme-Product Complexes of Human MMP12, PDB code: 1os9:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 1os9

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Calcium binding site 1 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:16.4
occ:1.00
O A:GLY176 2.2 19.1 1.0
OE2 A:GLU201 2.2 19.7 1.0
O A:GLY178 2.3 18.0 1.0
OD1 A:ASP198 2.3 17.5 1.0
O A:ILE180 2.4 17.7 1.0
OD2 A:ASP175 2.4 16.8 1.0
CG A:ASP198 3.4 16.9 1.0
C A:GLY176 3.4 18.4 1.0
C A:GLY178 3.4 18.1 1.0
CD A:GLU201 3.5 19.6 1.0
C A:ILE180 3.5 16.1 1.0
CG A:ASP175 3.6 18.7 1.0
N A:GLY178 3.8 18.9 1.0
N A:ILE180 4.0 17.7 1.0
CB A:ASP198 4.0 13.5 1.0
N A:GLY176 4.0 17.8 1.0
OD1 A:ASP175 4.1 18.0 1.0
C A:LYS177 4.1 21.6 1.0
CA A:GLY178 4.1 18.6 1.0
OE1 A:GLU201 4.2 16.7 1.0
C A:ASP175 4.2 18.4 1.0
OD2 A:ASP198 4.3 13.6 1.0
C A:GLY179 4.3 18.5 1.0
N A:ASP175 4.3 17.7 1.0
CA A:GLY176 4.3 18.5 1.0
CA A:ILE180 4.3 19.1 1.0
N A:LYS177 4.4 18.8 1.0
CA A:LYS177 4.4 20.1 1.0
N A:LEU181 4.5 16.2 1.0
N A:GLY179 4.5 16.8 1.0
O A:ASP175 4.6 20.7 1.0
CG A:GLU201 4.6 20.1 1.0
CA A:GLY179 4.6 16.8 1.0
CA A:LEU181 4.6 14.6 1.0
O A:LYS177 4.6 20.7 1.0
CA A:ASP175 4.6 18.7 1.0
CB A:ASP175 4.7 19.3 1.0
CB A:ILE180 4.8 19.0 1.0
O A:GLY179 4.9 18.8 1.0
CD2 A:LEU181 5.0 18.3 0.9

Calcium binding site 2 out of 18 in 1os9

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Calcium binding site 2 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:18.4
occ:1.00
O A:GLY192 2.2 15.2 1.0
O A:GLY190 2.3 20.4 1.0
O A:HOH938 2.3 19.8 1.0
O A:ASP158 2.4 17.1 1.0
OD2 A:ASP194 2.4 16.0 1.0
O A:HOH913 2.5 19.5 1.0
CG A:ASP194 3.4 16.6 1.0
C A:GLY192 3.4 16.6 1.0
C A:ASP158 3.5 16.9 1.0
C A:GLY190 3.6 22.4 1.0
OD1 A:ASP194 3.7 17.4 1.0
C A:ILE191 4.0 19.8 1.0
N A:GLY192 4.0 17.5 1.0
O A:ILE191 4.1 17.6 1.0
N A:ASP194 4.2 14.5 1.0
CA A:GLY192 4.2 16.8 1.0
O A:HOH950 4.2 36.2 1.0
N A:GLY190 4.4 23.3 1.0
O A:GLY188 4.4 22.2 1.0
CA A:ILE191 4.4 21.1 1.0
O A:ALA157 4.4 21.8 1.0
CA A:ASP158 4.4 18.6 1.0
N A:GLY193 4.4 14.4 1.0
N A:ILE191 4.4 20.0 1.0
N A:ILE159 4.4 15.4 1.0
CA A:GLY190 4.5 21.9 1.0
CA A:ILE159 4.5 14.5 1.0
N A:LEU160 4.6 13.5 1.0
CB A:ASP194 4.6 16.4 1.0
CA A:GLY193 4.6 16.5 1.0
C A:GLY193 4.7 15.2 1.0
O A:HOH936 4.7 23.6 1.0
C A:SER189 4.8 24.6 1.0
CA A:ASP194 4.8 15.9 1.0
CH2 A:TRP109 4.9 18.8 1.0

Calcium binding site 3 out of 18 in 1os9

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Calcium binding site 3 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:17.0
occ:1.00
OE2 A:GLU199 2.2 17.2 1.0
O A:GLU199 2.3 14.5 1.0
OD1 A:ASP124 2.3 17.5 1.0
O A:HOH909 2.4 16.2 1.0
O A:GLU201 2.4 17.0 1.0
O A:HOH919 2.4 19.2 1.0
OD2 A:ASP124 2.6 20.2 1.0
CG A:ASP124 2.9 18.4 1.0
CD A:GLU199 3.4 12.8 1.0
C A:GLU199 3.4 15.9 1.0
C A:GLU201 3.6 17.3 1.0
CG A:GLU199 3.9 13.1 1.0
CA A:GLU199 4.1 14.8 1.0
OG1 A:THR122 4.2 16.0 1.0
O A:HOH1051 4.2 45.6 1.0
CA A:PHE202 4.2 18.0 1.0
CD1 A:TRP203 4.3 16.8 1.0
N A:PHE202 4.4 18.1 1.0
CB A:ASP124 4.4 16.7 1.0
NH2 A:ARG165 4.4 20.8 0.8
N A:GLU201 4.4 16.5 1.0
OE1 A:GLU199 4.5 17.2 1.0
C A:ASP200 4.5 16.5 1.0
N A:ASP200 4.5 15.0 1.0
O A:HOH962 4.5 28.3 1.0
O A:HOH1074 4.5 51.5 1.0
CB A:GLU199 4.6 15.0 1.0
O A:HOH943 4.6 23.1 1.0
CA A:GLU201 4.7 16.9 1.0
CA A:ASP200 4.7 16.1 1.0
O A:HOH910 4.8 16.6 1.0
N A:TRP203 4.8 18.2 1.0
NE1 A:TRP203 4.9 15.7 1.0
CD1 A:PHE202 4.9 22.9 1.0
O A:ASP200 4.9 17.5 1.0

Calcium binding site 4 out of 18 in 1os9

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Calcium binding site 4 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca908

b:15.8
occ:1.00
O B:GLY176 2.2 19.2 1.0
OE2 B:GLU201 2.3 20.5 1.0
O B:GLY178 2.3 19.5 1.0
OD1 B:ASP198 2.3 16.9 1.0
OD2 B:ASP175 2.3 18.3 1.0
O B:ILE180 2.3 17.7 1.0
CG B:ASP198 3.4 17.5 1.0
C B:GLY176 3.4 18.2 1.0
C B:GLY178 3.5 18.1 1.0
C B:ILE180 3.5 15.6 1.0
CG B:ASP175 3.5 18.9 1.0
CD B:GLU201 3.6 18.6 1.0
N B:GLY178 3.8 19.4 1.0
N B:ILE180 3.9 17.3 1.0
N B:GLY176 4.0 18.6 1.0
CB B:ASP198 4.0 15.4 1.0
OD1 B:ASP175 4.1 17.2 1.0
C B:LYS177 4.1 21.3 1.0
CA B:GLY178 4.2 19.6 1.0
C B:ASP175 4.2 19.8 1.0
OE1 B:GLU201 4.3 15.6 1.0
C B:GLY179 4.3 18.1 1.0
OD2 B:ASP198 4.3 14.2 1.0
N B:ASP175 4.3 19.3 1.0
CA B:GLY176 4.3 18.8 1.0
CA B:ILE180 4.3 18.4 1.0
N B:LYS177 4.3 18.0 1.0
CA B:LYS177 4.4 19.5 1.0
N B:LEU181 4.5 15.7 1.0
N B:GLY179 4.5 16.8 1.0
CA B:LEU181 4.5 13.8 1.0
CA B:GLY179 4.6 16.7 1.0
CA B:ASP175 4.6 19.8 1.0
O B:LYS177 4.6 20.0 1.0
O B:ASP175 4.6 20.9 1.0
CG B:GLU201 4.6 19.3 1.0
CB B:ASP175 4.7 19.6 1.0
CB B:ILE180 4.8 18.3 1.0
O B:GLY179 4.9 19.0 1.0
CD2 B:LEU181 4.9 18.3 0.9

Calcium binding site 5 out of 18 in 1os9

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Calcium binding site 5 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca909

b:18.5
occ:1.00
O B:GLY192 2.2 15.9 1.0
O B:GLY190 2.3 21.3 1.0
O B:HOH920 2.3 19.9 1.0
O B:HOH938 2.4 20.7 1.0
O B:ASP158 2.4 18.3 1.0
OD2 B:ASP194 2.4 14.6 1.0
CG B:ASP194 3.4 16.9 1.0
C B:GLY192 3.4 17.6 1.0
C B:ASP158 3.5 17.5 1.0
C B:GLY190 3.6 22.7 1.0
OD1 B:ASP194 3.7 16.8 1.0
C B:ILE191 3.9 21.2 1.0
N B:GLY192 4.0 19.0 1.0
O B:ILE191 4.0 20.4 1.0
CA B:GLY192 4.2 17.5 1.0
N B:ASP194 4.2 13.6 1.0
O B:HOH977 4.3 38.2 1.0
CA B:ILE191 4.3 22.8 1.0
O B:ALA157 4.4 22.1 1.0
N B:ILE159 4.4 15.8 1.0
N B:GLY190 4.4 23.1 1.0
N B:GLY193 4.4 15.0 1.0
CA B:ASP158 4.4 19.3 1.0
N B:ILE191 4.4 20.8 1.0
O B:GLY188 4.4 22.8 1.0
CA B:ILE159 4.5 14.9 1.0
CA B:GLY190 4.5 22.2 1.0
N B:LEU160 4.6 14.4 1.0
CA B:GLY193 4.6 16.3 1.0
CB B:ASP194 4.7 16.5 1.0
C B:GLY193 4.7 15.7 1.0
C B:SER189 4.7 25.0 1.0
O B:HOH922 4.7 21.9 1.0
CA B:ASP194 4.8 15.9 1.0
CH2 B:TRP109 4.9 20.3 1.0
O B:SER189 4.9 24.7 1.0

Calcium binding site 6 out of 18 in 1os9

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Calcium binding site 6 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca910

b:16.3
occ:1.00
OE2 B:GLU199 2.3 18.0 1.0
O B:HOH911 2.3 16.0 1.0
O B:GLU199 2.4 14.7 1.0
OD1 B:ASP124 2.4 18.6 1.0
O B:HOH937 2.4 20.9 1.0
O B:GLU201 2.4 17.8 1.0
OD2 B:ASP124 2.6 21.3 1.0
CG B:ASP124 2.9 19.8 1.0
CD B:GLU199 3.4 12.1 1.0
C B:GLU199 3.5 15.9 1.0
C B:GLU201 3.6 17.4 1.0
CG B:GLU199 3.8 15.0 1.0
CA B:GLU199 4.1 15.3 1.0
CA B:PHE202 4.2 17.8 1.0
OG1 B:THR122 4.3 16.1 1.0
NH2 B:ARG165 4.3 19.8 0.8
CD1 B:TRP203 4.3 16.7 1.0
N B:PHE202 4.4 16.5 1.0
N B:GLU201 4.4 16.6 1.0
CB B:ASP124 4.4 16.2 1.0
C B:ASP200 4.5 15.3 1.0
O B:HOH1046 4.5 47.7 1.0
OE1 B:GLU199 4.5 17.4 1.0
N B:ASP200 4.5 16.4 1.0
O B:HOH976 4.6 29.5 1.0
CB B:GLU199 4.6 14.6 1.0
CA B:GLU201 4.7 15.9 1.0
CA B:ASP200 4.7 17.2 1.0
O B:HOH985 4.8 32.8 1.0
N B:TRP203 4.8 17.7 1.0
CD1 B:PHE202 4.8 21.9 1.0
O B:HOH916 4.9 17.9 1.0
O B:ASP200 4.9 17.4 1.0
NE1 B:TRP203 4.9 14.9 1.0

Calcium binding site 7 out of 18 in 1os9

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Calcium binding site 7 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca913

b:16.8
occ:1.00
OE2 C:GLU201 2.1 23.9 1.0
OD2 C:ASP175 2.2 19.7 1.0
O C:GLY176 2.2 19.4 1.0
OD1 C:ASP198 2.3 16.4 1.0
O C:ILE180 2.3 17.9 1.0
O C:GLY178 2.4 20.7 1.0
CD C:GLU201 3.4 23.0 1.0
CG C:ASP198 3.4 19.4 1.0
CG C:ASP175 3.4 16.3 1.0
C C:GLY176 3.4 20.3 1.0
C C:ILE180 3.5 14.6 1.0
C C:GLY178 3.5 21.0 1.0
N C:GLY178 3.9 19.2 1.0
CB C:ASP198 4.0 18.2 1.0
N C:ILE180 4.0 18.6 1.0
OD1 C:ASP175 4.0 18.5 1.0
C C:LYS177 4.1 20.7 1.0
N C:GLY176 4.1 19.2 1.0
OE1 C:GLU201 4.1 19.6 1.0
CA C:GLY178 4.2 20.4 1.0
C C:ASP175 4.2 20.4 1.0
N C:ASP175 4.3 17.4 1.0
CA C:ILE180 4.3 16.9 1.0
OD2 C:ASP198 4.3 17.8 1.0
C C:GLY179 4.3 18.8 1.0
CA C:GLY176 4.3 19.7 1.0
N C:LEU181 4.4 14.5 1.0
N C:LYS177 4.4 19.4 1.0
CG C:GLU201 4.4 21.5 1.0
CA C:LYS177 4.4 20.6 1.0
CA C:LEU181 4.5 14.8 1.0
N C:GLY179 4.5 19.2 1.0
O C:LYS177 4.6 20.5 1.0
O C:ASP175 4.6 19.4 1.0
CB C:ASP175 4.6 18.1 1.0
CA C:ASP175 4.6 19.6 1.0
CA C:GLY179 4.7 18.9 1.0
CB C:ILE180 4.7 17.4 1.0
O C:GLY179 4.8 20.2 1.0

Calcium binding site 8 out of 18 in 1os9

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Calcium binding site 8 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca914

b:21.8
occ:1.00
O C:ASP158 2.3 19.0 1.0
O C:HOH927 2.3 27.6 1.0
O C:GLY192 2.3 19.4 1.0
O C:GLY190 2.3 25.6 1.0
O C:HOH931 2.4 24.5 1.0
OD2 C:ASP194 2.4 19.1 1.0
CG C:ASP194 3.4 21.5 1.0
C C:ASP158 3.4 19.8 1.0
C C:GLY190 3.5 25.8 1.0
C C:GLY192 3.5 19.1 1.0
OD1 C:ASP194 3.9 18.3 1.0
C C:ILE191 4.0 22.9 1.0
N C:GLY192 4.2 19.7 1.0
O C:ILE191 4.2 23.7 1.0
O C:ALA157 4.2 23.5 1.0
CA C:ASP158 4.3 18.2 1.0
N C:ASP194 4.3 16.2 1.0
CA C:ILE191 4.3 25.0 1.0
N C:ILE191 4.4 24.1 1.0
O C:GLY188 4.4 25.4 1.0
CA C:GLY192 4.4 19.3 1.0
N C:ILE159 4.4 20.0 1.0
CA C:GLY190 4.4 26.4 1.0
O C:HOH981 4.5 38.1 1.0
N C:GLY190 4.5 25.2 1.0
N C:GLY193 4.5 17.7 1.0
CA C:ILE159 4.5 19.8 1.0
N C:LEU160 4.6 18.2 1.0
CA C:GLY193 4.6 17.5 1.0
CB C:ASP194 4.7 17.5 1.0
C C:GLY193 4.7 17.8 1.0
O C:HOH928 4.7 21.6 1.0
CA C:ASP194 4.8 16.9 1.0
CH2 C:TRP109 4.8 22.3 1.0
C C:SER189 4.9 26.5 1.0

Calcium binding site 9 out of 18 in 1os9

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Calcium binding site 9 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca915

b:21.0
occ:1.00
OD1 C:ASP124 2.1 21.2 1.0
O C:HOH947 2.3 30.5 1.0
OE2 C:GLU199 2.4 18.4 1.0
O C:GLU199 2.4 20.9 1.0
O C:GLU201 2.5 20.5 1.0
OD2 C:ASP124 2.6 21.7 1.0
CG C:ASP124 2.8 23.1 1.0
CD C:GLU199 3.4 24.6 1.0
C C:GLU199 3.5 18.9 1.0
C C:GLU201 3.6 21.1 1.0
CG C:GLU199 3.8 22.8 1.0
CA C:GLU199 4.1 19.4 1.0
OG1 C:THR122 4.2 27.0 1.0
CA C:PHE202 4.2 21.4 1.0
CD1 C:TRP203 4.2 15.9 1.0
CB C:ASP124 4.3 25.5 1.0
O C:HOH1059 4.3 32.8 1.0
N C:PHE202 4.3 20.9 1.0
N C:GLU201 4.5 19.7 1.0
C C:ASP200 4.5 22.1 1.0
OE1 C:GLU199 4.5 21.4 1.0
N C:ASP200 4.6 20.0 1.0
CB C:GLU199 4.6 20.4 1.0
NH2 C:ARG165 4.7 31.6 0.8
CA C:GLU201 4.7 20.7 1.0
NE1 C:TRP203 4.7 18.4 1.0
CA C:ASP200 4.8 21.6 1.0
N C:TRP203 4.8 21.4 1.0
O C:HOH1034 4.8 33.9 1.0
O C:HOH998 4.8 34.2 1.0
CD1 C:PHE202 4.9 27.8 1.0
O C:ASP200 4.9 23.4 1.0

Calcium binding site 10 out of 18 in 1os9

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Calcium binding site 10 out of 18 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca918

b:17.1
occ:1.00
OE2 D:GLU201 2.1 23.4 1.0
OD2 D:ASP175 2.2 19.0 1.0
O D:ILE180 2.3 17.5 1.0
OD1 D:ASP198 2.3 17.3 1.0
O D:GLY176 2.3 20.0 1.0
O D:GLY178 2.3 20.4 1.0
CD D:GLU201 3.4 20.7 1.0
CG D:ASP198 3.4 19.7 1.0
C D:ILE180 3.4 15.3 1.0
CG D:ASP175 3.5 14.6 1.0
C D:GLY178 3.5 20.6 1.0
C D:GLY176 3.6 20.8 1.0
N D:GLY178 3.8 19.8 1.0
CB D:ASP198 4.0 17.5 1.0
OD1 D:ASP175 4.0 16.8 1.0
N D:ILE180 4.0 18.4 1.0
N D:GLY176 4.1 18.6 1.0
C D:LYS177 4.1 20.8 1.0
OE1 D:GLU201 4.2 19.3 1.0
C D:ASP175 4.2 20.7 1.0
CA D:ILE180 4.2 18.0 1.0
CA D:GLY178 4.3 19.9 1.0
N D:ASP175 4.3 18.3 1.0
OD2 D:ASP198 4.3 17.1 1.0
N D:LEU181 4.3 14.4 1.0
C D:GLY179 4.3 17.3 1.0
CA D:GLY176 4.4 19.6 1.0
CG D:GLU201 4.4 21.2 1.0
CA D:LYS177 4.5 21.0 1.0
N D:LYS177 4.5 19.3 1.0
CA D:LEU181 4.5 15.2 1.0
N D:GLY179 4.6 19.0 1.0
O D:ASP175 4.6 18.7 1.0
CA D:ASP175 4.6 19.8 1.0
CB D:ASP175 4.6 18.5 1.0
O D:LYS177 4.6 21.4 1.0
CB D:ILE180 4.7 18.2 1.0
CA D:GLY179 4.7 18.2 1.0
O D:GLY179 4.8 18.6 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, S.Mangani, B.Terni. X-Ray Structures of Binary and Ternary Enzyme-Product-Inhibitor Complexes of Matrix Metalloproteinases Angew.Chem.Int.Ed.Engl. V. 42 2673 2003.
ISSN: ISSN 1433-7851
PubMed: 12813751
DOI: 10.1002/ANIE.200350957
Page generated: Sat Dec 12 03:12:55 2020

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