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Zinc 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:

Calcium (Ca) 18 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Binary Enzyme-Product Complexes of Human MMP12 (pdb code 1os9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Binary Enzyme-Product Complexes of Human MMP12, PDB code: 1os9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 1os9

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Zinc binding site 1 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:18.4
occ:1.00
NE2 A:HIS222 2.0 18.4 1.0
NE2 A:HIS218 2.1 17.1 1.0
NE2 A:HIS228 2.1 17.9 1.0
O E:HOH951 2.3 32.0 1.0
O A:HOH1026 2.6 39.9 1.0
O A:HOH988 2.8 46.8 1.0
CE1 A:HIS218 3.0 18.1 1.0
CD2 A:HIS228 3.0 16.6 1.0
CD2 A:HIS222 3.0 14.9 1.0
CE1 A:HIS222 3.0 18.8 1.0
CD2 A:HIS218 3.1 19.4 1.0
CE1 A:HIS228 3.1 21.3 1.0
O C:HOH954 4.0 30.3 1.0
O A:HOH960 4.0 27.9 1.0
ND1 A:HIS218 4.1 19.5 1.0
ND1 A:HIS222 4.1 18.6 1.0
N E:MET104 4.1 24.7 1.0
CG A:HIS222 4.2 18.0 1.0
CG A:HIS228 4.2 16.2 1.0
CG A:HIS218 4.2 17.9 1.0
ND1 A:HIS228 4.2 18.1 1.0
CA E:MET104 4.5 25.9 1.0
OE2 A:GLU219 4.6 23.9 1.0
OE1 A:GLU219 4.8 22.1 1.0
O A:HOH1009 4.9 35.0 1.0
CE A:MET236 4.9 15.9 1.0

Zinc binding site 2 out of 12 in 1os9

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Zinc binding site 2 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:18.4
occ:1.00
OD1 A:ASP170 1.8 10.3 0.7
NE2 A:HIS168 2.0 18.9 1.0
NE2 A:HIS183 2.0 6.7 0.5
ND1 A:HIS196 2.0 17.8 1.0
CE1 A:HIS183 2.8 13.7 0.5
CG A:ASP170 2.8 15.8 0.7
CD2 A:HIS168 2.9 20.1 1.0
CE1 A:HIS196 3.0 17.0 1.0
CG A:HIS196 3.0 16.5 1.0
CE1 A:HIS168 3.1 16.3 1.0
OD2 A:ASP170 3.1 10.7 0.7
CD2 A:HIS183 3.2 6.2 0.5
CB A:HIS196 3.4 13.9 1.0
ND1 A:HIS183 4.0 13.9 0.5
CG A:HIS168 4.1 17.7 1.0
NE2 A:HIS196 4.1 17.5 1.0
ND1 A:HIS168 4.2 19.1 1.0
CD2 A:HIS196 4.2 14.3 1.0
O A:HIS172 4.2 24.9 1.0
CB A:ASP170 4.2 17.8 0.7
CG A:HIS183 4.2 8.6 0.5
CE1 A:PHE185 4.2 28.3 1.0
CZ A:PHE185 4.4 28.7 1.0
CB A:HIS172 4.6 27.3 1.0
CZ A:PHE174 4.7 15.8 1.0
CE2 A:PHE174 4.8 12.4 1.0
CA A:HIS196 4.9 14.6 1.0
C A:HIS172 5.0 25.8 1.0

Zinc binding site 3 out of 12 in 1os9

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Zinc binding site 3 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn906

b:18.5
occ:1.00
NE2 B:HIS218 2.0 18.1 1.0
NE2 B:HIS222 2.1 17.4 1.0
NE2 B:HIS228 2.1 17.1 1.0
O F:HOH946 2.5 30.3 1.0
O F:HOH1017 2.5 49.1 1.0
O B:HOH997 2.9 37.1 1.0
CE1 B:HIS218 3.0 19.0 1.0
CD2 B:HIS222 3.0 15.2 1.0
CD2 B:HIS228 3.0 16.7 1.0
CD2 B:HIS218 3.1 21.8 1.0
CE1 B:HIS222 3.1 16.1 1.0
CE1 B:HIS228 3.1 20.7 1.0
N F:MET104 3.9 26.4 1.0
O D:HOH949 4.0 28.8 1.0
O B:HOH957 4.1 25.1 1.0
ND1 B:HIS218 4.1 19.6 1.0
CG B:HIS222 4.2 17.8 1.0
CG B:HIS218 4.2 17.2 1.0
ND1 B:HIS222 4.2 19.5 1.0
CG B:HIS228 4.2 15.8 1.0
ND1 B:HIS228 4.2 15.4 1.0
CA F:MET104 4.4 26.9 1.0
O B:HOH1066 4.6 44.4 1.0
OE1 B:GLU219 4.7 23.8 1.0
OE2 B:GLU219 4.8 27.9 1.0
O D:HOH982 4.8 31.9 1.0
CE B:MET236 4.9 15.1 1.0

Zinc binding site 4 out of 12 in 1os9

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Zinc binding site 4 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn907

b:17.9
occ:1.00
OD1 B:ASP170 1.8 12.2 0.7
NE2 B:HIS168 2.0 15.0 1.0
NE2 B:HIS183 2.0 19.2 1.0
ND1 B:HIS196 2.1 17.9 1.0
CD2 B:HIS168 2.8 20.8 1.0
CE1 B:HIS183 2.8 26.0 1.0
CG B:ASP170 2.9 18.2 0.7
CE1 B:HIS196 3.0 18.2 1.0
CG B:HIS196 3.1 17.6 1.0
CE1 B:HIS168 3.1 17.6 1.0
CD2 B:HIS183 3.1 23.2 1.0
OD2 B:ASP170 3.2 12.8 0.7
CB B:HIS196 3.4 15.3 1.0
CG B:HIS168 4.0 17.0 1.0
ND1 B:HIS183 4.0 23.6 1.0
ND1 B:HIS168 4.1 19.7 1.0
NE2 B:HIS196 4.1 16.6 1.0
O B:HIS172 4.2 23.5 1.0
CG B:HIS183 4.2 18.6 1.0
CD2 B:HIS196 4.2 17.9 1.0
CB B:ASP170 4.3 19.0 0.7
CE1 B:PHE185 4.3 33.5 1.0
CZ B:PHE185 4.5 33.3 1.0
CB B:HIS172 4.6 27.4 1.0
CZ B:PHE174 4.7 16.1 1.0
CE2 B:PHE174 4.8 12.1 1.0
CA B:HIS196 5.0 14.4 1.0
O B:HOH925 5.0 19.2 1.0

Zinc binding site 5 out of 12 in 1os9

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Zinc binding site 5 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn911

b:24.2
occ:1.00
NE2 C:HIS228 2.0 25.2 1.0
NE2 C:HIS222 2.1 21.6 1.0
NE2 C:HIS218 2.2 17.1 1.0
O A:HOH1079 2.4 49.6 1.0
O C:HOH1058 2.5 55.7 1.0
CE1 C:HIS228 3.0 29.7 1.0
CD2 C:HIS228 3.0 27.4 1.0
CD2 C:HIS222 3.0 19.9 1.0
CD2 C:HIS218 3.1 18.8 1.0
CE1 C:HIS222 3.1 22.4 1.0
CE1 C:HIS218 3.2 16.5 1.0
N A:MET104 3.9 31.5 1.0
CA A:MET104 4.1 32.1 1.0
ND1 C:HIS228 4.1 23.3 1.0
CG C:HIS228 4.1 26.9 1.0
CG C:HIS222 4.2 18.9 1.0
ND1 C:HIS222 4.2 22.6 1.0
CG C:HIS218 4.3 18.2 1.0
O C:HOH930 4.3 25.8 1.0
ND1 C:HIS218 4.3 18.8 1.0
OE2 C:GLU219 4.5 34.4 1.0
CB A:MET104 4.6 32.4 1.0
OE1 C:GLU219 4.6 27.0 1.0
O C:HOH1048 4.8 49.0 1.0
CE C:MET236 4.9 16.1 1.0
CD C:GLU219 5.0 28.4 1.0

Zinc binding site 6 out of 12 in 1os9

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Zinc binding site 6 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn912

b:22.0
occ:1.00
OD1 C:ASP170 1.9 14.1 0.7
NE2 C:HIS168 2.0 23.7 1.0
NE2 C:HIS183 2.1 8.2 0.5
ND1 C:HIS196 2.1 18.2 1.0
CE1 C:HIS183 2.9 8.0 0.5
CG C:ASP170 2.9 22.2 0.7
CE1 C:HIS168 3.0 20.8 1.0
CD2 C:HIS168 3.0 21.5 1.0
CE1 C:HIS196 3.0 23.4 1.0
CD2 C:HIS183 3.1 7.5 0.5
CG C:HIS196 3.2 19.6 1.0
OD2 C:ASP170 3.2 18.7 0.7
CB C:HIS196 3.5 16.4 1.0
ND1 C:HIS183 4.1 7.8 0.5
ND1 C:HIS168 4.1 23.4 1.0
CG C:HIS168 4.1 24.1 1.0
NE2 C:HIS196 4.2 19.0 1.0
CE1 C:PHE185 4.2 27.8 1.0
CG C:HIS183 4.2 7.8 0.5
O C:HIS172 4.2 24.5 1.0
CD2 C:HIS196 4.3 19.2 1.0
CB C:ASP170 4.3 24.4 0.7
CE2 C:PHE174 4.6 14.7 1.0
CZ C:PHE174 4.6 15.0 1.0
CZ C:PHE185 4.8 30.7 1.0
CB C:HIS172 4.8 30.1 1.0
O C:HOH919 4.8 26.0 1.0
CA C:HIS196 5.0 16.9 1.0

Zinc binding site 7 out of 12 in 1os9

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Zinc binding site 7 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn916

b:24.5
occ:1.00
NE2 D:HIS222 2.1 24.6 1.0
NE2 D:HIS228 2.1 23.6 1.0
NE2 D:HIS218 2.1 18.0 1.0
O B:HOH1054 2.1 37.8 1.0
CD2 D:HIS228 3.0 26.9 1.0
O D:HOH1015 3.1 57.6 1.0
CD2 D:HIS222 3.1 20.8 1.0
CD2 D:HIS218 3.1 19.7 1.0
CE1 D:HIS218 3.1 16.5 1.0
CE1 D:HIS222 3.1 24.5 1.0
CE1 D:HIS228 3.2 28.9 1.0
N B:MET104 3.9 31.7 1.0
CA B:MET104 4.2 32.1 1.0
CG D:HIS228 4.2 26.4 1.0
ND1 D:HIS218 4.2 18.7 1.0
CG D:HIS222 4.2 19.8 1.0
ND1 D:HIS228 4.2 25.3 1.0
CG D:HIS218 4.2 15.7 1.0
ND1 D:HIS222 4.2 23.7 1.0
OE2 D:GLU219 4.4 35.8 1.0
O D:HOH936 4.4 26.4 1.0
OE1 D:GLU219 4.7 28.3 1.0
CB B:MET104 4.7 33.3 1.0
CE D:MET236 4.9 14.8 1.0
CD D:GLU219 4.9 25.6 1.0

Zinc binding site 8 out of 12 in 1os9

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Zinc binding site 8 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn917

b:22.3
occ:1.00
NE2 D:HIS168 2.0 22.5 1.0
OD1 D:ASP170 2.0 16.7 0.7
ND1 D:HIS196 2.1 17.6 1.0
NE2 D:HIS183 2.1 10.7 0.5
CE1 D:HIS196 2.9 23.5 1.0
CG D:ASP170 2.9 21.8 0.7
CE1 D:HIS168 2.9 22.9 1.0
CD2 D:HIS168 3.0 23.3 1.0
CE1 D:HIS183 3.0 10.2 0.5
CG D:HIS196 3.1 17.7 1.0
OD2 D:ASP170 3.1 17.6 0.7
CD2 D:HIS183 3.2 12.0 0.5
CB D:HIS196 3.5 16.6 1.0
ND1 D:HIS168 4.1 25.9 1.0
NE2 D:HIS196 4.1 20.1 1.0
CG D:HIS168 4.1 25.3 1.0
ND1 D:HIS183 4.2 10.3 0.5
CD2 D:HIS196 4.2 21.7 1.0
CE1 D:PHE185 4.2 25.0 1.0
O D:HIS172 4.3 23.9 1.0
CG D:HIS183 4.3 9.9 0.5
CB D:ASP170 4.3 23.8 0.7
CE2 D:PHE174 4.6 17.9 1.0
CZ D:PHE174 4.6 17.8 1.0
CZ D:PHE185 4.7 29.8 1.0
CB D:HIS172 4.8 29.9 1.0
O D:HOH925 5.0 27.9 1.0
CA D:HIS196 5.0 16.7 1.0

Zinc binding site 9 out of 12 in 1os9

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Zinc binding site 9 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn921

b:22.3
occ:1.00
NE2 E:HIS218 2.0 20.7 1.0
NE2 E:HIS222 2.0 16.6 1.0
NE2 E:HIS228 2.0 21.0 1.0
O E:HOH1006 2.4 46.0 1.0
O E:HOH1047 2.4 37.7 1.0
CD2 E:HIS222 2.9 20.7 1.0
CE1 E:HIS228 3.0 20.7 1.0
CE1 E:HIS218 3.0 17.9 1.0
CD2 E:HIS218 3.0 20.4 1.0
CD2 E:HIS228 3.1 17.5 1.0
CE1 E:HIS222 3.1 17.4 1.0
O E:HOH1046 4.0 49.4 1.0
O E:HOH954 4.1 26.3 1.0
ND1 E:HIS218 4.1 19.3 1.0
ND1 E:HIS228 4.1 18.8 1.0
CG E:HIS222 4.1 20.7 1.0
CG E:HIS218 4.2 18.1 1.0
ND1 E:HIS222 4.2 20.7 1.0
CG E:HIS228 4.2 20.0 1.0
O E:HOH959 4.2 27.5 1.0
OE2 E:GLU219 4.7 33.5 1.0
CE E:MET236 4.8 18.6 1.0
OE1 E:GLU219 4.8 37.0 1.0
O E:HOH1008 5.0 42.2 1.0

Zinc binding site 10 out of 12 in 1os9

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Zinc binding site 10 out of 12 in the Binary Enzyme-Product Complexes of Human MMP12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Binary Enzyme-Product Complexes of Human MMP12 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn922

b:35.7
occ:1.00
NE2 E:HIS183 1.9 12.9 0.5
NE2 E:HIS168 2.1 33.1 1.0
ND1 E:HIS196 2.2 32.7 1.0
OD1 E:ASP170 2.2 37.2 0.7
CE1 E:HIS183 2.6 17.4 0.5
CD2 E:HIS168 3.0 32.0 1.0
CG E:ASP170 3.0 38.0 0.7
OD2 E:ASP170 3.1 35.0 0.7
CD2 E:HIS183 3.1 17.5 0.5
CE1 E:HIS168 3.1 33.1 1.0
CE1 E:HIS196 3.2 33.5 1.0
CG E:HIS196 3.2 31.1 1.0
CB E:HIS196 3.5 26.8 1.0
ND1 E:HIS183 3.8 19.1 0.5
CG E:HIS183 4.1 17.1 0.5
CG E:HIS168 4.1 33.8 1.0
ND1 E:HIS168 4.2 34.6 1.0
CE1 E:PHE185 4.3 38.3 1.0
NE2 E:HIS196 4.3 33.3 1.0
CD2 E:HIS196 4.3 34.1 1.0
CZ E:PHE185 4.4 38.5 1.0
O E:HIS172 4.4 45.0 1.0
CB E:ASP170 4.5 40.4 0.7
CZ E:PHE174 4.7 29.3 1.0
CE2 E:PHE174 4.8 31.2 1.0
O E:HOH994 5.0 39.6 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: Wed Dec 16 02:59:59 2020

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