Atomistry » Zinc » PDB 1oj7-1p1r » 1os9
Atomistry »
  Zinc »
    PDB 1oj7-1p1r »
      1os9 »

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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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

Go back to Zinc Binding Sites List in 1os9
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 Oct 16 17:33:58 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy