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Zinc in PDB 2j0t: Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1

Enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1:
3.4.24.7;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1, PDB code: 2j0t was solved by S.Iyer, S.Wei, K.Brew, K.R.Acharya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.00 / 2.54
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.098, 67.850, 86.241, 90.00, 100.29, 90.00
R / Rfree (%) 24.8 / 27.5

Other elements in 2j0t:

The structure of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 also contains other interesting chemical elements:

Calcium (Ca) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 (pdb code 2j0t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1, PDB code: 2j0t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2j0t

Go back to Zinc Binding Sites List in 2j0t
Zinc binding site 1 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1266

b:33.4
occ:1.00
 OD2 A:ASP170 1.9 49.3 1.0
NE2 A:HIS183 2.0 47.0 1.0
NE2 A:HIS168 2.0 48.0 1.0
ND1 A:HIS196 2.1 42.7 1.0
CG A:ASP170 2.9 49.5 1.0
CE1 A:HIS183 2.9 47.0 1.0
CD2 A:HIS183 3.0 47.0 1.0
CD2 A:HIS168 3.0 47.9 1.0
CE1 A:HIS168 3.1 47.6 1.0
CE1 A:HIS196 3.1 42.3 1.0
CG A:HIS196 3.1 42.5 1.0
OD1 A:ASP170 3.3 49.5 1.0
CB A:HIS196 3.4 42.4 1.0
O A:SER172 4.0 50.5 1.0
ND1 A:HIS183 4.0 47.3 1.0
CB A:ASP170 4.1 49.8 1.0
CG A:HIS183 4.1 47.0 1.0
ND1 A:HIS168 4.2 48.0 1.0
CG A:HIS168 4.2 48.1 1.0
NE2 A:HIS196 4.2 42.4 1.0
CD2 A:HIS196 4.2 42.6 1.0
CE1 A:PHE185 4.3 45.3 1.0
CZ A:PHE185 4.5 45.4 1.0
CE2 A:PHE174 4.6 48.8 1.0
CZ A:PHE174 4.7 49.0 1.0
CA A:HIS196 4.9 42.2 1.0
CB A:SER172 5.0 50.8 1.0

Zinc binding site 2 out of 6 in 2j0t

Go back to Zinc Binding Sites List in 2j0t
Zinc binding site 2 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1267

b:29.4
occ:1.00
 NE2 A:HIS228 2.0 44.9 1.0
N D:CYS1 2.1 38.4 1.0
NE2 A:HIS218 2.1 46.1 1.0
NE2 A:HIS222 2.2 42.5 1.0
O D:CYS1 2.3 38.4 1.0
CA D:CYS1 2.9 38.5 1.0
C D:CYS1 2.9 38.5 1.0
CD2 A:HIS228 2.9 44.4 1.0
CD2 A:HIS222 3.0 42.9 1.0
CE1 A:HIS218 3.1 46.8 1.0
CD2 A:HIS218 3.1 46.2 1.0
CE1 A:HIS228 3.1 44.1 1.0
CE1 A:HIS222 3.3 42.6 1.0
CB D:CYS1 3.5 38.7 1.0
CG A:HIS228 4.1 44.5 1.0
OE1 A:GLU219 4.1 45.9 1.0
N D:THR2 4.1 38.5 1.0
ND1 A:HIS228 4.2 44.6 1.0
ND1 A:HIS218 4.2 46.2 1.0
OE2 A:GLU219 4.2 46.8 1.0
CG A:HIS218 4.2 46.4 1.0
CG A:HIS222 4.2 43.3 1.0
ND1 A:HIS222 4.4 42.9 1.0
CD A:GLU219 4.5 46.5 1.0
O D:SER68 4.6 40.0 1.0
O D:GLU67 4.8 40.1 1.0
CA D:SER68 4.8 39.9 1.0
CA A:PRO238 4.8 43.7 1.0
CA D:THR2 5.0 38.6 1.0
OG1 D:THR2 5.0 38.4 1.0

Zinc binding site 3 out of 6 in 2j0t

Go back to Zinc Binding Sites List in 2j0t
Zinc binding site 3 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1267

b:30.1
occ:1.00
 OD2 B:ASP170 1.9 47.4 1.0
NE2 B:HIS183 2.0 44.7 1.0
NE2 B:HIS168 2.0 48.8 1.0
ND1 B:HIS196 2.1 43.8 1.0
CG B:ASP170 2.9 48.2 1.0
CE1 B:HIS183 2.9 44.5 1.0
CE1 B:HIS168 3.0 48.5 1.0
CD2 B:HIS168 3.0 48.3 1.0
CE1 B:HIS196 3.1 43.6 1.0
CG B:HIS196 3.1 43.5 1.0
CD2 B:HIS183 3.1 44.4 1.0
OD1 B:ASP170 3.3 47.8 1.0
CB B:HIS196 3.4 43.1 1.0
O B:SER172 4.0 48.5 1.0
ND1 B:HIS183 4.1 44.8 1.0
CB B:ASP170 4.1 48.5 1.0
ND1 B:HIS168 4.1 48.5 1.0
CG B:HIS168 4.2 48.4 1.0
NE2 B:HIS196 4.2 43.7 1.0
CG B:HIS183 4.2 44.7 1.0
CD2 B:HIS196 4.2 43.4 1.0
CE1 B:PHE185 4.4 43.5 1.0
CE2 B:PHE174 4.5 46.3 1.0
CZ B:PHE185 4.5 43.5 1.0
CZ B:PHE174 4.6 46.3 1.0
CB B:SER172 4.6 48.6 1.0
CA B:HIS196 4.9 43.1 1.0
C B:SER172 5.0 48.3 1.0

Zinc binding site 4 out of 6 in 2j0t

Go back to Zinc Binding Sites List in 2j0t
Zinc binding site 4 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1268

b:34.1
occ:1.00
 N E:CYS1 2.0 42.6 1.0
NE2 B:HIS218 2.1 46.2 1.0
NE2 B:HIS228 2.1 44.9 1.0
NE2 B:HIS222 2.2 44.8 1.0
O E:CYS1 2.4 42.7 1.0
CA E:CYS1 2.9 42.6 1.0
C E:CYS1 3.0 42.7 1.0
CD2 B:HIS228 3.0 44.9 1.0
CD2 B:HIS222 3.0 44.9 1.0
CD2 B:HIS218 3.0 46.3 1.0
CE1 B:HIS228 3.1 44.5 1.0
CE1 B:HIS218 3.2 46.7 1.0
CE1 B:HIS222 3.3 45.0 1.0
CB E:CYS1 3.5 42.7 1.0
CG B:HIS228 4.2 44.8 1.0
ND1 B:HIS228 4.2 45.0 1.0
CG B:HIS222 4.2 44.8 1.0
CG B:HIS218 4.2 46.2 1.0
N E:THR2 4.2 42.7 1.0
OE1 B:GLU219 4.2 46.6 1.0
ND1 B:HIS218 4.2 46.1 1.0
ND1 B:HIS222 4.3 44.9 1.0
OE2 B:GLU219 4.4 48.0 1.0
CD B:GLU219 4.7 47.2 1.0
O E:SER68 4.7 43.1 1.0
O E:GLU67 4.7 43.2 1.0
CA E:SER68 4.8 43.2 1.0
CA B:PRO238 4.9 43.0 1.0
OG1 E:THR2 4.9 42.5 1.0

Zinc binding site 5 out of 6 in 2j0t

Go back to Zinc Binding Sites List in 2j0t
Zinc binding site 5 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1264

b:45.9
occ:1.00
 NE2 C:HIS168 2.0 44.9 1.0
ND1 C:HIS196 2.1 42.6 1.0
OD2 C:ASP170 2.1 44.6 1.0
NE2 C:HIS183 2.1 45.2 1.0
CD2 C:HIS168 2.9 44.7 1.0
CE1 C:HIS183 2.9 45.2 1.0
CE1 C:HIS196 3.0 42.8 1.0
CG C:ASP170 3.1 45.0 1.0
CG C:HIS196 3.1 43.3 1.0
CE1 C:HIS168 3.1 44.9 1.0
CD2 C:HIS183 3.2 45.5 1.0
CB C:HIS196 3.5 43.5 1.0
OD1 C:ASP170 3.5 45.0 1.0
O C:SER172 3.9 45.4 1.0
NE2 C:HIS196 4.1 42.9 1.0
CG C:HIS168 4.1 44.5 1.0
ND1 C:HIS183 4.1 45.4 1.0
CD2 C:HIS196 4.2 43.1 1.0
ND1 C:HIS168 4.2 44.8 1.0
CG C:HIS183 4.3 45.5 1.0
CB C:ASP170 4.3 44.9 1.0
CE1 C:PHE185 4.4 45.6 1.0
CZ C:PHE185 4.5 45.8 1.0
CE2 C:PHE174 4.7 45.3 1.0
CZ C:PHE174 4.7 45.3 1.0
CA C:HIS196 5.0 43.5 1.0
C C:SER172 5.0 45.4 1.0

Zinc binding site 6 out of 6 in 2j0t

Go back to Zinc Binding Sites List in 2j0t
Zinc binding site 6 out of 6 in the Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Catalytic Domain of Mmp-1 in Complex with the Inhibitory Domain of Timp-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1265

b:46.1
occ:1.00
 N F:CYS1 2.0 41.1 1.0
NE2 C:HIS218 2.1 44.4 1.0
NE2 C:HIS228 2.1 46.4 1.0
NE2 C:HIS222 2.2 45.0 1.0
O F:CYS1 2.5 40.9 1.0
CA F:CYS1 2.9 41.0 1.0
C F:CYS1 3.0 40.9 1.0
CD2 C:HIS222 3.0 44.7 1.0
CD2 C:HIS228 3.0 46.3 1.0
CD2 C:HIS218 3.1 44.4 1.0
CE1 C:HIS218 3.1 44.6 1.0
CE1 C:HIS228 3.1 46.2 1.0
CE1 C:HIS222 3.3 45.1 1.0
CB F:CYS1 3.6 41.1 1.0
OE1 C:GLU219 4.0 44.5 1.0
CG C:HIS228 4.2 46.4 1.0
ND1 C:HIS228 4.2 46.5 1.0
N F:THR2 4.2 40.8 1.0
ND1 C:HIS218 4.2 44.5 1.0
CG C:HIS222 4.2 44.8 1.0
CG C:HIS218 4.2 44.4 1.0
ND1 C:HIS222 4.3 45.0 1.0
OE2 C:GLU219 4.5 45.1 1.0
O F:GLU67 4.5 44.0 1.0
O F:SER68 4.6 44.0 1.0
CD C:GLU219 4.7 45.2 1.0
CA F:SER68 4.7 44.0 1.0
CA C:PRO238 4.7 44.4 1.0
CB C:PRO238 4.8 44.3 1.0

Reference:

S.Iyer, S.Wei, K.Brew, K.R.Acharya. Crystal Structure of the Catalytic Domain of Matrix Metalloproteinase-1 in Complex with the Inhibitory Domain of Tissue Inhibitor of Metalloproteinase-1. J.Biol.Chem. V. 282 364 2007.
ISSN: ISSN 0021-9258
PubMed: 17050530
DOI: 10.1074/JBC.M607625200
Page generated: Thu Oct 17 01:03:00 2024

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