Atomistry » Zinc » PDB 2iux-2ja7 » 2j0t
Atomistry »
  Zinc »
    PDB 2iux-2ja7 »
      2j0t »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy