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Calcium 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:

Zinc (Zn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 9 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 1 out of 9 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 Calcium with other atoms in the Ca 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:Ca1268

b:32.2
occ:1.00
 O A:GLY190 2.4 43.8 1.0
O A:GLY192 2.4 43.0 1.0
O A:ASP158 2.4 43.5 1.0
OD1 A:ASP194 2.6 42.9 1.0
C A:GLY190 3.5 43.8 1.0
C A:GLY192 3.5 42.9 1.0
CG A:ASP194 3.5 42.7 1.0
C A:ASP158 3.5 43.7 1.0
OD2 A:ASP194 3.9 43.2 1.0
C A:ILE191 4.0 43.2 1.0
N A:GLY192 4.0 43.1 1.0
O A:ALA157 4.1 44.5 1.0
O A:ILE191 4.2 43.1 1.0
N A:ASP194 4.2 42.4 1.0
O A:GLY188 4.3 45.1 1.0
CA A:GLY192 4.3 43.0 1.0
CA A:ASP158 4.4 43.9 1.0
N A:ILE191 4.4 43.5 1.0
CA A:ILE191 4.4 43.3 1.0
N A:GLY193 4.5 42.9 1.0
N A:ILE159 4.5 43.6 1.0
CA A:GLY190 4.5 43.9 1.0
N A:GLY190 4.5 44.2 1.0
CA A:GLY193 4.6 42.7 1.0
N A:MET160 4.6 43.2 1.0
CA A:ILE159 4.6 43.5 1.0
C A:GLY193 4.7 42.6 1.0
CG A:MET160 4.7 42.6 1.0
CB A:ASP194 4.7 42.4 1.0
CH2 A:TRP109 4.8 53.6 1.0
C A:PRO189 4.9 44.4 1.0
CA A:ASP194 4.9 42.4 1.0

Calcium binding site 2 out of 9 in 2j0t

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Calcium binding site 2 out of 9 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 Calcium with other atoms in the Ca 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:Ca1269

b:42.8
occ:1.00
 O A:ASN180 2.2 48.0 1.0
O A:GLY176 2.3 48.0 1.0
O A:GLY178 2.4 48.1 1.0
OD2 A:ASP198 2.4 43.1 1.0
OE1 A:GLU201 2.4 44.8 1.0
OD1 A:ASP175 2.5 47.5 1.0
C A:ASN180 3.3 47.9 1.0
CG A:ASP198 3.5 43.1 1.0
C A:GLY176 3.6 48.0 1.0
CD A:GLU201 3.6 44.8 1.0
C A:GLY178 3.6 48.1 1.0
CG A:ASP175 3.6 48.0 1.0
N A:GLY178 3.9 48.0 1.0
N A:ASN180 3.9 48.1 1.0
CB A:ASP198 4.0 43.1 1.0
OE2 A:GLU201 4.0 45.3 1.0
CA A:ASN180 4.1 48.1 1.0
N A:GLY176 4.2 48.0 1.0
C A:PRO177 4.2 48.0 1.0
OD2 A:ASP175 4.2 48.1 1.0
N A:LEU181 4.3 47.8 1.0
CA A:GLY178 4.3 48.0 1.0
N A:ASP175 4.4 48.5 1.0
C A:GLY179 4.4 48.2 1.0
C A:ASP175 4.4 48.1 1.0
CA A:LEU181 4.4 47.5 1.0
CA A:PRO177 4.4 48.0 1.0
N A:PRO177 4.5 48.0 1.0
CA A:GLY176 4.5 48.0 1.0
OD1 A:ASP198 4.5 43.3 1.0
CB A:ASN180 4.6 48.2 1.0
N A:GLY179 4.6 48.1 1.0
CA A:ASP175 4.7 48.2 1.0
O A:PRO177 4.8 48.1 1.0
CB A:ASP175 4.8 48.1 1.0
CG A:GLU201 4.8 44.3 1.0
CA A:GLY179 4.8 48.1 1.0
O A:ASP175 4.9 48.1 1.0
O A:GLY179 4.9 48.3 1.0
CD1 A:PHE174 5.0 49.0 1.0
CD2 A:LEU181 5.0 46.9 1.0

Calcium binding site 3 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 3 out of 9 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 Calcium with other atoms in the Ca 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
A:Ca1270

b:51.6
occ:1.00
 O A:GLU199 2.3 43.7 1.0
O A:GLU201 2.5 44.3 1.0
OD2 A:ASP124 2.6 48.0 1.0
OD1 A:ASP124 2.8 48.4 1.0
OE2 A:GLU199 3.0 44.6 1.0
CG A:ASP124 3.1 48.0 1.0
C A:GLU199 3.5 43.7 1.0
C A:GLU201 3.6 44.3 1.0
CD A:GLU199 4.0 44.4 1.0
CG A:GLU199 4.2 43.9 1.0
CA A:ARG202 4.3 44.4 1.0
N A:ARG202 4.3 44.4 1.0
CA A:GLU199 4.3 43.6 1.0
C A:ASP200 4.3 43.9 1.0
N A:GLU201 4.4 44.1 1.0
N A:ASP200 4.5 43.7 1.0
OG1 A:THR122 4.5 47.5 1.0
CA A:ASP200 4.6 43.9 1.0
CB A:ASP124 4.6 47.9 1.0
O A:ASP200 4.6 44.0 1.0
CA A:GLU201 4.7 44.2 1.0
NH2 A:ARG165 4.8 47.8 1.0
CD1 A:TRP203 4.8 44.4 1.0
CB A:GLU199 4.9 43.7 1.0
N A:TRP203 5.0 44.4 1.0

Calcium binding site 4 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 4 out of 9 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 Calcium with other atoms in the Ca 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:Ca1269

b:40.8
occ:1.00
 O B:ASP158 2.4 43.6 1.0
O B:GLY192 2.4 42.6 1.0
O B:GLY190 2.4 42.7 1.0
OD1 B:ASP194 2.5 41.5 1.0
C B:ASP158 3.5 43.6 1.0
CG B:ASP194 3.5 41.6 1.0
C B:GLY192 3.6 42.6 1.0
C B:GLY190 3.6 42.8 1.0
O B:ALA157 4.0 44.1 1.0
N B:GLY192 4.0 42.7 1.0
OD2 B:ASP194 4.0 41.2 1.0
C B:ILE191 4.0 42.8 1.0
N B:ASP194 4.2 42.2 1.0
O B:GLY188 4.2 43.5 1.0
CA B:GLY192 4.3 42.6 1.0
CA B:ASP158 4.3 43.8 1.0
O B:ILE191 4.3 42.9 1.0
N B:GLY190 4.4 43.1 1.0
N B:ILE159 4.5 43.5 1.0
N B:ILE191 4.5 42.8 1.0
CA B:GLY190 4.5 42.9 1.0
CA B:ILE191 4.5 42.9 1.0
N B:GLY193 4.6 42.5 1.0
CA B:ILE159 4.7 43.4 1.0
CB B:ASP194 4.7 42.0 1.0
N B:MET160 4.7 43.1 1.0
CG B:MET160 4.7 42.5 1.0
C B:GLY193 4.7 42.3 1.0
CA B:GLY193 4.8 42.4 1.0
C B:PRO189 4.8 43.2 1.0
CA B:ASP194 4.8 42.1 1.0
C B:ALA157 4.9 44.1 1.0
CH2 B:TRP109 4.9 52.2 1.0

Calcium binding site 5 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 5 out of 9 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 Calcium with other atoms in the Ca 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
B:Ca1270

b:40.7
occ:1.00
 O B:ASN180 2.2 46.0 1.0
O B:GLY176 2.3 46.1 1.0
O B:GLY178 2.3 46.0 1.0
OD2 B:ASP198 2.5 44.4 1.0
OD1 B:ASP175 2.6 46.6 1.0
OE1 B:GLU201 2.6 45.3 1.0
C B:ASN180 3.3 46.0 1.0
C B:GLY178 3.5 46.0 1.0
CG B:ASP198 3.5 44.5 1.0
C B:GLY176 3.6 46.0 1.0
CD B:GLU201 3.6 45.2 1.0
CG B:ASP175 3.8 46.5 1.0
N B:ASN180 3.8 46.2 1.0
N B:GLY178 3.9 45.9 1.0
OE2 B:GLU201 4.0 45.8 1.0
CB B:ASP198 4.0 44.4 1.0
CA B:ASN180 4.1 46.2 1.0
C B:PRO177 4.1 45.9 1.0
N B:GLY176 4.2 46.2 1.0
CA B:GLY178 4.3 46.0 1.0
C B:GLY179 4.3 46.2 1.0
N B:LEU181 4.3 45.8 1.0
N B:ASP175 4.4 46.5 1.0
C B:ASP175 4.4 46.2 1.0
CA B:PRO177 4.4 46.0 1.0
OD2 B:ASP175 4.4 47.2 1.0
N B:PRO177 4.4 46.0 1.0
CB B:ASN180 4.5 46.5 1.0
CA B:GLY176 4.5 46.0 1.0
CA B:LEU181 4.5 45.7 1.0
N B:GLY179 4.6 46.0 1.0
OD1 B:ASP198 4.6 44.7 1.0
O B:PRO177 4.7 46.0 1.0
CA B:ASP175 4.8 46.3 1.0
CA B:GLY179 4.8 46.1 1.0
O B:ASP175 4.8 46.2 1.0
CB B:ASP175 4.9 46.3 1.0
O B:GLY179 4.9 46.2 1.0
CG B:GLU201 5.0 45.1 1.0

Calcium binding site 6 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 6 out of 9 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 Calcium with other atoms in the Ca 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
B:Ca1271

b:48.6
occ:1.00
 O B:GLU199 2.3 44.9 1.0
O B:GLU201 2.4 44.7 1.0
OD2 B:ASP124 2.7 48.7 1.0
OE2 B:GLU199 2.7 45.6 1.0
OD1 B:ASP124 2.8 49.3 1.0
CG B:ASP124 3.1 49.0 1.0
C B:GLU199 3.5 44.9 1.0
C B:GLU201 3.5 44.8 1.0
CD B:GLU199 3.8 45.7 1.0
CG B:GLU199 4.2 45.1 1.0
N B:GLU201 4.2 44.9 1.0
OG1 B:THR122 4.2 48.7 1.0
CA B:GLU199 4.3 44.8 1.0
CA B:ARG202 4.3 44.8 1.0
N B:ARG202 4.3 44.8 1.0
C B:ASP200 4.5 44.9 1.0
CA B:GLU201 4.5 44.9 1.0
N B:ASP200 4.5 44.9 1.0
CB B:ASP124 4.6 49.1 1.0
CA B:ASP200 4.7 44.9 1.0
CD1 B:TRP203 4.7 44.4 1.0
CB B:GLU199 4.8 44.9 1.0
OE1 B:GLU199 4.9 46.4 1.0
N B:TRP203 4.9 44.7 1.0
O B:ASP200 5.0 45.0 1.0

Calcium binding site 7 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 7 out of 9 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 Calcium with other atoms in the Ca binding site number 7 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:Ca1266

b:66.8
occ:1.00
 O C:GLY192 2.4 45.3 1.0
O C:ASP158 2.5 43.6 1.0
O C:GLY190 2.6 45.8 1.0
OD1 C:ASP194 2.6 45.2 1.0
C C:GLY192 3.6 45.3 1.0
CG C:ASP194 3.6 44.9 1.0
C C:ASP158 3.6 43.5 1.0
C C:GLY190 3.6 45.8 1.0
O C:ALA157 3.7 43.7 1.0
OD2 C:ASP194 4.0 45.5 1.0
N C:GLY192 4.0 45.5 1.0
O C:GLY188 4.1 45.9 1.0
C C:ILE191 4.2 45.7 1.0
CA C:GLY192 4.3 45.4 1.0
N C:ASP194 4.3 44.6 1.0
CA C:ASP158 4.4 43.6 1.0
N C:GLY190 4.4 45.8 1.0
CG C:MET160 4.4 42.8 1.0
CA C:GLY190 4.5 45.8 1.0
N C:ILE191 4.5 45.8 1.0
N C:GLY193 4.6 45.1 1.0
O C:ILE191 4.6 45.6 1.0
N C:ILE159 4.6 43.4 1.0
CA C:ILE191 4.6 45.8 1.0
N C:MET160 4.7 43.1 1.0
CA C:GLY193 4.7 44.9 1.0
C C:PRO189 4.8 45.8 1.0
C C:ALA157 4.8 43.7 1.0
CA C:ILE159 4.8 43.3 1.0
C C:GLY193 4.8 44.8 1.0
CB C:ASP194 4.8 44.5 1.0
CA C:ASP194 5.0 44.4 1.0

Calcium binding site 8 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 8 out of 9 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 Calcium with other atoms in the Ca binding site number 8 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:Ca1267

b:40.9
occ:1.00
 O C:GLY176 2.3 45.0 1.0
O C:GLY178 2.4 45.1 1.0
OD2 C:ASP198 2.4 43.7 1.0
O C:ASN180 2.5 45.9 1.0
OD1 C:ASP175 2.5 45.1 1.0
OE1 C:GLU201 2.5 43.9 1.0
C C:GLY176 3.5 45.1 1.0
C C:ASN180 3.5 46.0 1.0
CG C:ASP198 3.5 43.7 1.0
C C:GLY178 3.6 45.3 1.0
CD C:GLU201 3.7 44.5 1.0
CG C:ASP175 3.7 45.0 1.0
N C:ASN180 4.0 46.0 1.0
N C:GLY178 4.1 45.1 1.0
N C:GLY176 4.1 45.0 1.0
CB C:ASP198 4.1 43.7 1.0
OE2 C:GLU201 4.1 44.9 1.0
OD2 C:ASP175 4.2 45.3 1.0
C C:PRO177 4.3 45.2 1.0
N C:LEU181 4.3 45.9 1.0
CA C:ASN180 4.4 46.1 1.0
CA C:GLY176 4.4 45.0 1.0
C C:GLY179 4.4 45.9 1.0
CA C:LEU181 4.4 45.8 1.0
N C:PRO177 4.4 45.1 1.0
CA C:GLY178 4.4 45.2 1.0
OD1 C:ASN180 4.4 48.6 1.0
CA C:PRO177 4.5 45.2 1.0
N C:ASP175 4.5 45.0 1.0
N C:GLY179 4.6 45.4 1.0
OD1 C:ASP198 4.6 44.4 1.0
C C:ASP175 4.6 45.0 1.0
CA C:GLY179 4.7 45.7 1.0
CB C:ASP175 4.9 44.9 1.0
CA C:ASP175 4.9 45.0 1.0
CG C:GLU201 4.9 44.4 1.0
O C:PRO177 4.9 45.2 1.0
CD2 C:LEU181 4.9 46.0 1.0
O C:GLY179 5.0 45.8 1.0
CG C:ASN180 5.0 47.1 1.0

Calcium binding site 9 out of 9 in 2j0t

Go back to Calcium Binding Sites List in 2j0t
Calcium binding site 9 out of 9 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 Calcium with other atoms in the Ca binding site number 9 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:Ca1268

b:43.2
occ:1.00
 O C:GLU199 2.3 43.6 1.0
OD2 C:ASP124 2.4 44.6 1.0
OE2 C:GLU199 2.7 44.0 1.0
O C:GLU201 2.7 44.0 1.0
CG C:ASP124 3.2 45.3 1.0
OD1 C:ASP124 3.2 45.6 1.0
C C:GLU199 3.5 43.7 1.0
C C:GLU201 3.6 44.0 1.0
CD C:GLU199 3.7 44.2 1.0
CG C:GLU199 4.1 43.8 1.0
N C:GLU201 4.2 44.0 1.0
CA C:GLU199 4.3 43.7 1.0
N C:ARG202 4.3 44.1 1.0
CA C:ARG202 4.3 44.2 1.0
OG1 C:THR122 4.4 46.8 1.0
C C:ASP200 4.4 43.8 1.0
N C:ASP200 4.5 43.7 1.0
CA C:GLU201 4.5 44.0 1.0
CB C:ASP124 4.6 45.5 1.0
CA C:ASP200 4.7 43.8 1.0
CB C:GLU199 4.8 43.7 1.0
OE1 C:GLU199 4.8 44.5 1.0
CD1 C:TRP203 4.9 44.0 1.0
NH2 C:ARG165 5.0 47.8 1.0
O C:ASP200 5.0 43.9 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: Fri Jul 12 13:14:34 2024

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