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Calcium in PDB 2d1o: Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor

Enzymatic activity of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor

All present enzymatic activity of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor:
3.4.24.17;

Protein crystallography data

The structure of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1o was solved by T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.02
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.360, 50.950, 80.790, 90.00, 105.00, 90.00
R / Rfree (%) 18.3 / 20.6

Other elements in 2d1o:

The structure of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor (pdb code 2d1o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor, PDB code: 2d1o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2d1o

Go back to Calcium Binding Sites List in 2d1o
Calcium binding site 1 out of 6 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca259

b:16.0
occ:1.00
 O A:GLY159 2.2 22.7 1.0
O A:VAL163 2.2 13.9 1.0
OE2 A:GLU184 2.2 16.5 1.0
OD2 A:ASP181 2.4 14.1 1.0
OD2 A:ASP158 2.4 18.5 1.0
O A:GLY161 2.5 20.1 1.0
C A:VAL163 3.4 15.0 1.0
CG A:ASP181 3.4 14.4 1.0
C A:GLY159 3.4 22.6 1.0
CD A:GLU184 3.4 15.9 1.0
CG A:ASP158 3.6 19.4 1.0
C A:GLY161 3.6 20.0 1.0
N A:GLY161 3.9 20.8 1.0
N A:VAL163 3.9 16.2 1.0
N A:GLY159 4.0 21.1 1.0
CB A:ASP181 4.0 13.3 1.0
CA A:VAL163 4.1 15.7 1.0
C A:PRO160 4.1 22.5 1.0
OD1 A:ASP158 4.2 18.9 1.0
OE1 A:GLU184 4.3 15.7 1.0
OD1 A:ASP181 4.3 13.7 1.0
CA A:GLY159 4.3 22.3 1.0
CG A:GLU184 4.3 15.8 1.0
C A:ASP158 4.3 20.7 1.0
CA A:GLY161 4.3 20.5 1.0
N A:PRO160 4.3 22.6 1.0
C A:ASN162 4.4 17.6 1.0
N A:ASP158 4.4 20.2 1.0
CA A:PRO160 4.4 22.5 1.0
N A:LEU164 4.4 13.9 1.0
CB A:VAL163 4.4 15.7 1.0
CA A:LEU164 4.6 14.2 1.0
N A:ASN162 4.6 19.3 1.0
O A:HOH1040 4.7 35.0 1.0
O A:PRO160 4.7 22.6 1.0
CA A:ASP158 4.7 20.1 1.0
CB A:ASP158 4.7 19.8 1.0
CA A:ASN162 4.9 19.1 1.0
O A:ASP158 4.9 19.8 1.0
O A:ASN162 4.9 17.2 1.0
CB A:ASN162 4.9 20.2 1.0

Calcium binding site 2 out of 6 in 2d1o

Go back to Calcium Binding Sites List in 2d1o
Calcium binding site 2 out of 6 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca260

b:15.2
occ:1.00
 OD2 A:ASP107 2.3 18.1 1.0
O A:ASP182 2.3 16.3 1.0
OD2 A:ASP182 2.3 13.7 1.0
O A:GLU184 2.4 18.1 1.0
OD1 A:ASP107 2.6 17.3 1.0
CG A:ASP107 2.8 17.9 1.0
C A:ASP182 3.3 15.8 1.0
CG A:ASP182 3.4 14.2 1.0
C A:GLU184 3.6 18.1 1.0
CA A:ASP182 3.8 14.6 1.0
OG1 A:THR105 4.0 14.3 1.0
CB A:ASP182 4.1 13.8 1.0
CD1 A:TRP186 4.2 15.6 1.0
N A:GLU184 4.2 16.6 1.0
CB A:ASP107 4.3 17.5 1.0
OD1 A:ASP182 4.3 15.2 1.0
CA A:GLN185 4.3 20.6 1.0
N A:ASP183 4.4 16.2 1.0
N A:GLN185 4.4 19.1 1.0
C A:ASP183 4.5 16.8 1.0
N A:TRP186 4.6 18.6 1.0
CA A:GLU184 4.7 17.1 1.0
NE1 A:TRP186 4.7 15.7 1.0
CA A:ASP183 4.7 16.4 1.0
O A:HOH1029 4.8 32.6 1.0
OE1 A:GLN185 5.0 31.6 1.0

Calcium binding site 3 out of 6 in 2d1o

Go back to Calcium Binding Sites List in 2d1o
Calcium binding site 3 out of 6 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca261

b:13.4
occ:1.00
 OD2 A:ASP177 2.3 15.4 1.0
O A:ASP141 2.4 13.9 1.0
O A:HOH1022 2.4 24.6 1.0
O A:GLY173 2.4 16.1 1.0
O A:ASN175 2.4 13.6 1.0
CG A:ASP177 3.3 14.4 1.0
C A:ASP141 3.5 13.8 1.0
C A:ASN175 3.6 13.9 1.0
C A:GLY173 3.6 17.2 1.0
OD1 A:ASP177 3.8 15.0 1.0
N A:ASP177 4.1 12.8 1.0
C A:ILE174 4.1 15.2 1.0
O A:ALA140 4.1 17.7 1.0
N A:ASN175 4.2 14.2 1.0
O A:ILE174 4.2 13.5 1.0
CA A:ASP141 4.3 14.4 1.0
C A:GLY176 4.3 13.3 1.0
O A:GLY171 4.3 16.3 1.0
CA A:GLY176 4.4 13.3 1.0
N A:GLY176 4.4 13.3 1.0
O A:HOH1026 4.4 19.5 1.0
N A:GLY173 4.5 18.5 1.0
CA A:ASN175 4.5 14.0 1.0
N A:ILE142 4.5 12.9 1.0
N A:ILE174 4.5 16.3 1.0
CB A:ASP177 4.5 13.8 1.0
CA A:GLY173 4.5 17.7 1.0
CA A:ILE174 4.5 15.8 1.0
N A:MET143 4.6 13.4 1.0
CA A:ASP177 4.7 13.3 1.0
CA A:ILE142 4.7 13.6 1.0
CG A:MET143 4.7 17.0 1.0
O A:HOH1039 4.8 22.6 1.0
C A:PRO172 4.8 18.2 1.0
CH2 A:TRP92 4.9 14.9 1.0
O A:GLY176 5.0 13.2 1.0

Calcium binding site 4 out of 6 in 2d1o

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Calcium binding site 4 out of 6 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca264

b:12.7
occ:1.00
 OE2 B:GLU184 2.2 13.3 1.0
O B:GLY159 2.2 17.1 1.0
O B:VAL163 2.3 12.8 1.0
OD2 B:ASP181 2.4 13.1 1.0
O B:GLY161 2.4 14.0 1.0
OD1 B:ASP158 2.4 17.7 1.0
CG B:ASP181 3.4 13.8 1.0
C B:VAL163 3.4 12.7 1.0
CD B:GLU184 3.4 12.2 1.0
C B:GLY159 3.4 16.7 1.0
C B:GLY161 3.6 13.7 1.0
CG B:ASP158 3.6 17.2 1.0
N B:VAL163 3.9 12.0 1.0
N B:GLY161 3.9 15.1 1.0
N B:GLY159 3.9 17.1 1.0
CB B:ASP181 4.0 13.3 1.0
OE1 B:GLU184 4.2 12.0 1.0
C B:PRO160 4.2 16.1 1.0
CA B:VAL163 4.2 12.5 1.0
C B:ASP158 4.2 17.8 1.0
CA B:GLY159 4.3 17.1 1.0
OD2 B:ASP158 4.3 16.3 1.0
OD1 B:ASP181 4.3 14.6 1.0
CA B:GLY161 4.3 14.6 1.0
C B:ASN162 4.3 11.5 1.0
N B:ASP158 4.4 18.4 1.0
N B:PRO160 4.4 17.2 1.0
CG B:GLU184 4.4 12.4 1.0
N B:LEU164 4.4 11.8 1.0
CA B:PRO160 4.5 16.8 1.0
N B:ASN162 4.6 13.0 1.0
CA B:ASP158 4.6 17.4 1.0
O B:PRO160 4.6 15.7 1.0
CA B:LEU164 4.7 12.0 1.0
CB B:VAL163 4.7 12.8 1.0
CB B:ASP158 4.7 18.5 1.0
O B:HOH1011 4.7 22.8 1.0
CB B:ASN162 4.7 13.4 1.0
CA B:ASN162 4.8 12.7 1.0
O B:ASP158 4.8 17.4 1.0
O B:ASN162 4.9 11.5 1.0

Calcium binding site 5 out of 6 in 2d1o

Go back to Calcium Binding Sites List in 2d1o
Calcium binding site 5 out of 6 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca265

b:13.3
occ:1.00
 OD2 B:ASP107 2.3 16.1 1.0
OD2 B:ASP182 2.4 18.3 1.0
O B:ASP182 2.4 15.0 1.0
O B:GLU184 2.4 13.6 1.0
OD1 B:ASP107 2.6 14.7 1.0
CG B:ASP107 2.8 16.4 1.0
C B:ASP182 3.3 14.3 1.0
CG B:ASP182 3.5 17.2 1.0
C B:GLU184 3.6 15.0 1.0
CA B:ASP182 3.9 14.6 1.0
OG1 B:THR105 4.1 13.0 1.0
CB B:ASP182 4.2 15.0 1.0
N B:GLU184 4.2 13.6 1.0
CD1 B:TRP186 4.2 13.9 1.0
CB B:ASP107 4.3 16.9 1.0
O B:HOH1026 4.3 30.3 1.0
CA B:GLN185 4.3 17.4 1.0
OD1 B:ASP182 4.4 16.1 1.0
N B:ASP183 4.4 14.9 1.0
N B:GLN185 4.4 16.1 1.0
C B:ASP183 4.5 14.1 1.0
N B:TRP186 4.6 16.6 1.0
CA B:GLU184 4.6 13.8 1.0
CA B:ASP183 4.7 14.4 1.0
NE1 B:TRP186 4.8 13.7 1.0
O B:HOH1047 4.8 34.7 1.0
OE1 B:GLN185 5.0 28.5 1.0

Calcium binding site 6 out of 6 in 2d1o

Go back to Calcium Binding Sites List in 2d1o
Calcium binding site 6 out of 6 in the Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Stromelysin-1 (Mmp-3) Complexed to A Hydroxamic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca266

b:16.8
occ:1.00
 O B:ASN175 2.3 19.0 1.0
OD1 B:ASP177 2.3 14.2 1.0
O B:ASP141 2.4 18.1 1.0
O B:GLY173 2.4 19.8 1.0
O B:HOH1005 2.4 19.0 1.0
O B:HOH1010 2.5 24.7 1.0
CG B:ASP177 3.4 16.4 1.0
C B:ASN175 3.5 19.0 1.0
C B:ASP141 3.5 18.8 1.0
C B:GLY173 3.6 20.6 1.0
OD2 B:ASP177 3.9 14.9 1.0
N B:ASP177 4.0 16.6 1.0
C B:ILE174 4.1 20.4 1.0
O B:ALA140 4.1 22.6 1.0
O B:ILE174 4.2 20.0 1.0
O B:GLY171 4.2 21.8 1.0
N B:ASN175 4.2 20.0 1.0
C B:GLY176 4.3 17.3 1.0
CA B:GLY176 4.3 18.0 1.0
CA B:ASP141 4.3 19.6 1.0
N B:GLY176 4.3 18.6 1.0
N B:GLY173 4.4 21.4 1.0
CA B:GLY173 4.5 20.7 1.0
N B:ILE142 4.5 18.0 1.0
CA B:ASN175 4.5 20.1 1.0
N B:ILE174 4.5 20.4 1.0
CB B:ASP177 4.6 15.2 1.0
O B:HOH1038 4.6 39.6 1.0
CA B:ILE174 4.6 20.4 1.0
N B:MET143 4.6 16.8 1.0
CA B:ILE142 4.6 17.6 1.0
CA B:ASP177 4.6 15.9 1.0
C B:PRO172 4.7 22.0 1.0
CH2 B:TRP92 4.8 19.5 1.0
CG B:MET143 4.8 16.6 1.0
O B:HOH1040 4.9 30.3 1.0

Reference:

T.Kohno, H.Hochigai, E.Yamashita, T.Tsukihara, M.Kanaoka. Crystal Structures of the Catalytic Domain of Human Stromelysin-1 (Mmp-3) and Collagenase-3 (Mmp-13) with A Hydroxamic Acid Inhibitor Sm-25453 Biochem.Biophys.Res.Commun. V. 344 315 2006.
ISSN: ISSN 0006-291X
PubMed: 16603129
DOI: 10.1016/J.BBRC.2006.03.098
Page generated: Tue Jul 8 04:57:36 2025

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