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Calcium in PDB 4dpe: Structure of MMP3 Complexed with A Platinum-Based Inhibitor.

Enzymatic activity of Structure of MMP3 Complexed with A Platinum-Based Inhibitor.

All present enzymatic activity of Structure of MMP3 Complexed with A Platinum-Based Inhibitor.:
3.4.24.17;

Protein crystallography data

The structure of Structure of MMP3 Complexed with A Platinum-Based Inhibitor., PDB code: 4dpe was solved by B.D.Belviso, F.Arnesano, V.Calderone, R.Caliandro, G.Natile, D.Siliqi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.86 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.206, 77.714, 105.615, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 23.1

Other elements in 4dpe:

The structure of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. also contains other interesting chemical elements:

Platinum (Pt) 6 atoms
Chlorine (Cl) 2 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor. (pdb code 4dpe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor., PDB code: 4dpe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4dpe

Go back to Calcium Binding Sites List in 4dpe
Calcium binding site 1 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:17.7
occ:1.00
 OE2 A:GLU184 2.2 20.9 1.0
OD1 A:ASP158 2.3 16.8 1.0
OD2 A:ASP181 2.3 17.0 1.0
O A:VAL163 2.3 13.0 1.0
O A:GLY159 2.4 22.6 1.0
O A:GLY161 2.5 19.5 1.0
CG A:ASP181 3.4 16.9 1.0
CD A:GLU184 3.4 20.1 1.0
CG A:ASP158 3.5 17.4 1.0
C A:VAL163 3.5 12.9 1.0
C A:GLY159 3.6 25.4 1.0
C A:GLY161 3.6 20.1 1.0
N A:GLY161 3.9 21.5 1.0
CB A:ASP181 4.0 12.5 1.0
N A:VAL163 4.0 16.1 1.0
OD2 A:ASP158 4.0 16.9 1.0
OE1 A:GLU184 4.1 19.5 1.0
C A:PRO160 4.1 22.6 1.0
CA A:VAL163 4.2 15.8 1.0
N A:GLY159 4.2 23.5 1.0
CA A:GLY161 4.3 20.6 1.0
OD1 A:ASP181 4.3 15.6 1.0
C A:ASP158 4.3 22.5 1.0
N A:ASP158 4.4 19.9 1.0
C A:ASN162 4.5 18.4 1.0
N A:LEU164 4.5 12.4 1.0
CA A:GLY159 4.5 24.4 1.0
CG A:GLU184 4.5 17.2 1.0
N A:PRO160 4.5 25.4 1.0
CA A:PRO160 4.5 23.9 1.0
O A:ASP158 4.5 22.3 1.0
O A:PRO160 4.5 21.6 1.0
CB A:VAL163 4.6 13.8 1.0
CA A:LEU164 4.6 12.3 1.0
N A:ASN162 4.7 18.7 1.0
CA A:ASP158 4.7 21.4 1.0
CB A:ASP158 4.7 21.2 1.0
CA A:ASN162 4.9 19.3 1.0

Calcium binding site 2 out of 6 in 4dpe

Go back to Calcium Binding Sites List in 4dpe
Calcium binding site 2 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:18.2
occ:1.00
 O A:GLY173 2.2 19.4 1.0
O A:HOH411 2.3 21.6 1.0
O A:ASP141 2.4 17.7 1.0
OD1 A:ASP177 2.4 18.0 1.0
O A:ASN175 2.4 17.2 1.0
O A:HOH402 2.4 16.6 1.0
CG A:ASP177 3.4 16.5 1.0
C A:GLY173 3.4 19.3 1.0
C A:ASP141 3.5 17.1 1.0
C A:ASN175 3.6 16.6 1.0
OD2 A:ASP177 3.8 19.6 1.0
C A:ILE174 4.0 19.1 1.0
O A:ALA140 4.1 23.8 1.0
N A:ASN175 4.2 19.0 1.0
N A:GLY173 4.2 20.7 1.0
N A:ASP177 4.2 14.2 1.0
O A:ILE174 4.2 18.7 1.0
CA A:ASP141 4.3 18.7 1.0
CA A:GLY173 4.3 22.1 1.0
O A:GLY171 4.3 23.5 1.0
N A:ILE174 4.3 21.4 1.0
CA A:ILE174 4.4 20.2 1.0
CA A:GLY176 4.4 16.1 1.0
N A:GLY176 4.5 12.7 1.0
N A:ILE142 4.5 16.6 1.0
C A:GLY176 4.5 15.7 1.0
CA A:ASN175 4.5 17.9 1.0
N A:MET143 4.6 16.3 1.0
CB A:ASP177 4.6 12.3 1.0
C A:PRO172 4.6 22.6 1.0
CA A:ILE142 4.7 16.3 1.0
CA A:ASP177 4.8 13.0 1.0
O A:HOH459 4.8 37.2 1.0
CH2 A:TRP92 4.9 18.9 1.0
O A:PRO172 5.0 20.6 1.0

Calcium binding site 3 out of 6 in 4dpe

Go back to Calcium Binding Sites List in 4dpe
Calcium binding site 3 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:19.6
occ:1.00
 O A:GLU184 2.3 17.1 1.0
O A:ASP182 2.4 18.7 1.0
OD1 A:ASP182 2.5 17.6 1.0
OD2 A:ASP107 2.5 17.6 1.0
OD1 A:ASP107 2.7 17.3 1.0
CG A:ASP107 3.0 20.6 1.0
C A:ASP182 3.3 18.0 1.0
C A:GLU184 3.5 19.0 1.0
CG A:ASP182 3.5 18.2 1.0
CA A:ASP182 3.8 17.2 1.0
CB A:ASP182 4.1 16.9 1.0
OG1 A:THR105 4.1 15.1 1.0
CA A:GLN185 4.2 18.3 1.0
N A:GLN185 4.3 18.5 1.0
CD1 A:TRP186 4.4 17.1 1.0
N A:GLU184 4.4 19.1 1.0
N A:ASP183 4.4 19.8 1.0
CB A:ASP107 4.5 17.0 1.0
OD2 A:ASP182 4.5 14.1 1.0
C A:ASP183 4.6 20.9 1.0
CA A:GLU184 4.6 18.8 1.0
N A:TRP186 4.6 17.2 1.0
CA A:ASP183 4.7 20.7 1.0
OE1 A:GLN185 4.7 23.3 1.0
NE1 A:TRP186 4.9 17.3 1.0
C A:GLN185 5.0 18.0 1.0

Calcium binding site 4 out of 6 in 4dpe

Go back to Calcium Binding Sites List in 4dpe
Calcium binding site 4 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:27.4
occ:1.00
 OE2 B:GLU184 2.2 32.1 1.0
OD1 B:ASP158 2.2 28.6 1.0
O B:VAL163 2.3 28.4 1.0
O B:GLY161 2.4 31.6 1.0
OD2 B:ASP181 2.4 21.6 1.0
O B:GLY159 2.4 33.8 1.0
C B:VAL163 3.4 26.4 1.0
CD B:GLU184 3.4 30.7 1.0
CG B:ASP181 3.5 19.7 1.0
CG B:ASP158 3.5 32.2 1.0
C B:GLY161 3.6 31.9 1.0
C B:GLY159 3.7 33.6 1.0
N B:VAL163 3.9 28.7 1.0
N B:GLY161 4.0 33.6 1.0
CB B:ASP181 4.0 22.1 1.0
N B:GLY159 4.1 32.6 1.0
CA B:VAL163 4.1 28.1 1.0
C B:ASN162 4.2 29.1 1.0
OD2 B:ASP158 4.2 31.9 1.0
OE1 B:GLU184 4.2 27.9 1.0
C B:PRO160 4.2 34.0 1.0
C B:ASP158 4.3 31.6 1.0
CA B:GLY161 4.3 31.8 1.0
N B:ASP158 4.4 30.1 1.0
OD1 B:ASP181 4.4 22.1 1.0
N B:LEU164 4.4 25.4 1.0
CG B:GLU184 4.5 28.7 1.0
O B:ASN162 4.5 28.4 1.0
CA B:GLY159 4.5 32.7 1.0
N B:PRO160 4.6 34.0 1.0
O B:PRO160 4.6 35.4 1.0
N B:ASN162 4.6 29.9 1.0
CA B:ASP158 4.6 31.7 1.0
O B:ASP158 4.6 34.6 1.0
CA B:PRO160 4.6 34.3 1.0
CA B:LEU164 4.7 23.5 1.0
CB B:ASP158 4.7 30.4 1.0
O B:HOH428 4.7 27.1 1.0
CB B:VAL163 4.7 28.1 1.0
CA B:ASN162 4.8 30.8 1.0
CB B:ASN162 5.0 30.7 1.0

Calcium binding site 5 out of 6 in 4dpe

Go back to Calcium Binding Sites List in 4dpe
Calcium binding site 5 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:23.2
occ:1.00
 O B:ASN175 2.1 22.7 1.0
O B:HOH408 2.1 19.8 1.0
O B:GLY173 2.3 28.4 1.0
O B:HOH416 2.3 23.9 1.0
OD1 B:ASP177 2.4 18.3 1.0
O B:ASP141 2.4 21.2 1.0
C B:ASN175 3.3 22.9 1.0
CG B:ASP177 3.4 22.5 1.0
C B:ASP141 3.5 21.0 1.0
C B:GLY173 3.5 28.0 1.0
OD2 B:ASP177 3.9 22.4 1.0
C B:ILE174 4.0 26.6 1.0
N B:ASP177 4.1 18.2 1.0
N B:ASN175 4.1 25.8 1.0
O B:ILE174 4.1 24.7 1.0
N B:GLY176 4.2 22.3 1.0
O B:ALA140 4.2 23.2 1.0
CA B:ASP141 4.2 22.3 1.0
N B:GLY173 4.2 27.0 1.0
CA B:GLY176 4.3 20.3 1.0
C B:GLY176 4.3 20.4 1.0
CA B:ASN175 4.4 26.1 1.0
N B:ILE174 4.4 27.6 1.0
CA B:GLY173 4.4 28.7 1.0
O B:GLY171 4.4 29.8 1.0
CA B:ILE174 4.5 27.4 1.0
N B:ILE142 4.5 20.5 1.0
C B:PRO172 4.5 28.2 1.0
CB B:ASP177 4.6 18.0 1.0
CA B:ILE142 4.6 18.8 1.0
O B:HOH439 4.6 30.3 1.0
N B:MET143 4.7 17.9 1.0
O B:HOH473 4.7 37.9 1.0
CA B:ASP177 4.7 17.9 1.0
O B:PRO172 4.8 26.6 1.0
CH2 B:TRP92 4.9 30.2 1.0
O B:HOH501 5.0 36.1 1.0
CG B:MET143 5.0 24.6 1.0

Calcium binding site 6 out of 6 in 4dpe

Go back to Calcium Binding Sites List in 4dpe
Calcium binding site 6 out of 6 in the Structure of MMP3 Complexed with A Platinum-Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of MMP3 Complexed with A Platinum-Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:28.0
occ:0.82
 O B:GLU184 2.3 25.4 1.0
O B:ASP182 2.4 26.0 1.0
OD1 B:ASP182 2.5 27.2 1.0
OD2 B:ASP107 2.5 26.1 1.0
O B:HOH422 2.5 34.5 1.0
OD1 B:ASP107 2.8 29.1 1.0
CG B:ASP107 3.0 24.6 1.0
C B:ASP182 3.3 24.7 1.0
C B:GLU184 3.4 26.0 1.0
CG B:ASP182 3.6 25.8 1.0
CA B:ASP182 3.9 23.0 1.0
N B:GLU184 4.1 26.1 1.0
CB B:ASP182 4.2 20.2 1.0
OG1 B:THR105 4.2 17.3 1.0
N B:GLN185 4.3 24.2 1.0
N B:ASP183 4.3 26.6 1.0
CD1 B:TRP186 4.4 20.1 1.0
C B:ASP183 4.4 27.6 1.0
CA B:GLN185 4.4 25.2 1.0
CA B:GLU184 4.4 26.7 1.0
O B:HOH468 4.5 27.4 1.0
CB B:ASP107 4.5 23.6 1.0
CA B:ASP183 4.5 26.9 1.0
O B:HOH479 4.5 35.9 1.0
OD2 B:ASP182 4.6 21.3 1.0
N B:TRP186 4.8 21.3 1.0
NE1 B:TRP186 4.9 22.5 1.0
O B:ASP183 5.0 26.8 1.0

Reference:

B.D.Belviso, R.Caliandro, D.Siliqi, V.Calderone, F.Arnesano, G.Natile. Structure of Matrix Metalloproteinase-3 with A Platinum-Based Inhibitor. Chem.Commun.(Camb.) V. 49 5492 2013.
ISSN: ISSN 1359-7345
PubMed: 23660647
DOI: 10.1039/C3CC41278D
Page generated: Tue Jul 8 19:32:21 2025

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