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Calcium in PDB 4ja1: 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: 4ja1 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) 34.22 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.119, 77.615, 106.048, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 24.4

Other elements in 4ja1:

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

Platinum (Pt) 3 atoms
Chlorine (Cl) 4 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 4ja1). 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: 4ja1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4ja1

Go back to Calcium Binding Sites List in 4ja1
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:16.3
occ:1.00
 OE2 A:GLU184 2.2 17.0 1.0
O A:VAL163 2.3 13.8 1.0
OD1 A:ASP158 2.3 17.7 1.0
OD2 A:ASP181 2.3 17.5 1.0
O A:GLY161 2.3 19.0 1.0
O A:GLY159 2.3 18.0 1.0
CG A:ASP181 3.4 14.5 1.0
C A:VAL163 3.5 14.0 1.0
CG A:ASP158 3.5 17.5 1.0
CD A:GLU184 3.5 17.2 1.0
C A:GLY161 3.5 18.6 1.0
C A:GLY159 3.6 20.0 1.0
N A:GLY161 4.0 20.1 1.0
OD2 A:ASP158 4.0 15.9 1.0
CB A:ASP181 4.0 11.9 1.0
C A:PRO160 4.1 20.1 1.0
N A:VAL163 4.1 16.6 1.0
OE1 A:GLU184 4.2 17.3 1.0
CA A:GLY161 4.2 18.1 1.0
N A:GLY159 4.2 20.2 1.0
CA A:VAL163 4.2 15.3 1.0
C A:ASP158 4.3 20.9 1.0
OD1 A:ASP181 4.3 15.1 1.0
N A:ASP158 4.4 20.2 1.0
O A:PRO160 4.4 20.7 1.0
N A:LEU164 4.4 12.9 1.0
C A:ASN162 4.4 17.4 1.0
N A:PRO160 4.4 20.3 1.0
CA A:PRO160 4.5 20.6 1.0
CA A:GLY159 4.5 19.8 1.0
CG A:GLU184 4.5 17.0 1.0
O A:HOH426 4.5 24.9 1.0
O A:ASP158 4.6 21.6 1.0
CA A:LEU164 4.6 12.6 1.0
N A:ASN162 4.6 18.0 1.0
CA A:ASP158 4.6 20.6 1.0
CB A:VAL163 4.6 14.2 1.0
CB A:ASP158 4.6 19.9 1.0
O A:ASN162 4.9 18.2 1.0
CA A:ASN162 4.9 18.2 1.0

Calcium binding site 2 out of 6 in 4ja1

Go back to Calcium Binding Sites List in 4ja1
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:17.4
occ:1.00
 O A:GLY173 2.3 17.2 1.0
O A:HOH443 2.3 30.8 1.0
O A:HOH401 2.3 17.9 1.0
O A:ASN175 2.3 17.6 1.0
O A:ASP141 2.3 18.1 1.0
OD1 A:ASP177 2.4 15.9 1.0
CG A:ASP177 3.4 15.0 1.0
C A:ASP141 3.5 18.2 1.0
C A:GLY173 3.5 19.2 1.0
C A:ASN175 3.5 17.7 1.0
OD2 A:ASP177 3.9 16.0 1.0
C A:ILE174 4.0 20.3 1.0
O A:ALA140 4.1 23.7 1.0
N A:ASN175 4.1 18.6 1.0
N A:ASP177 4.2 13.9 1.0
O A:ILE174 4.2 20.7 1.0
CA A:ASP141 4.3 19.3 1.0
N A:GLY173 4.3 20.2 1.0
N A:ILE174 4.4 19.0 1.0
CA A:GLY176 4.4 15.0 1.0
O A:GLY171 4.4 23.5 1.0
CA A:ILE174 4.4 19.7 1.0
N A:GLY176 4.4 15.8 1.0
CA A:GLY173 4.4 20.1 1.0
CA A:ASN175 4.5 19.2 1.0
N A:ILE142 4.5 16.7 1.0
C A:GLY176 4.5 15.0 1.0
CB A:ASP177 4.6 13.6 1.0
CA A:ILE142 4.6 16.5 1.0
N A:MET143 4.6 17.5 1.0
C A:PRO172 4.7 21.0 1.0
O A:HOH422 4.7 19.5 1.0
O A:HOH444 4.7 23.2 0.6
CA A:ASP177 4.8 13.8 1.0
CH2 A:TRP92 4.9 17.7 1.0
O A:PRO172 5.0 19.4 1.0

Calcium binding site 3 out of 6 in 4ja1

Go back to Calcium Binding Sites List in 4ja1
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:17.4
occ:1.00
 O A:HOH405 2.3 21.4 1.0
O A:HOH415 2.3 22.4 1.0
O A:ASP182 2.3 15.3 1.0
OD2 A:ASP107 2.4 14.9 1.0
O A:GLU184 2.4 16.3 1.0
OD1 A:ASP182 2.5 15.3 1.0
OD1 A:ASP107 2.6 13.5 1.0
CG A:ASP107 2.9 15.7 1.0
C A:ASP182 3.3 15.1 1.0
CG A:ASP182 3.5 15.6 1.0
C A:GLU184 3.6 17.2 1.0
CA A:ASP182 3.8 14.5 1.0
OG1 A:THR105 4.0 14.8 1.0
CB A:ASP182 4.1 13.8 1.0
CA A:GLN185 4.3 17.1 1.0
CD1 A:TRP186 4.3 12.2 1.0
N A:GLN185 4.3 17.5 1.0
CB A:ASP107 4.4 16.3 1.0
N A:ASP183 4.4 15.7 1.0
N A:GLU184 4.4 17.7 1.0
OD2 A:ASP182 4.5 18.1 1.0
C A:ASP183 4.6 17.4 1.0
CA A:GLU184 4.7 17.4 1.0
NE2 A:GLN185 4.7 20.8 1.0
O B:HOH415 4.7 22.1 1.0
CA A:ASP183 4.7 16.4 1.0
N A:TRP186 4.7 15.7 1.0
NE1 A:TRP186 4.9 13.0 1.0

Calcium binding site 4 out of 6 in 4ja1

Go back to Calcium Binding Sites List in 4ja1
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:23.4
occ:1.00
 OD1 B:ASP158 2.2 28.1 1.0
O B:VAL163 2.3 24.0 1.0
OE2 B:GLU184 2.3 24.9 1.0
OD2 B:ASP181 2.3 21.5 1.0
O B:GLY159 2.4 29.6 1.0
O B:GLY161 2.4 26.9 1.0
CG B:ASP181 3.4 19.2 1.0
C B:VAL163 3.5 24.6 1.0
CG B:ASP158 3.5 31.0 1.0
CD B:GLU184 3.5 26.8 1.0
C B:GLY161 3.6 27.5 1.0
C B:GLY159 3.6 29.5 1.0
N B:VAL163 3.9 26.0 1.0
CB B:ASP181 4.0 20.2 1.0
N B:GLY161 4.1 28.6 1.0
N B:GLY159 4.1 30.1 1.0
OD2 B:ASP158 4.1 31.6 1.0
CA B:VAL163 4.2 25.6 1.0
C B:PRO160 4.2 29.4 1.0
C B:ASN162 4.3 26.0 1.0
N B:ASP158 4.3 29.1 1.0
OD1 B:ASP181 4.3 19.6 1.0
C B:ASP158 4.3 30.3 1.0
OE1 B:GLU184 4.3 26.5 1.0
CA B:GLY161 4.4 27.9 1.0
N B:LEU164 4.5 23.3 1.0
CG B:GLU184 4.5 23.3 1.0
CA B:GLY159 4.5 29.8 1.0
CA B:PRO160 4.6 29.4 1.0
N B:PRO160 4.6 29.4 1.0
CA B:ASP158 4.6 30.1 1.0
O B:ASN162 4.6 25.6 1.0
CB B:ASP158 4.6 30.1 1.0
N B:ASN162 4.6 26.7 1.0
O B:PRO160 4.7 29.0 1.0
CA B:LEU164 4.7 21.6 1.0
O B:HOH432 4.7 24.2 1.0
CA B:ASN162 4.8 27.1 1.0
CB B:VAL163 4.8 25.8 1.0
O B:ASP158 4.9 32.1 1.0
CB B:ASN162 5.0 27.4 1.0

Calcium binding site 5 out of 6 in 4ja1

Go back to Calcium Binding Sites List in 4ja1
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:23.8
occ:1.00
 O B:HOH404 2.2 17.3 1.0
O B:HOH402 2.3 29.8 1.0
O B:ASP141 2.4 19.6 1.0
O B:GLY173 2.4 26.6 1.0
O B:ASN175 2.4 22.6 1.0
OD1 B:ASP177 2.4 16.8 1.0
CG B:ASP177 3.4 18.0 1.0
C B:ASP141 3.5 19.8 1.0
C B:ASN175 3.6 22.3 1.0
C B:GLY173 3.6 25.8 1.0
OD2 B:ASP177 3.8 18.1 1.0
C B:ILE174 4.0 25.1 1.0
N B:ASN175 4.1 24.4 1.0
O B:ILE174 4.2 25.3 1.0
N B:ASP177 4.2 18.2 1.0
CA B:ASP141 4.2 20.8 1.0
O B:ALA140 4.3 22.5 1.0
N B:GLY173 4.3 26.4 1.0
O B:GLY171 4.3 26.6 1.0
C B:GLY176 4.4 19.0 1.0
CA B:GLY173 4.5 26.6 1.0
CA B:ASN175 4.5 24.1 1.0
N B:ILE142 4.5 18.5 1.0
N B:GLY176 4.5 21.3 1.0
N B:ILE174 4.5 25.8 1.0
CA B:ILE174 4.5 25.3 1.0
CA B:GLY176 4.5 19.6 1.0
CB B:ASP177 4.6 18.9 1.0
C B:PRO172 4.7 26.5 1.0
CA B:ILE142 4.7 18.7 1.0
N B:MET143 4.7 18.6 1.0
CA B:ASP177 4.8 18.4 1.0
CH2 B:TRP92 4.8 23.3 1.0
O B:PRO172 4.9 26.4 1.0
O B:HOH440 4.9 29.4 0.6

Calcium binding site 6 out of 6 in 4ja1

Go back to Calcium Binding Sites List in 4ja1
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:23.2
occ:1.00
 O B:GLU184 2.3 23.5 1.0
O B:ASP182 2.3 22.9 1.0
OD1 B:ASP182 2.4 23.2 1.0
O B:HOH444 2.5 20.4 1.0
OD2 B:ASP107 2.5 19.6 1.0
O B:HOH454 2.5 25.9 1.0
OD1 B:ASP107 2.5 20.5 1.0
CG B:ASP107 2.9 18.7 1.0
C B:ASP182 3.3 22.3 1.0
C B:GLU184 3.5 23.3 1.0
CG B:ASP182 3.6 22.3 1.0
CA B:ASP182 3.9 21.5 1.0
OG1 B:THR105 4.1 15.6 1.0
CB B:ASP182 4.1 20.6 1.0
CA B:GLN185 4.3 22.5 1.0
N B:GLN185 4.3 22.0 1.0
CB B:ASP107 4.4 19.0 1.0
CD1 B:TRP186 4.4 17.2 1.0
N B:ASP183 4.4 23.8 1.0
N B:GLU184 4.4 23.3 1.0
O A:HOH430 4.5 22.2 1.0
C B:ASP183 4.5 24.2 1.0
OD2 B:ASP182 4.6 21.5 1.0
CA B:GLU184 4.6 23.1 1.0
O B:HOH418 4.6 24.7 1.0
CA B:ASP183 4.7 24.0 1.0
N B:TRP186 4.7 19.6 1.0
NE2 B:GLN185 4.8 37.5 1.0
NE1 B:TRP186 4.9 18.3 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: Sun Jul 14 08:26:26 2024

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