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Calcium in PDB 4g9l: Structure of MMP3 Complexed with Nngh Inhibitor.

Enzymatic activity of Structure of MMP3 Complexed with Nngh Inhibitor.

All present enzymatic activity of Structure of MMP3 Complexed with Nngh Inhibitor.:
3.4.24.17;

Protein crystallography data

The structure of Structure of MMP3 Complexed with Nngh Inhibitor., PDB code: 4g9l 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) 28.81 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.990, 78.840, 106.730, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 27

Other elements in 4g9l:

The structure of Structure of MMP3 Complexed with Nngh Inhibitor. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of MMP3 Complexed with Nngh Inhibitor. (pdb code 4g9l). 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 Nngh Inhibitor., PDB code: 4g9l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4g9l

Go back to Calcium Binding Sites List in 4g9l
Calcium binding site 1 out of 6 in the Structure of MMP3 Complexed with Nngh 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 Nngh Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:10.4
occ:1.00
 OE2 A:GLU184 2.1 10.6 1.0
O A:VAL163 2.3 7.0 1.0
O A:GLY161 2.4 12.0 1.0
OD2 A:ASP181 2.4 8.5 1.0
OD1 A:ASP158 2.4 11.5 1.0
O A:GLY159 2.4 12.8 1.0
CD A:GLU184 3.4 7.2 1.0
CG A:ASP181 3.4 10.4 1.0
C A:VAL163 3.4 8.6 1.0
C A:GLY161 3.5 12.7 1.0
CG A:ASP158 3.6 12.3 1.0
C A:GLY159 3.6 14.0 1.0
N A:GLY161 3.9 11.4 1.0
N A:VAL163 4.0 8.3 1.0
CB A:ASP181 4.0 7.7 1.0
C A:PRO160 4.1 12.4 1.0
OE1 A:GLU184 4.2 11.3 1.0
OD2 A:ASP158 4.2 12.0 1.0
CA A:VAL163 4.2 8.6 1.0
CA A:GLY161 4.2 11.4 1.0
OD1 A:ASP181 4.3 10.6 1.0
CG A:GLU184 4.3 12.8 1.0
CA A:PRO160 4.4 13.3 1.0
N A:GLY159 4.4 14.1 1.0
C A:ASN162 4.4 11.0 1.0
N A:ASP158 4.4 13.2 1.0
N A:LEU164 4.4 7.4 1.0
O A:PRO160 4.4 11.1 1.0
O A:HOH418 4.5 12.4 1.0
C A:ASP158 4.5 14.2 1.0
N A:PRO160 4.5 13.9 1.0
N A:ASN162 4.6 11.4 1.0
CA A:GLY159 4.6 13.8 1.0
CA A:LEU164 4.6 8.1 1.0
CB A:VAL163 4.6 8.4 1.0
CB A:ASP158 4.7 12.9 1.0
CA A:ASP158 4.8 12.4 1.0
O A:ASP158 4.8 14.7 1.0
CA A:ASN162 4.9 11.6 1.0
O A:ASN162 4.9 10.4 1.0

Calcium binding site 2 out of 6 in 4g9l

Go back to Calcium Binding Sites List in 4g9l
Calcium binding site 2 out of 6 in the Structure of MMP3 Complexed with Nngh 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 Nngh Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:11.5
occ:1.00
 O A:GLY173 2.1 13.6 1.0
O A:HOH402 2.2 14.0 1.0
O A:HOH401 2.2 4.4 1.0
O A:ASP141 2.3 8.8 1.0
OD1 A:ASP177 2.4 9.6 1.0
O A:ASN175 2.5 10.7 1.0
C A:GLY173 3.4 14.6 1.0
CG A:ASP177 3.4 9.9 1.0
C A:ASP141 3.4 10.6 1.0
C A:ASN175 3.7 11.1 1.0
OD2 A:ASP177 3.8 8.6 1.0
O A:ALA140 4.0 15.3 1.0
C A:ILE174 4.1 12.9 1.0
N A:ASN175 4.1 12.8 1.0
CA A:ASP141 4.2 11.6 1.0
N A:ASP177 4.2 8.8 1.0
O A:HOH410 4.2 18.0 1.0
N A:ILE174 4.3 15.2 1.0
CA A:GLY173 4.3 15.1 1.0
N A:GLY173 4.3 16.8 1.0
O A:ILE174 4.3 13.5 1.0
CA A:ILE174 4.4 15.0 1.0
O A:GLY171 4.4 17.5 1.0
N A:ILE142 4.5 10.7 1.0
OE2 A:GLU139 4.5 30.3 1.0
CA A:GLY176 4.5 10.7 1.0
CA A:ASN175 4.5 11.3 1.0
C A:GLY176 4.5 10.6 1.0
N A:GLY176 4.6 10.1 1.0
CB A:ASP177 4.6 9.8 1.0
C A:PRO172 4.7 16.1 1.0
CA A:ASP177 4.8 10.1 1.0
CH2 A:TRP92 4.8 11.3 1.0
CA A:ILE142 4.8 10.4 1.0
N A:MET143 4.8 12.0 1.0
CG A:MET143 4.9 10.2 1.0
C A:ALA140 5.0 12.9 1.0
O A:PRO172 5.0 14.4 1.0

Calcium binding site 3 out of 6 in 4g9l

Go back to Calcium Binding Sites List in 4g9l
Calcium binding site 3 out of 6 in the Structure of MMP3 Complexed with Nngh 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 Nngh Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:12.9
occ:1.00
 O A:HOH416 2.1 12.7 1.0
O A:ASP182 2.3 9.7 1.0
OD2 A:ASP107 2.3 8.9 1.0
O A:GLU184 2.4 14.7 1.0
OD1 A:ASP182 2.5 17.8 1.0
OD1 A:ASP107 2.6 13.8 1.0
CG A:ASP107 2.8 15.5 1.0
C A:ASP182 3.3 10.8 1.0
CG A:ASP182 3.5 12.5 1.0
C A:GLU184 3.6 13.4 1.0
CA A:ASP182 3.9 9.8 1.0
OG1 A:THR105 4.1 11.9 1.0
CB A:ASP182 4.2 9.9 1.0
CB A:ASP107 4.2 13.6 1.0
CA A:GLN185 4.2 14.2 1.0
N A:GLN185 4.3 13.9 1.0
OD2 A:ASP182 4.4 16.0 1.0
N A:GLU184 4.4 12.8 1.0
N A:ASP183 4.4 11.5 1.0
CD1 A:TRP186 4.4 7.0 1.0
C A:ASP183 4.6 13.8 1.0
NE2 A:GLN185 4.7 20.4 1.0
N A:TRP186 4.7 12.1 1.0
CA A:GLU184 4.7 13.1 1.0
CA A:ASP183 4.7 13.1 1.0
NE1 A:TRP186 4.9 6.1 1.0

Calcium binding site 4 out of 6 in 4g9l

Go back to Calcium Binding Sites List in 4g9l
Calcium binding site 4 out of 6 in the Structure of MMP3 Complexed with Nngh 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 Nngh Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:17.6
occ:1.00
 O B:VAL163 2.2 19.7 1.0
OE2 B:GLU184 2.3 21.7 1.0
OD2 B:ASP181 2.3 10.3 1.0
OD1 B:ASP158 2.3 20.9 1.0
O B:GLY159 2.4 23.0 1.0
O B:GLY161 2.5 23.2 1.0
CG B:ASP181 3.4 13.5 1.0
C B:VAL163 3.4 18.8 1.0
CD B:GLU184 3.5 22.2 1.0
CG B:ASP158 3.5 23.8 1.0
C B:GLY159 3.6 23.3 1.0
C B:GLY161 3.7 22.2 1.0
N B:GLY161 3.9 23.4 1.0
CB B:ASP181 4.0 13.8 1.0
N B:VAL163 4.1 20.6 1.0
OD2 B:ASP158 4.1 21.5 1.0
CA B:VAL163 4.2 20.1 1.0
N B:GLY159 4.2 23.4 1.0
C B:PRO160 4.2 23.6 1.0
OE1 B:GLU184 4.2 18.1 1.0
OD1 B:ASP181 4.3 12.0 1.0
C B:ASP158 4.3 23.5 1.0
CA B:GLY161 4.4 22.8 1.0
N B:LEU164 4.4 18.7 1.0
N B:ASP158 4.4 20.3 1.0
C B:ASN162 4.4 21.9 1.0
CA B:GLY159 4.4 23.2 1.0
N B:PRO160 4.5 23.9 1.0
CA B:PRO160 4.5 23.8 1.0
CG B:GLU184 4.5 19.4 1.0
CA B:LEU164 4.6 17.0 1.0
CB B:VAL163 4.7 19.2 1.0
N B:ASN162 4.7 23.6 1.0
CA B:ASP158 4.7 22.5 1.0
O B:PRO160 4.7 24.3 1.0
CB B:ASP158 4.7 22.7 1.0
O B:ASP158 4.8 24.4 1.0
CB B:ASN162 4.8 23.9 1.0
O B:ASN162 4.9 20.7 1.0
CA B:ASN162 4.9 22.2 1.0

Calcium binding site 5 out of 6 in 4g9l

Go back to Calcium Binding Sites List in 4g9l
Calcium binding site 5 out of 6 in the Structure of MMP3 Complexed with Nngh 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 Nngh Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:12.3
occ:1.00
 O B:HOH401 2.1 7.6 1.0
O B:GLY173 2.2 19.1 1.0
O B:ASN175 2.2 14.5 1.0
O B:HOH403 2.3 20.8 1.0
OD1 B:ASP177 2.4 12.2 1.0
O B:ASP141 2.5 14.7 1.0
CG B:ASP177 3.3 13.8 1.0
C B:GLY173 3.4 18.2 1.0
C B:ASN175 3.5 16.3 1.0
C B:ASP141 3.5 13.4 1.0
OD2 B:ASP177 3.9 11.9 1.0
C B:ILE174 4.0 17.6 1.0
N B:ASP177 4.0 12.0 1.0
O B:HOH439 4.0 55.7 1.0
O B:ILE174 4.1 17.0 1.0
O B:ALA140 4.2 12.6 1.0
N B:ASN175 4.2 16.7 1.0
CA B:ASP141 4.2 13.4 1.0
N B:GLY173 4.2 17.5 1.0
N B:ILE174 4.2 17.6 1.0
N B:GLY176 4.3 14.5 1.0
CA B:ILE174 4.3 17.2 1.0
CA B:GLY173 4.3 17.7 1.0
CA B:GLY176 4.4 14.3 1.0
CA B:ASN175 4.4 17.5 1.0
C B:GLY176 4.4 14.8 1.0
CB B:ASP177 4.5 13.1 1.0
N B:ILE142 4.6 14.3 1.0
O B:GLY171 4.6 17.2 1.0
C B:PRO172 4.7 17.3 1.0
N B:MET143 4.7 14.9 1.0
CA B:ASP177 4.7 14.1 1.0
CA B:ILE142 4.8 14.5 1.0
CG B:MET143 4.9 13.2 1.0
O B:HOH421 4.9 20.7 1.0
CH2 B:TRP92 4.9 16.2 1.0

Calcium binding site 6 out of 6 in 4g9l

Go back to Calcium Binding Sites List in 4g9l
Calcium binding site 6 out of 6 in the Structure of MMP3 Complexed with Nngh 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 Nngh Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca306

b:17.0
occ:1.00
 O B:ASP182 2.3 19.8 1.0
OD1 B:ASP182 2.3 22.4 1.0
OD2 B:ASP107 2.4 12.1 1.0
O B:GLU184 2.4 14.7 1.0
OD1 B:ASP107 2.6 14.5 1.0
CG B:ASP107 2.8 14.9 1.0
C B:ASP182 3.4 19.1 1.0
CG B:ASP182 3.5 19.4 1.0
C B:GLU184 3.6 16.0 1.0
CA B:ASP182 4.0 18.3 1.0
OG1 B:THR105 4.1 9.4 1.0
CB B:ASP107 4.2 11.7 1.0
CB B:ASP182 4.2 18.0 1.0
CD1 B:TRP186 4.3 8.9 1.0
CA B:GLN185 4.3 16.0 1.0
N B:GLN185 4.4 15.5 1.0
OD2 B:ASP182 4.4 18.2 1.0
N B:ASP183 4.5 18.3 1.0
N B:GLU184 4.5 19.3 1.0
C B:ASP183 4.6 19.0 1.0
O B:HOH424 4.6 14.2 1.0
CA B:GLU184 4.7 17.0 1.0
CA B:ASP183 4.7 19.0 1.0
N B:TRP186 4.7 15.4 1.0
NE1 B:TRP186 4.8 15.4 1.0
O B:HOH425 4.8 13.2 1.0
CD B:PRO106 4.8 12.8 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 20:14:19 2025

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