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Calcium in PDB 1g49: A Carboxylic Acid Based Inhibitor in Complex with MMP3

Enzymatic activity of A Carboxylic Acid Based Inhibitor in Complex with MMP3

All present enzymatic activity of A Carboxylic Acid Based Inhibitor in Complex with MMP3:
3.4.24.17;

Protein crystallography data

The structure of A Carboxylic Acid Based Inhibitor in Complex with MMP3, PDB code: 1g49 was solved by M.G.Natchus, R.G.Bookland, B.De, N.G.Almstead, S.Pikul, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.70 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.668, 77.112, 106.145, 90.00, 90.00, 90.00
R / Rfree (%) n/a / 25.3

Other elements in 1g49:

The structure of A Carboxylic Acid Based Inhibitor in Complex with MMP3 also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the A Carboxylic Acid Based Inhibitor in Complex with MMP3 (pdb code 1g49). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the A Carboxylic Acid Based Inhibitor in Complex with MMP3, PDB code: 1g49:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1g49

Go back to Calcium Binding Sites List in 1g49
Calcium binding site 1 out of 6 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

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

b:13.8
occ:1.00
 OE2 A:GLU184 2.2 15.2 1.0
O A:VAL163 2.3 11.2 1.0
O A:GLY159 2.3 17.4 1.0
OD1 A:ASP158 2.3 15.0 1.0
O A:GLY161 2.4 13.0 1.0
OD2 A:ASP181 2.4 15.5 1.0
CD A:GLU184 3.4 15.0 1.0
C A:VAL163 3.4 13.6 1.0
CG A:ASP181 3.4 15.0 1.0
CG A:ASP158 3.5 17.0 1.0
C A:GLY159 3.6 19.0 1.0
C A:GLY161 3.6 17.4 1.0
N A:GLY161 3.9 15.5 1.0
N A:VAL163 4.0 14.5 1.0
OD2 A:ASP158 4.0 15.9 1.0
CB A:ASP181 4.0 11.7 1.0
N A:GLY159 4.0 18.9 1.0
C A:PRO160 4.1 15.9 1.0
OE1 A:GLU184 4.1 16.7 1.0
CA A:VAL163 4.2 13.9 1.0
C A:ASP158 4.2 20.0 1.0
N A:ASP158 4.3 17.8 1.0
CA A:GLY161 4.3 14.9 1.0
OD1 A:ASP181 4.4 16.0 1.0
C A:ASN162 4.4 17.1 1.0
N A:LEU164 4.4 11.4 1.0
O A:PRO160 4.4 16.0 1.0
CA A:GLY159 4.4 19.9 1.0
CG A:GLU184 4.5 13.2 1.0
N A:PRO160 4.5 18.3 1.0
CA A:PRO160 4.5 17.8 1.0
O A:HOH313 4.5 21.2 1.0
CB A:VAL163 4.5 13.9 1.0
CA A:ASP158 4.6 18.3 1.0
CA A:LEU164 4.6 13.6 1.0
CB A:ASP158 4.6 18.1 1.0
O A:ASP158 4.7 19.7 1.0
N A:ASN162 4.7 16.5 1.0
CB A:ASN162 4.9 15.9 1.0
CA A:ASN162 4.9 18.0 1.0
O A:ASN162 4.9 17.7 1.0

Calcium binding site 2 out of 6 in 1g49

Go back to Calcium Binding Sites List in 1g49
Calcium binding site 2 out of 6 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

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

b:15.8
occ:1.00
 O A:ASP182 2.4 15.1 1.0
OD2 A:ASP107 2.4 19.1 1.0
OD1 A:ASP182 2.4 15.3 1.0
O A:HOH316 2.4 13.5 1.0
O A:HOH314 2.5 18.4 1.0
O A:GLU184 2.5 13.6 1.0
OD1 A:ASP107 2.6 17.9 1.0
CG A:ASP107 2.9 18.6 1.0
C A:ASP182 3.3 17.1 1.0
CG A:ASP182 3.3 15.1 1.0
C A:GLU184 3.7 14.7 1.0
CA A:ASP182 3.8 17.2 1.0
CB A:ASP182 3.9 17.2 1.0
OG1 A:THR105 4.0 15.3 1.0
OD2 A:ASP182 4.3 14.5 1.0
CA A:GLN185 4.3 14.6 1.0
CD1 A:TRP186 4.4 15.4 1.0
CB A:ASP107 4.4 18.6 1.0
N A:GLU184 4.4 16.4 1.0
N A:GLN185 4.4 15.3 1.0
N A:ASP183 4.5 18.1 1.0
C A:ASP183 4.6 18.4 1.0
CA A:GLU184 4.7 15.9 1.0
N A:TRP186 4.7 14.9 1.0
CA A:ASP183 4.8 17.4 1.0
OE1 A:GLN185 4.8 22.9 1.0
NE1 A:TRP186 4.9 14.3 1.0

Calcium binding site 3 out of 6 in 1g49

Go back to Calcium Binding Sites List in 1g49
Calcium binding site 3 out of 6 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

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

b:15.1
occ:1.00
 O A:GLY173 2.1 17.7 1.0
O A:HOH325 2.2 15.3 1.0
O A:ASP141 2.3 13.0 1.0
O A:ASN175 2.3 15.2 1.0
O A:HOH326 2.3 16.7 1.0
OD1 A:ASP177 2.4 15.2 1.0
C A:GLY173 3.3 18.0 1.0
CG A:ASP177 3.4 13.7 1.0
C A:ASP141 3.4 15.9 1.0
C A:ASN175 3.5 15.4 1.0
OD2 A:ASP177 3.9 12.5 1.0
N A:ASP177 4.0 12.6 1.0
C A:ILE174 4.0 15.4 1.0
O A:ALA140 4.1 16.6 1.0
N A:ASN175 4.1 14.0 1.0
CA A:ASP141 4.2 15.8 1.0
O A:ILE174 4.2 15.2 1.0
N A:GLY173 4.2 20.2 1.0
CA A:GLY173 4.2 17.5 1.0
CA A:GLY176 4.3 12.6 1.0
N A:ILE174 4.3 15.7 1.0
O A:GLY171 4.3 18.4 1.0
N A:GLY176 4.3 13.6 1.0
C A:GLY176 4.4 13.6 1.0
CA A:ILE174 4.4 16.7 1.0
CA A:ASN175 4.5 16.1 1.0
N A:ILE142 4.5 14.4 1.0
CB A:ASP177 4.6 12.9 1.0
C A:PRO172 4.6 19.9 1.0
O A:HOH311 4.7 21.0 1.0
CA A:ASP177 4.7 13.4 1.0
CA A:ILE142 4.7 14.9 1.0
O A:HOH322 4.7 20.6 1.0
N A:MET143 4.7 16.7 1.0
CH2 A:TRP92 4.9 18.5 1.0
CG A:MET143 4.9 14.6 1.0
O A:PRO172 4.9 17.2 1.0

Calcium binding site 4 out of 6 in 1g49

Go back to Calcium Binding Sites List in 1g49
Calcium binding site 4 out of 6 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:21.3
occ:1.00
 OD1 B:ASP658 2.2 22.1 1.0
OE2 B:GLU684 2.3 21.8 1.0
O B:GLY659 2.3 24.5 1.0
O B:VAL663 2.3 19.3 1.0
O B:GLY661 2.4 23.3 1.0
OD2 B:ASP681 2.4 21.4 1.0
CG B:ASP658 3.4 21.1 1.0
C B:VAL663 3.4 18.1 1.0
CD B:GLU684 3.5 19.4 1.0
CG B:ASP681 3.5 17.9 1.0
C B:GLY659 3.5 23.6 1.0
C B:GLY661 3.6 23.8 1.0
OD2 B:ASP658 3.9 22.6 1.0
N B:VAL663 3.9 20.5 1.0
N B:GLY661 4.0 22.7 1.0
CB B:ASP681 4.1 16.5 1.0
OE1 B:GLU684 4.1 19.4 1.0
C B:PRO660 4.2 23.4 1.0
CA B:VAL663 4.2 19.6 1.0
N B:GLY659 4.2 23.2 1.0
C B:ASP658 4.2 23.3 1.0
C B:ASN662 4.2 21.0 1.0
N B:ASP658 4.3 21.6 1.0
CA B:GLY661 4.4 24.1 1.0
OD1 B:ASP681 4.4 16.5 1.0
N B:LEU664 4.4 17.1 1.0
CA B:GLY659 4.5 25.1 1.0
N B:PRO660 4.5 23.5 1.0
CA B:PRO660 4.5 23.8 1.0
CG B:GLU684 4.5 17.9 1.0
CA B:ASP658 4.5 20.8 1.0
CB B:ASP658 4.5 20.6 1.0
O B:ASP658 4.5 23.6 1.0
O B:ASN662 4.6 20.4 1.0
CB B:VAL663 4.6 19.9 1.0
CA B:LEU664 4.6 17.3 1.0
O B:PRO660 4.6 22.7 1.0
N B:ASN662 4.6 23.1 1.0
CA B:ASN662 4.7 23.4 1.0
CB B:ASN662 4.8 24.0 1.0

Calcium binding site 5 out of 6 in 1g49

Go back to Calcium Binding Sites List in 1g49
Calcium binding site 5 out of 6 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:19.1
occ:1.00
 O B:ASP682 2.2 17.9 1.0
O B:GLU684 2.4 17.3 1.0
OD2 B:ASP607 2.4 15.1 1.0
OD1 B:ASP682 2.4 14.2 1.0
O B:HOH60 2.5 19.8 1.0
O B:HOH86 2.5 19.8 1.0
OD1 B:ASP607 2.5 17.8 1.0
CG B:ASP607 2.9 15.8 1.0
C B:ASP682 3.2 17.6 1.0
CG B:ASP682 3.5 16.2 1.0
C B:GLU684 3.6 16.9 1.0
CA B:ASP682 3.7 15.5 1.0
CB B:ASP682 4.0 14.4 1.0
OG1 B:THR605 4.1 16.0 1.0
CA B:GLN685 4.2 17.5 1.0
CD1 B:TRP686 4.2 13.3 1.0
N B:GLU684 4.3 16.9 1.0
N B:GLN685 4.3 15.4 1.0
N B:ASP683 4.3 18.0 1.0
CB B:ASP607 4.3 16.3 1.0
OD2 B:ASP682 4.5 15.8 1.0
C B:ASP683 4.5 18.5 1.0
O A:HOH312 4.6 18.1 1.0
N B:TRP686 4.6 16.4 1.0
CA B:GLU684 4.6 18.7 1.0
CA B:ASP683 4.7 17.3 1.0
NE1 B:TRP686 4.7 14.4 1.0
OE1 B:GLN685 4.8 27.2 1.0
O B:HOH63 4.9 19.9 1.0
CD B:PRO606 5.0 15.9 1.0
C B:GLN685 5.0 16.7 1.0

Calcium binding site 6 out of 6 in 1g49

Go back to Calcium Binding Sites List in 1g49
Calcium binding site 6 out of 6 in the A Carboxylic Acid Based Inhibitor in Complex with MMP3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of A Carboxylic Acid Based Inhibitor in Complex with MMP3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:15.2
occ:1.00
 O B:ASP641 2.3 18.6 1.0
O B:ASN675 2.3 16.3 1.0
O B:HOH44 2.4 16.9 1.0
O B:GLY673 2.4 18.1 1.0
OD1 B:ASP677 2.4 16.9 1.0
O B:HOH40 2.4 18.3 1.0
C B:ASP641 3.4 18.9 1.0
CG B:ASP677 3.5 15.4 1.0
C B:ASN675 3.5 15.6 1.0
C B:GLY673 3.6 17.2 1.0
OD2 B:ASP677 3.9 14.1 1.0
C B:ILE674 4.0 17.2 1.0
N B:ASP677 4.0 13.8 1.0
O B:ALA640 4.1 18.2 1.0
CA B:ASP641 4.2 17.9 1.0
O B:ILE674 4.2 16.5 1.0
N B:ASN675 4.2 16.5 1.0
O B:GLY671 4.3 19.2 1.0
CA B:GLY676 4.3 12.8 1.0
C B:GLY676 4.3 15.1 1.0
N B:GLY676 4.4 15.5 1.0
N B:GLY673 4.4 17.6 1.0
N B:ILE642 4.4 15.8 1.0
CA B:ILE674 4.5 18.0 1.0
N B:ILE674 4.5 15.3 1.0
CA B:GLY673 4.5 17.6 1.0
CA B:ASN675 4.5 16.8 1.0
CB B:ASP677 4.6 14.4 1.0
CA B:ILE642 4.6 15.8 1.0
C B:PRO672 4.6 20.7 1.0
N B:MET643 4.6 12.3 1.0
CA B:ASP677 4.7 13.4 1.0
O B:HOH55 4.7 15.7 1.0
O B:PRO672 4.8 22.1 1.0
CG B:MET643 4.8 13.1 1.0
CH2 B:TRP592 4.8 18.8 1.0

Reference:

M.G.Natchus, R.G.Bookland, B.De, N.G.Almstead, S.Pikul. Development of New Hydroxamate Matrix Metalloproteinase Inhibitors Derived From Functionalized 4-Aminoprolines. J.Med.Chem. V. 43 4948 2000.
ISSN: ISSN 0022-2623
PubMed: 11150165
DOI: 10.1021/JM000246E
Page generated: Thu Jul 11 08:29:45 2024

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