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Calcium in PDB 1hy7: 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: 1hy7 was solved by M.G.Natchus, R.G.Bookland, M.J.Laufersweiler, S.Pikul, N.G.Almstead, B.De, M.J.Janusz, L.C.Hsieh, F.Gu, M.E.Pokross, V.S.Patel, S.M.Garver, S.X.Peng, T.M.Branch, S.L.King, T.R.Baker, D.J.Foltz, G.E.Mieling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.25 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.918, 78.059, 105.801, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22

Other elements in 1hy7:

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 1hy7). 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: 1hy7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1hy7

Go back to Calcium Binding Sites List in 1hy7
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:10.8
occ:1.00
 O A:VAL163 2.3 10.5 1.0
OE2 A:GLU184 2.3 13.5 1.0
O A:GLY159 2.3 12.2 1.0
OD2 A:ASP181 2.3 11.1 1.0
OD1 A:ASP158 2.4 12.7 1.0
O A:GLY161 2.4 12.6 1.0
CG A:ASP181 3.4 9.6 1.0
C A:VAL163 3.5 10.9 1.0
C A:GLY159 3.5 14.0 1.0
CD A:GLU184 3.5 10.3 1.0
CG A:ASP158 3.5 12.6 1.0
C A:GLY161 3.5 11.9 1.0
N A:GLY161 3.8 11.9 1.0
N A:VAL163 4.0 10.6 1.0
C A:PRO160 4.0 13.1 1.0
CB A:ASP181 4.1 9.9 1.0
OD2 A:ASP158 4.1 12.1 1.0
N A:GLY159 4.1 12.8 1.0
CA A:GLY161 4.2 12.2 1.0
CA A:VAL163 4.2 10.6 1.0
OE1 A:GLU184 4.2 11.8 1.0
OD1 A:ASP181 4.3 10.6 1.0
C A:ASP158 4.3 12.6 1.0
N A:ASP158 4.4 12.1 1.0
CA A:GLY159 4.4 13.3 1.0
N A:PRO160 4.4 14.0 1.0
CA A:PRO160 4.4 13.9 1.0
C A:ASN162 4.5 12.4 1.0
N A:LEU164 4.5 8.9 1.0
O A:PRO160 4.5 13.6 1.0
CG A:GLU184 4.5 11.6 1.0
N A:ASN162 4.6 11.9 1.0
CB A:VAL163 4.6 9.9 1.0
CA A:LEU164 4.6 9.4 1.0
O A:HOH335 4.6 18.8 1.0
CA A:ASP158 4.7 11.7 1.0
CB A:ASP158 4.7 12.4 1.0
O A:ASP158 4.7 14.4 1.0
CA A:ASN162 4.9 12.7 1.0

Calcium binding site 2 out of 6 in 1hy7

Go back to Calcium Binding Sites List in 1hy7
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:11.8
occ:1.00
 O A:HOH326 2.4 15.4 1.0
O A:HOH341 2.4 17.4 1.0
O A:ASP182 2.4 13.4 1.0
O A:GLU184 2.4 12.4 1.0
OD1 A:ASP182 2.4 11.9 1.0
OD2 A:ASP107 2.4 12.7 1.0
OD1 A:ASP107 2.6 14.7 1.0
CG A:ASP107 2.9 12.6 1.0
C A:ASP182 3.3 12.2 1.0
CG A:ASP182 3.5 12.4 1.0
C A:GLU184 3.6 11.6 1.0
CA A:ASP182 3.8 11.1 1.0
CB A:ASP182 4.0 11.2 1.0
OG1 A:THR105 4.1 11.9 1.0
CA A:GLN185 4.3 12.5 1.0
CD1 A:TRP186 4.3 12.5 1.0
N A:GLN185 4.4 12.8 1.0
O B:HOH186 4.4 25.6 1.0
O A:HOH371 4.4 23.1 1.0
N A:GLU184 4.4 12.1 1.0
OD2 A:ASP182 4.4 12.2 1.0
CB A:ASP107 4.4 12.9 1.0
N A:ASP183 4.5 10.6 1.0
O A:HOH458 4.5 35.6 1.0
C A:ASP183 4.6 12.6 1.0
O A:HOH365 4.6 20.2 1.0
O B:HOH73 4.6 16.6 1.0
CA A:GLU184 4.7 11.5 1.0
OE1 A:GLN185 4.7 19.1 1.0
CA A:ASP183 4.7 12.2 1.0
N A:TRP186 4.7 12.7 1.0
NE1 A:TRP186 4.9 11.8 1.0
O A:HOH386 4.9 40.6 1.0

Calcium binding site 3 out of 6 in 1hy7

Go back to Calcium Binding Sites List in 1hy7
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:10.8
occ:1.00
 O A:GLY173 2.3 12.2 1.0
O A:HOH307 2.3 12.6 1.0
O A:HOH306 2.3 11.2 1.0
O A:ASP141 2.3 10.6 1.0
O A:ASN175 2.3 11.6 1.0
OD1 A:ASP177 2.4 10.5 1.0
CG A:ASP177 3.4 11.0 1.0
C A:ASP141 3.4 11.3 1.0
C A:GLY173 3.5 12.2 1.0
C A:ASN175 3.5 10.9 1.0
OD2 A:ASP177 3.9 10.7 1.0
O A:ALA140 4.0 12.0 1.0
C A:ILE174 4.0 11.0 1.0
N A:ASP177 4.1 10.0 1.0
N A:ASN175 4.1 11.2 1.0
O A:ILE174 4.1 11.5 1.0
CA A:ASP141 4.2 10.9 1.0
N A:GLY173 4.3 13.3 1.0
N A:GLY176 4.4 10.2 1.0
CA A:GLY173 4.4 13.1 1.0
O A:GLY171 4.4 11.8 1.0
CA A:GLY176 4.4 9.0 1.0
N A:ILE174 4.4 11.6 1.0
C A:GLY176 4.4 8.9 1.0
CA A:ILE174 4.4 11.1 1.0
CA A:ASN175 4.5 11.5 1.0
N A:ILE142 4.5 10.3 1.0
O A:HOH338 4.5 20.5 1.0
O A:HOH330 4.6 16.9 1.0
CB A:ASP177 4.6 9.5 1.0
C A:PRO172 4.7 13.9 1.0
CA A:ASP177 4.7 9.5 1.0
O A:HOH317 4.7 16.0 1.0
N A:MET143 4.7 9.4 1.0
CA A:ILE142 4.7 10.0 1.0
CG A:MET143 4.8 11.0 1.0
CH2 A:TRP92 4.9 12.1 1.0
O A:PRO172 4.9 13.8 1.0
C A:ALA140 5.0 11.4 1.0

Calcium binding site 4 out of 6 in 1hy7

Go back to Calcium Binding Sites List in 1hy7
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:15.9
occ:1.00
 OE2 B:GLU684 2.2 15.4 1.0
O B:VAL663 2.3 17.5 1.0
OD1 B:ASP658 2.3 18.6 1.0
OD2 B:ASP681 2.3 14.4 1.0
O B:GLY659 2.3 20.0 1.0
O B:GLY661 2.3 19.4 1.0
CG B:ASP681 3.4 13.6 1.0
C B:VAL663 3.4 17.0 1.0
CD B:GLU684 3.5 18.5 1.0
CG B:ASP658 3.5 15.8 1.0
C B:GLY661 3.5 18.9 1.0
C B:GLY659 3.5 20.3 1.0
N B:GLY661 3.9 18.3 1.0
N B:VAL663 3.9 19.7 1.0
OD2 B:ASP658 4.0 18.6 1.0
CB B:ASP681 4.0 11.7 1.0
N B:GLY659 4.1 19.5 1.0
C B:PRO660 4.1 21.0 1.0
CA B:VAL663 4.2 17.9 1.0
OE1 B:GLU684 4.2 16.3 1.0
C B:ASN662 4.2 20.4 1.0
OD1 B:ASP681 4.2 13.9 1.0
C B:ASP658 4.3 19.2 1.0
CA B:GLY661 4.3 19.4 1.0
N B:ASP658 4.3 17.4 1.0
CA B:GLY659 4.4 19.8 1.0
N B:LEU664 4.4 15.3 1.0
N B:PRO660 4.5 20.9 1.0
CA B:PRO660 4.5 20.2 1.0
CG B:GLU684 4.5 16.3 1.0
N B:ASN662 4.5 21.2 1.0
O B:ASN662 4.6 21.6 1.0
CA B:ASP658 4.6 18.0 1.0
CA B:LEU664 4.6 14.7 1.0
CB B:ASP658 4.7 18.2 1.0
O B:PRO660 4.7 22.1 1.0
CB B:VAL663 4.7 17.5 1.0
O B:ASP658 4.7 20.8 1.0
O B:HOH138 4.7 24.5 1.0
CA B:ASN662 4.8 20.6 1.0
CB B:ASN662 4.9 21.8 1.0

Calcium binding site 5 out of 6 in 1hy7

Go back to Calcium Binding Sites List in 1hy7
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:13.4
occ:1.00
 O B:HOH20 2.3 19.2 1.0
O B:HOH52 2.4 15.8 1.0
O B:ASP682 2.4 14.1 1.0
OD1 B:ASP682 2.4 12.3 1.0
OD2 B:ASP607 2.4 13.7 1.0
O B:GLU684 2.5 13.2 1.0
OD1 B:ASP607 2.6 15.3 1.0
CG B:ASP607 2.9 11.7 1.0
C B:ASP682 3.3 13.2 1.0
CG B:ASP682 3.4 13.1 1.0
C B:GLU684 3.6 13.7 1.0
CA B:ASP682 3.8 12.0 1.0
CB B:ASP682 3.9 12.5 1.0
OG1 B:THR605 4.1 11.6 1.0
CA B:GLN685 4.2 13.8 1.0
CD1 B:TRP686 4.3 12.6 1.0
CB B:ASP607 4.4 12.6 1.0
N B:GLN685 4.4 13.0 1.0
OD2 B:ASP682 4.4 13.2 1.0
N B:GLU684 4.4 13.9 1.0
N B:ASP683 4.5 14.2 1.0
O B:HOH36 4.6 18.7 1.0
O A:HOH364 4.6 20.0 1.0
C B:ASP683 4.6 16.6 1.0
CA B:GLU684 4.7 13.6 1.0
O A:HOH357 4.7 18.1 1.0
N B:TRP686 4.7 12.5 1.0
CA B:ASP683 4.8 15.2 1.0
OE1 B:GLN685 4.8 26.7 1.0
NE1 B:TRP686 4.9 12.8 1.0

Calcium binding site 6 out of 6 in 1hy7

Go back to Calcium Binding Sites List in 1hy7
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:12.9
occ:1.00
 O B:GLY673 2.2 13.4 1.0
O B:ASP641 2.3 11.5 1.0
O B:ASN675 2.3 14.0 1.0
OD1 B:ASP677 2.4 12.7 1.0
O B:HOH64 2.4 14.8 1.0
O B:HOH12 2.4 12.8 1.0
CG B:ASP677 3.4 10.9 1.0
C B:ASP641 3.4 12.6 1.0
C B:GLY673 3.5 14.2 1.0
C B:ASN675 3.5 12.9 1.0
OD2 B:ASP677 3.8 12.1 1.0
C B:ILE674 4.0 13.2 1.0
N B:ASP677 4.0 10.6 1.0
O B:ALA640 4.1 13.2 1.0
O B:ILE674 4.1 13.6 1.0
N B:ASN675 4.2 13.9 1.0
CA B:ASP641 4.2 11.9 1.0
N B:GLY673 4.3 16.1 1.0
N B:ILE674 4.4 14.8 1.0
CA B:GLY673 4.4 15.4 1.0
O B:GLY671 4.4 17.6 1.0
N B:GLY676 4.4 12.0 1.0
CA B:ILE674 4.4 14.2 1.0
C B:GLY676 4.4 11.4 1.0
CA B:GLY676 4.4 11.5 1.0
CA B:ASN675 4.4 14.2 1.0
N B:ILE642 4.4 11.7 1.0
O B:HOH98 4.5 20.3 1.0
O B:HOH272 4.5 25.4 1.0
CB B:ASP677 4.5 12.2 1.0
CA B:ILE642 4.6 11.4 1.0
CA B:ASP677 4.7 10.5 1.0
C B:PRO672 4.7 15.7 1.0
N B:MET643 4.7 10.9 1.0
O B:HOH51 4.8 16.2 1.0
CH2 B:TRP592 4.9 16.6 1.0
CG B:MET643 4.9 12.8 1.0
O B:PRO672 4.9 16.3 1.0

Reference:

M.G.Natchus, R.G.Bookland, M.J.Laufersweiler, S.Pikul, N.G.Almstead, B.De, M.J.Janusz, L.C.Hsieh, F.Gu, M.E.Pokross, V.S.Patel, S.M.Garver, S.X.Peng, T.M.Branch, S.L.King, T.R.Baker, D.J.Foltz, G.E.Mieling. Development of New Carboxylic Acid-Based Mmp Inhibitors Derived From Functionalized Propargylglycines. J.Med.Chem. V. 44 1060 2001.
ISSN: ISSN 0022-2623
PubMed: 11297453
DOI: 10.1021/JM000477L
Page generated: Mon Jul 7 15:44:10 2025

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