Atomistry » Calcium » PDB 1hov-1i6t » 1hy7
Atomistry »
  Calcium »
    PDB 1hov-1i6t »
      1hy7 »

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: Thu Jul 11 10:11:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy