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Calcium in PDB 1d7x: Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.

Enzymatic activity of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.

All present enzymatic activity of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.:
3.4.24.17;

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor., PDB code: 1d7x was solved by M.Y.Cheng, M.G.Natchus, 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) 10.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.850, 78.220, 104.740, 90.00, 90.00, 90.00
R / Rfree (%) 26.2 / 22.7

Other elements in 1d7x:

The structure of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. (pdb code 1d7x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor., PDB code: 1d7x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1d7x

Go back to Calcium Binding Sites List in 1d7x
Calcium binding site 1 out of 6 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:6.1
occ:1.00
 OE2 A:GLU184 2.3 8.9 1.0
O A:GLY159 2.3 8.2 1.0
OD2 A:ASP181 2.3 7.0 1.0
O A:VAL163 2.4 2.1 1.0
OD1 A:ASP158 2.5 2.0 1.0
O A:GLY161 2.5 5.8 1.0
CG A:ASP181 3.3 4.2 1.0
CD A:GLU184 3.4 6.5 1.0
C A:GLY159 3.5 6.4 1.0
C A:VAL163 3.6 2.0 1.0
CG A:ASP158 3.6 2.8 1.0
C A:GLY161 3.6 3.3 1.0
CB A:ASP181 3.9 2.0 1.0
N A:GLY161 3.9 3.3 1.0
OE1 A:GLU184 4.1 8.1 1.0
C A:PRO160 4.1 7.0 1.0
OD2 A:ASP158 4.2 4.4 1.0
C A:ASP158 4.2 7.6 1.0
N A:VAL163 4.2 3.1 1.0
N A:GLY159 4.2 4.1 1.0
OD1 A:ASP181 4.2 4.3 1.0
CA A:GLY161 4.3 2.0 1.0
N A:ASP158 4.3 7.7 1.0
CA A:VAL163 4.4 3.5 1.0
O A:HOH452 4.4 5.7 1.0
CG A:GLU184 4.4 6.7 1.0
N A:PRO160 4.4 8.5 1.0
O A:ASP158 4.4 7.6 1.0
CA A:GLY159 4.5 4.9 1.0
C A:ASN162 4.5 4.9 1.0
CA A:PRO160 4.5 8.2 1.0
N A:LEU164 4.6 3.2 1.0
O A:PRO160 4.6 7.2 1.0
CA A:ASP158 4.6 6.2 1.0
CB A:VAL163 4.7 4.1 1.0
CB A:ASP158 4.7 3.8 1.0
O A:HOH492 4.7 11.8 1.0
N A:ASN162 4.7 4.6 1.0
CA A:LEU164 4.7 3.2 1.0
O A:ASN162 4.8 6.4 1.0

Calcium binding site 2 out of 6 in 1d7x

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Calcium binding site 2 out of 6 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:12.2
occ:1.00
 O A:HOH403 2.0 19.3 1.0
O A:ASP182 2.2 5.4 1.0
O A:HOH496 2.4 14.1 1.0
OD2 A:ASP107 2.4 9.4 1.0
OD1 A:ASP182 2.5 4.8 1.0
OD1 A:ASP107 2.6 6.4 1.0
O A:GLU184 2.6 4.2 1.0
CG A:ASP107 2.8 7.1 1.0
C A:ASP182 3.3 5.2 1.0
CG A:ASP182 3.5 3.3 1.0
C A:GLU184 3.7 3.9 1.0
CA A:ASP182 3.8 2.8 1.0
CB A:ASP182 4.0 2.0 1.0
OG1 A:THR105 4.0 5.5 1.0
CA A:GLN185 4.3 5.7 1.0
N A:GLU184 4.3 7.7 1.0
CB A:ASP107 4.3 5.5 1.0
CD1 A:TRP186 4.4 4.1 1.0
N A:ASP183 4.4 6.0 1.0
O A:HOH449 4.4 34.6 1.0
N A:GLN185 4.4 5.0 1.0
OD2 A:ASP182 4.5 4.5 1.0
C A:ASP183 4.6 7.1 1.0
OE1 A:GLN185 4.6 9.4 1.0
N A:TRP186 4.7 7.1 1.0
CA A:ASP183 4.7 7.0 1.0
NE1 A:TRP186 4.7 4.5 1.0
CA A:GLU184 4.7 6.5 1.0

Calcium binding site 3 out of 6 in 1d7x

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Calcium binding site 3 out of 6 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:8.2
occ:1.00
 O A:HOH470 2.1 13.7 1.0
O A:HOH473 2.2 19.6 1.0
O A:GLY173 2.2 7.6 1.0
O A:ASP141 2.4 4.8 1.0
O A:ASN175 2.4 6.1 1.0
OD1 A:ASP177 2.6 2.0 1.0
C A:GLY173 3.4 8.3 1.0
CG A:ASP177 3.5 2.9 1.0
C A:ASP141 3.5 2.0 1.0
C A:ASN175 3.6 6.3 1.0
OD2 A:ASP177 3.8 2.0 1.0
N A:GLY173 3.9 12.2 1.0
O A:ALA140 4.0 2.0 1.0
C A:ILE174 4.1 5.6 1.0
N A:ASN175 4.1 7.0 1.0
N A:ASP177 4.2 6.1 1.0
CA A:GLY173 4.2 11.2 1.0
CA A:ASP141 4.2 3.5 1.0
O A:GLY171 4.3 10.5 1.0
C A:PRO172 4.3 14.4 1.0
N A:ILE174 4.3 10.2 1.0
O A:ILE174 4.4 4.8 1.0
C A:GLY176 4.4 3.0 1.0
CA A:ILE174 4.4 8.3 1.0
CA A:GLY176 4.5 3.4 1.0
N A:GLY176 4.5 5.7 1.0
CA A:ASN175 4.5 7.2 1.0
N A:ILE142 4.5 3.4 1.0
O A:PRO172 4.6 13.4 1.0
O A:HOH427 4.7 19.1 1.0
CB A:ASP177 4.7 2.0 1.0
CG A:MET143 4.7 4.3 1.0
N A:MET143 4.7 4.5 1.0
O A:HOH414 4.8 5.0 1.0
CA A:ILE142 4.8 2.9 1.0
CA A:ASP177 4.8 3.5 1.0
O A:HOH447 4.9 11.2 1.0
C A:ALA140 5.0 2.0 1.0
CH2 A:TRP92 5.0 11.2 1.0

Calcium binding site 4 out of 6 in 1d7x

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Calcium binding site 4 out of 6 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:7.9
occ:1.00
 O B:GLY661 2.2 11.2 1.0
O B:GLY659 2.3 17.1 1.0
OD1 B:ASP658 2.3 12.2 1.0
O B:VAL663 2.4 8.4 1.0
OE2 B:GLU684 2.4 11.0 1.0
OD2 B:ASP681 2.5 4.8 1.0
C B:GLY661 3.3 10.9 1.0
CG B:ASP658 3.5 11.3 1.0
C B:GLY659 3.5 14.6 1.0
CG B:ASP681 3.5 4.6 1.0
C B:VAL663 3.5 7.6 1.0
CD B:GLU684 3.6 10.3 1.0
N B:GLY661 3.7 11.8 1.0
C B:PRO660 3.9 14.4 1.0
CA B:GLY661 4.0 10.7 1.0
N B:VAL663 4.1 9.9 1.0
OD2 B:ASP658 4.1 11.3 1.0
N B:GLY659 4.2 15.2 1.0
CB B:ASP681 4.2 6.0 1.0
C B:ASP658 4.2 15.3 1.0
C B:ASN662 4.2 9.9 1.0
CA B:VAL663 4.3 6.7 1.0
O B:PRO660 4.3 15.3 1.0
OE1 B:GLU684 4.3 13.5 1.0
O B:HOH110 4.4 16.6 1.0
N B:PRO660 4.4 15.3 1.0
N B:ASP658 4.4 12.3 1.0
CA B:PRO660 4.4 14.8 1.0
N B:ASN662 4.4 9.6 1.0
OD1 B:ASP681 4.4 7.0 1.0
CA B:GLY659 4.4 15.5 1.0
O B:ASN662 4.5 12.3 1.0
O B:ASP658 4.5 18.8 1.0
CA B:ASP658 4.5 13.3 1.0
CG B:GLU684 4.6 7.0 1.0
N B:LEU664 4.6 7.7 1.0
CB B:ASP658 4.6 13.3 1.0
CA B:ASN662 4.7 8.8 1.0
CB B:VAL663 4.7 3.4 1.0
CA B:LEU664 4.8 8.0 1.0
CB B:ASN662 4.8 9.0 1.0

Calcium binding site 5 out of 6 in 1d7x

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Calcium binding site 5 out of 6 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:9.2
occ:1.00
 O B:ASP682 2.2 10.5 1.0
O B:HOH14 2.4 12.2 1.0
O B:GLU684 2.5 8.0 1.0
OD1 B:ASP682 2.5 6.7 1.0
OD2 B:ASP607 2.5 6.6 1.0
OD1 B:ASP607 2.5 8.8 1.0
CG B:ASP607 2.9 5.1 1.0
C B:ASP682 3.2 7.6 1.0
CG B:ASP682 3.5 4.4 1.0
C B:GLU684 3.6 6.9 1.0
CA B:ASP682 3.8 6.3 1.0
CB B:ASP682 4.0 3.0 1.0
OG1 B:THR605 4.1 6.7 1.0
N B:GLU684 4.1 8.9 1.0
CD1 B:TRP686 4.2 3.0 1.0
N B:ASP683 4.3 10.1 1.0
CA B:GLN685 4.3 10.5 1.0
CB B:ASP607 4.4 5.6 1.0
N B:GLN685 4.4 8.1 1.0
C B:ASP683 4.5 10.1 1.0
OD2 B:ASP682 4.5 4.2 1.0
CA B:ASP683 4.6 7.1 1.0
CA B:GLU684 4.6 8.3 1.0
N B:TRP686 4.7 9.2 1.0
OE1 B:GLN685 4.8 27.3 1.0
NE1 B:TRP686 4.8 4.4 1.0
N B:ASP607 5.0 9.3 1.0

Calcium binding site 6 out of 6 in 1d7x

Go back to Calcium Binding Sites List in 1d7x
Calcium binding site 6 out of 6 in the Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of MMP3 Complexed with A Modified Proline Scaffold Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:8.8
occ:1.00
 O B:GLY673 2.2 12.7 1.0
O B:HOH6 2.2 3.1 1.0
O B:ASN675 2.3 6.5 1.0
O B:ASP641 2.4 5.8 1.0
OD1 B:ASP677 2.6 5.8 1.0
C B:GLY673 3.4 10.4 1.0
C B:ASN675 3.5 6.4 1.0
C B:ASP641 3.5 4.6 1.0
CG B:ASP677 3.6 6.3 1.0
C B:ILE674 4.0 8.0 1.0
O B:HOH43 4.0 21.9 1.0
O B:ILE674 4.1 10.8 1.0
OD2 B:ASP677 4.1 9.0 1.0
N B:ASN675 4.1 7.2 1.0
O B:ALA640 4.1 6.4 1.0
N B:ASP677 4.2 7.4 1.0
CA B:ASP641 4.2 4.2 1.0
N B:GLY673 4.3 7.4 1.0
O B:GLY671 4.3 8.1 1.0
CA B:GLY673 4.3 8.2 1.0
N B:ILE674 4.4 10.3 1.0
C B:GLY676 4.4 6.5 1.0
CA B:ASN675 4.4 7.2 1.0
CA B:GLY676 4.4 4.8 1.0
N B:GLY676 4.4 4.8 1.0
CA B:ILE674 4.5 8.2 1.0
C B:PRO672 4.6 10.3 1.0
N B:ILE642 4.6 4.4 1.0
O B:PRO672 4.7 11.2 1.0
O B:HOH32 4.7 21.9 1.0
CB B:ASP677 4.8 6.5 1.0
CH2 B:TRP592 4.8 6.9 1.0
N B:MET643 4.8 6.4 1.0
CA B:ILE642 4.8 6.3 1.0
CA B:ASP677 4.8 7.2 1.0
O B:HOH78 4.9 37.0 1.0
CG B:MET643 4.9 7.0 1.0

Reference:

M.Cheng, B.De, N.G.Almstead, S.Pikul, M.E.Dowty, C.R.Dietsch, C.M.Dunaway, F.Gu, L.C.Hsieh, M.J.Janusz, Y.O.Taiwo, M.G.Natchus, T.Hudlicky, M.Mandel. Design, Synthesis, and Biological Evaluation of Matrix Metalloproteinase Inhibitors Derived From A Modified Proline Scaffold. J.Med.Chem. V. 42 5426 1999.
ISSN: ISSN 0022-2623
PubMed: 10639284
DOI: 10.1021/JM9904699
Page generated: Sat Dec 12 02:52:33 2020

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