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Calcium in PDB 1d8f: Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.

Enzymatic activity of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor.

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

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Piperazine Based Inhibitor., PDB code: 1d8f was solved by M.Y.Cheng, B.De, S.Pikul, N.G.Almstead, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, L.Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.270, 78.540, 106.580, 90.00, 90.00, 90.00
R / Rfree (%) 29.4 / 25.2

Other elements in 1d8f:

The structure of Crystal Structure of MMP3 Complexed with A Piperazine 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 Piperazine Based Inhibitor. (pdb code 1d8f). 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 Piperazine Based Inhibitor., PDB code: 1d8f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1d8f

Go back to Calcium Binding Sites List in 1d8f
Calcium binding site 1 out of 6 in the Crystal Structure of MMP3 Complexed with A Piperazine 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 Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:2.0
occ:1.00
 O A:VAL163 2.3 3.6 1.0
O A:GLY159 2.3 8.7 1.0
OD2 A:ASP181 2.4 2.0 1.0
OE2 A:GLU184 2.4 2.0 1.0
O A:GLY161 2.4 5.5 1.0
OD1 A:ASP158 2.5 4.9 1.0
C A:VAL163 3.5 2.8 1.0
CG A:ASP181 3.5 2.0 1.0
C A:GLY159 3.5 5.7 1.0
C A:GLY161 3.6 4.6 1.0
CD A:GLU184 3.6 2.0 1.0
CG A:ASP158 3.8 6.5 1.0
N A:GLY161 3.9 2.0 1.0
C A:PRO160 4.0 5.0 1.0
N A:VAL163 4.0 2.0 1.0
CB A:ASP181 4.1 2.0 1.0
N A:GLY159 4.2 5.1 1.0
C A:ASP158 4.2 6.7 1.0
CA A:VAL163 4.3 2.0 1.0
CA A:GLY161 4.3 2.0 1.0
OE1 A:GLU184 4.3 8.3 1.0
N A:ASP158 4.3 4.6 1.0
O A:PRO160 4.3 4.4 1.0
N A:PRO160 4.4 5.8 1.0
N A:LEU164 4.4 3.3 1.0
C A:ASN162 4.4 5.3 1.0
CA A:PRO160 4.4 2.0 1.0
CA A:GLY159 4.5 2.2 1.0
O A:ASP158 4.5 8.8 1.0
OD2 A:ASP158 4.5 14.6 1.0
CG A:GLU184 4.5 4.0 1.0
OD1 A:ASP181 4.6 3.0 1.0
CA A:ASP158 4.6 5.3 1.0
N A:ASN162 4.6 5.6 1.0
CB A:VAL163 4.6 2.9 1.0
CA A:LEU164 4.6 2.0 1.0
CB A:ASP158 4.8 8.4 1.0
CA A:ASN162 4.9 5.9 1.0
CB A:ASN162 5.0 2.6 1.0

Calcium binding site 2 out of 6 in 1d8f

Go back to Calcium Binding Sites List in 1d8f
Calcium binding site 2 out of 6 in the Crystal Structure of MMP3 Complexed with A Piperazine 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 Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:5.5
occ:1.00
 O A:ASP182 2.3 12.6 1.0
OD1 A:ASP107 2.3 9.7 1.0
O A:GLU184 2.5 2.0 1.0
OD2 A:ASP107 2.6 14.1 1.0
OD1 A:ASP182 2.8 2.0 1.0
CG A:ASP107 2.9 2.0 1.0
C A:ASP182 3.3 5.8 1.0
O A:HOH22 3.4 17.6 1.0
C A:GLU184 3.6 2.0 1.0
CG A:ASP182 3.7 13.6 1.0
CA A:ASP182 3.9 4.2 1.0
N A:GLU184 4.1 3.9 1.0
CA A:GLN185 4.3 2.1 1.0
OG1 A:THR105 4.3 2.0 1.0
N A:ASP183 4.3 6.5 1.0
CB A:ASP182 4.3 9.0 1.0
CB A:ASP107 4.3 2.0 1.0
N A:GLN185 4.4 2.0 1.0
OE1 A:GLN185 4.4 2.0 1.0
C A:ASP183 4.5 6.8 1.0
CD1 A:TRP186 4.6 2.0 1.0
CA A:ASP183 4.6 5.0 1.0
CA A:GLU184 4.6 3.4 1.0
OD2 A:ASP182 4.6 17.6 1.0
N A:TRP186 4.7 4.4 1.0
CG A:PRO106 4.9 2.0 1.0

Calcium binding site 3 out of 6 in 1d8f

Go back to Calcium Binding Sites List in 1d8f
Calcium binding site 3 out of 6 in the Crystal Structure of MMP3 Complexed with A Piperazine 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 Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:2.0
occ:1.00
 O A:ASN175 2.4 2.2 1.0
O A:ASP141 2.4 7.2 1.0
O A:GLY173 2.5 2.0 1.0
OD1 A:ASP177 2.6 3.8 1.0
O A:HOH5 3.1 22.2 1.0
C A:ASP141 3.5 6.5 1.0
C A:ASN175 3.6 2.0 1.0
CG A:ASP177 3.6 2.0 1.0
C A:GLY173 3.7 5.2 1.0
O A:ALA140 3.9 9.0 1.0
OD2 A:ASP177 4.0 2.0 1.0
CA A:ASP141 4.1 7.2 1.0
N A:ASP177 4.2 2.6 1.0
N A:ASN175 4.3 5.7 1.0
N A:GLY173 4.3 7.3 1.0
O A:GLY171 4.4 2.0 1.0
C A:ILE174 4.4 5.6 1.0
CA A:GLY176 4.4 3.1 1.0
N A:GLY176 4.4 2.0 1.0
C A:GLY176 4.4 2.0 1.0
CA A:GLY173 4.5 7.9 1.0
CA A:ASN175 4.5 2.2 1.0
N A:ILE142 4.5 2.0 1.0
O A:ILE174 4.6 8.1 1.0
OE2 A:GLU139 4.6 33.0 1.0
N A:ILE174 4.7 6.1 1.0
CH2 A:TRP92 4.7 2.0 1.0
C A:PRO172 4.7 7.7 1.0
CB A:ASP177 4.8 2.0 1.0
CA A:ILE174 4.8 7.3 1.0
CA A:ILE142 4.8 4.0 1.0
CG A:MET143 4.9 2.0 1.0
C A:ALA140 4.9 8.0 1.0
CA A:ASP177 4.9 2.5 1.0
N A:MET143 4.9 6.2 1.0

Calcium binding site 4 out of 6 in 1d8f

Go back to Calcium Binding Sites List in 1d8f
Calcium binding site 4 out of 6 in the Crystal Structure of MMP3 Complexed with A Piperazine 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 Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:2.0
occ:1.00
 OE2 B:GLU684 2.3 2.0 1.0
OD1 B:ASP658 2.3 2.0 1.0
OD2 B:ASP681 2.3 2.0 1.0
O B:VAL663 2.4 10.5 1.0
O B:GLY659 2.4 7.9 1.0
O B:GLY661 2.6 8.0 1.0
CG B:ASP681 3.4 3.4 1.0
C B:VAL663 3.5 4.9 1.0
CG B:ASP658 3.5 2.0 1.0
CD B:GLU684 3.5 6.4 1.0
C B:GLY659 3.6 10.4 1.0
C B:GLY661 3.7 2.0 1.0
CB B:ASP681 4.1 3.7 1.0
N B:VAL663 4.1 2.0 1.0
OD2 B:ASP658 4.1 2.0 1.0
C B:ASP658 4.2 11.3 1.0
N B:GLY661 4.2 2.6 1.0
O B:ASP658 4.2 11.6 1.0
CA B:VAL663 4.3 2.0 1.0
OE1 B:GLU684 4.3 9.3 1.0
C B:ASN662 4.3 2.0 1.0
N B:GLY659 4.4 11.4 1.0
OD1 B:ASP681 4.4 2.2 1.0
CG B:GLU684 4.4 2.0 1.0
N B:LEU664 4.4 5.1 1.0
C B:PRO660 4.5 5.5 1.0
CA B:PRO660 4.5 9.5 1.0
CA B:GLY659 4.5 13.6 1.0
N B:PRO660 4.5 8.3 1.0
CA B:GLY661 4.5 2.0 1.0
CA B:LEU664 4.6 2.0 1.0
CB B:ASP658 4.6 6.7 1.0
N B:ASP658 4.6 8.3 1.0
N B:ASN662 4.7 5.1 1.0
CA B:ASP658 4.7 8.3 1.0
O B:ASN662 4.8 2.0 1.0
CB B:VAL663 4.8 2.0 1.0
CA B:ASN662 4.9 3.6 1.0

Calcium binding site 5 out of 6 in 1d8f

Go back to Calcium Binding Sites List in 1d8f
Calcium binding site 5 out of 6 in the Crystal Structure of MMP3 Complexed with A Piperazine 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 Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:12.9
occ:1.00
 OD2 B:ASP607 2.4 2.0 1.0
O B:ASP682 2.4 4.7 1.0
OD1 B:ASP607 2.4 4.0 1.0
OD1 B:ASP682 2.6 2.0 1.0
O B:GLU684 2.7 2.0 1.0
CG B:ASP607 2.7 2.0 1.0
C B:ASP682 3.4 2.4 1.0
CG B:ASP682 3.6 2.0 1.0
C B:GLU684 3.9 5.5 1.0
CA B:ASP682 3.9 2.0 1.0
OG1 B:THR605 4.0 8.5 1.0
CB B:ASP682 4.2 6.3 1.0
CB B:ASP607 4.3 2.7 1.0
CD1 B:TRP686 4.3 2.2 1.0
N B:GLU684 4.4 3.4 1.0
OD2 B:ASP682 4.4 6.1 1.0
N B:ASP683 4.5 5.8 1.0
CA B:GLN685 4.6 5.5 1.0
O B:HOH11 4.7 13.1 1.0
N B:GLN685 4.7 9.7 1.0
CD B:PRO606 4.7 2.0 1.0
C B:ASP683 4.8 2.0 1.0
CA B:GLU684 4.8 3.9 1.0
NE1 B:TRP686 4.9 2.0 1.0
N B:TRP686 4.9 6.8 1.0
CA B:ASP683 4.9 3.5 1.0
N B:ASP607 4.9 2.4 1.0

Calcium binding site 6 out of 6 in 1d8f

Go back to Calcium Binding Sites List in 1d8f
Calcium binding site 6 out of 6 in the Crystal Structure of MMP3 Complexed with A Piperazine 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 Piperazine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:6.5
occ:1.00
 O B:GLY673 2.4 9.0 1.0
OD1 B:ASP677 2.4 2.0 1.0
O B:HOH10 2.4 17.4 1.0
O B:ASP641 2.4 2.0 1.0
O B:ASN675 2.5 8.7 1.0
CG B:ASP677 3.4 8.5 1.0
C B:ASP641 3.6 2.0 1.0
C B:GLY673 3.6 6.3 1.0
C B:ASN675 3.6 4.9 1.0
OD2 B:ASP677 3.9 13.9 1.0
O B:ALA640 4.0 4.6 1.0
C B:ILE674 4.1 5.0 1.0
N B:ASP677 4.1 2.0 1.0
N B:ASN675 4.1 2.0 1.0
O B:ILE674 4.2 10.4 1.0
CA B:ASP641 4.3 2.0 1.0
CA B:ILE674 4.4 7.0 1.0
C B:GLY676 4.4 2.0 1.0
N B:ILE674 4.4 7.2 1.0
CA B:GLY676 4.5 2.0 1.0
N B:GLY676 4.5 3.6 1.0
N B:GLY673 4.5 2.0 1.0
O B:GLY671 4.5 2.0 1.0
CA B:ASN675 4.5 2.0 1.0
CA B:GLY673 4.5 3.5 1.0
O B:HOH30 4.6 17.3 1.0
N B:ILE642 4.6 2.0 1.0
CB B:ASP677 4.6 5.0 1.0
N B:MET643 4.6 4.2 1.0
CG B:MET643 4.7 2.0 1.0
C B:PRO672 4.7 2.0 1.0
CA B:ASP677 4.7 2.0 1.0
CA B:ILE642 4.8 2.0 1.0
O B:HOH2 4.9 4.1 1.0
O B:PRO672 4.9 4.7 1.0
C B:ALA640 5.0 4.4 1.0

Reference:

M.Cheng, B.De, S.Pikul, N.G.Almstead, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, L.Chen, C.M.Dunaway, F.Gu, M.E.Dowty, G.E.Mieling, M.J.Janusz, S.Wang-Weigand. Design and Synthesis of Piperazine-Based Matrix Metalloproteinase Inhibitors. J.Med.Chem. V. 43 369 2000.
ISSN: ISSN 0022-2623
PubMed: 10669564
DOI: 10.1021/JM990366Q
Page generated: Mon Jul 7 14:20:18 2025

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