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Calcium in PDB 1d8m: Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor

Enzymatic activity of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor

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

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Heterocycle- Based Inhibitor, PDB code: 1d8m was solved by S.Pikul, K.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, Y.O.Taiwo, L.E.Williams, B.A.Hynd, L.C.Hsieh, M.J.Janusz, F.Gu, G.E.Mieling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.960, 78.590, 105.930, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 31.5

Other elements in 1d8m:

The structure of Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor (pdb code 1d8m). 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 Heterocycle- Based Inhibitor, PDB code: 1d8m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1d8m

Go back to Calcium Binding Sites List in 1d8m
Calcium binding site 1 out of 6 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:3.9
occ:1.00
 O A:GLY161 2.2 9.6 1.0
O A:GLY159 2.2 3.9 1.0
O A:VAL163 2.3 2.0 1.0
OE2 A:GLU184 2.4 2.0 1.0
OD1 A:ASP158 2.5 3.1 1.0
OD2 A:ASP181 2.7 4.9 1.0
C A:GLY161 3.4 2.6 1.0
C A:VAL163 3.4 3.5 1.0
C A:GLY159 3.5 4.5 1.0
CD A:GLU184 3.6 2.0 1.0
CG A:ASP158 3.7 2.0 1.0
N A:GLY161 3.8 3.6 1.0
CG A:ASP181 3.8 2.0 1.0
N A:VAL163 3.8 2.8 1.0
C A:PRO160 3.9 2.0 1.0
O A:PRO160 4.1 2.0 1.0
CA A:VAL163 4.1 2.0 1.0
CA A:GLY161 4.2 2.0 1.0
OE1 A:GLU184 4.2 3.0 1.0
C A:ASP158 4.2 4.7 1.0
C A:ASN162 4.2 4.7 1.0
O A:ASP158 4.3 5.3 1.0
N A:GLY159 4.3 2.0 1.0
OD2 A:ASP158 4.3 4.0 1.0
N A:PRO160 4.3 4.5 1.0
CA A:PRO160 4.4 3.9 1.0
N A:ASP158 4.4 2.0 1.0
CA A:GLY159 4.4 4.2 1.0
N A:ASN162 4.5 4.6 1.0
CB A:ASP181 4.5 2.0 1.0
N A:LEU164 4.5 6.0 1.0
CB A:VAL163 4.5 5.2 1.0
CA A:ASP158 4.6 3.1 1.0
CA A:ASN162 4.7 4.0 1.0
CG A:GLU184 4.7 2.0 1.0
CB A:ASP158 4.7 2.0 1.0
CA A:LEU164 4.8 2.0 1.0
O A:ASN162 4.8 5.4 1.0
OD1 A:ASP181 4.8 2.0 1.0
CB A:ASN162 4.9 2.0 1.0

Calcium binding site 2 out of 6 in 1d8m

Go back to Calcium Binding Sites List in 1d8m
Calcium binding site 2 out of 6 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:3.2
occ:1.00
 O A:HOH28 2.1 21.2 1.0
O A:ASP182 2.3 2.9 1.0
O A:HOH4 2.3 2.0 1.0
O A:GLU184 2.8 2.0 1.0
OD2 A:ASP107 3.0 4.2 1.0
OD1 A:ASP107 3.0 2.0 1.0
CG A:ASP107 3.4 2.0 1.0
C A:ASP182 3.5 2.0 1.0
OD1 A:ASP182 3.6 2.0 1.0
C A:GLU184 3.8 2.0 1.0
OE1 A:GLN185 4.0 5.0 1.0
N A:GLU184 4.2 4.4 1.0
C A:ASP183 4.3 4.2 1.0
CA A:ASP183 4.4 2.0 1.0
CG A:ASP182 4.4 2.0 1.0
N A:ASP183 4.4 2.0 1.0
CA A:GLN185 4.4 3.5 1.0
CA A:ASP182 4.4 2.0 1.0
N A:GLN185 4.5 3.1 1.0
CB A:ASP182 4.6 2.0 1.0
CA A:GLU184 4.7 4.2 1.0
O A:ASP183 4.9 3.0 1.0
CB A:ASP107 4.9 2.0 1.0
CD A:GLN185 5.0 5.9 1.0

Calcium binding site 3 out of 6 in 1d8m

Go back to Calcium Binding Sites List in 1d8m
Calcium binding site 3 out of 6 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:2.3
occ:1.00
 O A:HOH24 2.2 2.0 1.0
O A:GLY173 2.3 4.2 1.0
O A:ASP141 2.4 2.0 1.0
O A:ASN175 2.6 5.3 1.0
OD1 A:ASP177 2.7 2.0 1.0
C A:ASP141 3.5 3.3 1.0
C A:GLY173 3.5 2.0 1.0
CG A:ASP177 3.6 2.0 1.0
O A:ALA140 3.6 9.1 1.0
C A:ASN175 3.8 2.0 1.0
OD2 A:ASP177 4.0 2.0 1.0
CA A:ASP141 4.1 2.6 1.0
O A:HOH36 4.2 10.4 1.0
N A:ASN175 4.2 6.0 1.0
C A:ILE174 4.3 6.3 1.0
N A:GLY173 4.3 2.9 1.0
O A:GLY171 4.4 2.0 1.0
N A:ASP177 4.4 2.0 1.0
CA A:GLY173 4.4 2.0 1.0
N A:ILE174 4.5 4.6 1.0
C A:PRO172 4.5 3.1 1.0
N A:ILE142 4.5 3.6 1.0
CA A:ILE174 4.5 6.0 1.0
O A:ILE174 4.6 5.1 1.0
CA A:ASN175 4.6 4.6 1.0
C A:ALA140 4.6 7.4 1.0
O A:PRO172 4.7 7.0 1.0
N A:GLY176 4.7 2.1 1.0
C A:GLY176 4.7 2.0 1.0
CA A:GLY176 4.8 2.0 1.0
CG A:MET143 4.8 2.0 1.0
CB A:ASP177 4.8 2.0 1.0
N A:MET143 4.8 2.0 1.0
CA A:ILE142 4.8 2.0 1.0
N A:ASP141 4.9 5.9 1.0
CH2 A:TRP92 5.0 7.1 1.0
CA A:ASP177 5.0 2.0 1.0

Calcium binding site 4 out of 6 in 1d8m

Go back to Calcium Binding Sites List in 1d8m
Calcium binding site 4 out of 6 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:2.5
occ:1.00
 O B:GLY661 2.2 5.2 1.0
O B:GLY659 2.2 8.6 1.0
O B:VAL663 2.4 7.8 1.0
OE2 B:GLU684 2.4 13.7 1.0
OD1 B:ASP658 2.4 2.0 1.0
OD2 B:ASP681 2.7 2.0 1.0
C B:GLY661 3.4 7.0 1.0
C B:GLY659 3.4 7.0 1.0
C B:VAL663 3.6 5.8 1.0
CD B:GLU684 3.6 10.7 1.0
CG B:ASP681 3.6 2.0 1.0
CG B:ASP658 3.6 5.1 1.0
N B:GLY661 3.8 6.8 1.0
N B:GLY659 3.9 9.7 1.0
N B:VAL663 4.0 7.7 1.0
C B:PRO660 4.0 9.7 1.0
CA B:GLY661 4.1 6.3 1.0
C B:ASN662 4.2 7.1 1.0
C B:ASP658 4.2 8.7 1.0
CA B:GLY659 4.3 7.7 1.0
OD2 B:ASP658 4.3 6.5 1.0
CA B:VAL663 4.3 6.1 1.0
CB B:ASP681 4.3 2.0 1.0
O B:PRO660 4.4 12.8 1.0
N B:PRO660 4.4 8.3 1.0
OE1 B:GLU684 4.4 12.7 1.0
N B:ASP658 4.4 7.2 1.0
N B:ASN662 4.4 6.9 1.0
OD1 B:ASP681 4.5 3.0 1.0
CG B:GLU684 4.5 2.0 1.0
CA B:PRO660 4.5 8.3 1.0
O B:ASN662 4.5 6.0 1.0
N B:LEU664 4.6 6.4 1.0
CA B:ASP658 4.6 6.2 1.0
CA B:ASN662 4.7 7.3 1.0
CB B:VAL663 4.7 4.3 1.0
O B:ASP658 4.7 12.1 1.0
CB B:ASP658 4.7 8.0 1.0
CB B:ASN662 4.8 10.6 1.0
CA B:LEU664 4.8 2.3 1.0
O B:HOH35 5.0 8.2 1.0

Calcium binding site 5 out of 6 in 1d8m

Go back to Calcium Binding Sites List in 1d8m
Calcium binding site 5 out of 6 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:8.6
occ:1.00
 O B:ASP682 2.2 4.4 1.0
O B:HOH25 2.2 17.2 1.0
O B:HOH38 2.3 4.8 1.0
OD1 B:ASP607 2.7 9.1 1.0
OD2 B:ASP607 3.0 6.0 1.0
O B:GLU684 3.0 4.1 1.0
OD1 B:ASP682 3.0 9.0 1.0
CG B:ASP607 3.2 5.9 1.0
C B:ASP682 3.4 3.7 1.0
C B:GLU684 3.9 2.8 1.0
CG B:ASP682 4.0 2.0 1.0
N B:GLU684 4.1 4.0 1.0
CA B:ASP682 4.3 2.9 1.0
N B:ASP683 4.3 2.8 1.0
CA B:ASP683 4.4 2.0 1.0
C B:ASP683 4.4 4.2 1.0
CB B:ASP682 4.4 2.4 1.0
O B:HOH64 4.5 13.6 1.0
CA B:GLN685 4.6 2.0 1.0
N B:GLN685 4.6 5.0 1.0
CA B:GLU684 4.7 2.4 1.0
CB B:ASP607 4.7 2.1 1.0
OG1 B:THR605 4.8 4.7 1.0
O B:HOH23 4.8 2.6 1.0
NH2 A:ARG100 5.0 8.8 1.0
OE1 B:GLN685 5.0 10.5 1.0
OD2 B:ASP682 5.0 2.0 1.0

Calcium binding site 6 out of 6 in 1d8m

Go back to Calcium Binding Sites List in 1d8m
Calcium binding site 6 out of 6 in the Crystal Structure of MMP3 Complexed with A Heterocycle- 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 Heterocycle- Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:3.0
occ:1.00
 O B:HOH27 2.2 6.4 1.0
O B:HOH3 2.3 2.0 1.0
O B:GLY673 2.3 2.0 1.0
O B:ASP641 2.3 2.0 1.0
O B:ASN675 2.5 2.0 1.0
OD1 B:ASP677 2.9 12.4 1.0
C B:ASP641 3.4 4.6 1.0
C B:GLY673 3.4 2.1 1.0
C B:ASN675 3.7 3.1 1.0
CG B:ASP677 3.7 5.6 1.0
N B:GLY673 3.8 3.1 1.0
O B:ALA640 3.9 2.0 1.0
CA B:ASP641 3.9 5.4 1.0
OD2 B:ASP677 4.0 7.6 1.0
CA B:GLY673 4.1 2.0 1.0
N B:ASN675 4.3 7.2 1.0
C B:PRO672 4.3 3.4 1.0
O B:GLY671 4.3 5.3 1.0
C B:ILE674 4.4 9.6 1.0
N B:ILE674 4.5 7.0 1.0
N B:ILE642 4.5 4.0 1.0
CA B:ASN675 4.6 5.2 1.0
N B:ASP677 4.6 2.0 1.0
O B:ILE674 4.6 13.2 1.0
N B:GLY676 4.7 5.1 1.0
O B:PRO672 4.7 2.8 1.0
O B:HOH60 4.8 22.0 1.0
C B:GLY676 4.8 2.0 1.0
CA B:GLY676 4.8 2.0 1.0
C B:ALA640 4.8 2.7 1.0
N B:MET643 4.8 2.0 1.0
CA B:ILE674 4.8 6.4 1.0
N B:ASP641 4.9 5.2 1.0
CH2 B:TRP592 4.9 2.0 1.0
CG B:MET643 4.9 2.0 1.0
CA B:ILE642 4.9 2.0 1.0
CB B:ASP641 5.0 7.6 1.0

Reference:

S.Pikul, K.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, Y.O.Taiwo, L.E.Williams, B.A.Hynd, L.C.Hsieh, M.J.Janusz, F.Gu, G.E.Mieling. Heterocycle-Based Mmp Inhibitors with P2' Substituents. Bioorg.Med.Chem.Lett. V. 11 1009 2001.
ISSN: ISSN 0960-894X
PubMed: 11327577
DOI: 10.1016/S0960-894X(01)00137-8
Page generated: Mon Jul 7 14:21:09 2025

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