Atomistry » Calcium » PDB 1cxk-1dds » 1d8m
Atomistry »
  Calcium »
    PDB 1cxk-1dds »
      1d8m »

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: Thu Jul 11 07:27:09 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