Atomistry » Calcium » PDB 1cxk-1dds » 1d5j
Atomistry »
  Calcium »
    PDB 1cxk-1dds »
      1d5j »

Calcium in PDB 1d5j: Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor.

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

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

Protein crystallography data

The structure of Crystal Structure of MMP3 Complexed with A Thiazepine Based Inhibitor., PDB code: 1d5j was solved by N.G.Almstead, R.S.Bradley, S.Pikul, B.De, M.G.Natchus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.780, 78.540, 105.270, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 25.7

Other elements in 1d5j:

The structure of Crystal Structure of MMP3 Complexed with A Thiazepine 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 Thiazepine Based Inhibitor. (pdb code 1d5j). 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 Thiazepine Based Inhibitor., PDB code: 1d5j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1d5j

Go back to Calcium Binding Sites List in 1d5j
Calcium binding site 1 out of 6 in the Crystal Structure of MMP3 Complexed with A Thiazepine 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 Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:7.1
occ:1.00
O A:GLY161 2.2 6.8 1.0
O A:VAL163 2.3 2.0 1.0
O A:GLY159 2.3 14.7 1.0
OE2 A:GLU184 2.4 11.4 1.0
OD1 A:ASP158 2.4 5.8 1.0
OD2 A:ASP181 2.6 2.0 1.0
C A:GLY161 3.4 6.5 1.0
C A:VAL163 3.4 2.0 1.0
CD A:GLU184 3.4 7.8 1.0
C A:GLY159 3.6 11.5 1.0
CG A:ASP158 3.6 3.7 1.0
CG A:ASP181 3.6 5.1 1.0
N A:VAL163 3.8 2.0 1.0
N A:GLY161 3.9 8.3 1.0
C A:PRO160 3.9 9.5 1.0
OE1 A:GLU184 4.0 8.9 1.0
CA A:VAL163 4.1 2.0 1.0
CA A:GLY161 4.1 7.0 1.0
O A:PRO160 4.2 11.1 1.0
C A:ASN162 4.2 2.8 1.0
OD2 A:ASP158 4.2 2.3 1.0
CB A:ASP181 4.3 2.0 1.0
C A:ASP158 4.3 9.6 1.0
N A:GLY159 4.4 8.3 1.0
N A:PRO160 4.4 8.4 1.0
N A:LEU164 4.4 2.0 1.0
N A:ASN162 4.4 3.1 1.0
CA A:PRO160 4.4 9.5 1.0
O A:ASP158 4.5 11.0 1.0
CG A:GLU184 4.5 8.8 1.0
N A:ASP158 4.5 8.6 1.0
CB A:VAL163 4.5 2.2 1.0
OD1 A:ASP181 4.6 6.4 1.0
CA A:GLY159 4.6 9.3 1.0
CA A:LEU164 4.7 2.0 1.0
CA A:ASN162 4.7 3.7 1.0
CA A:ASP158 4.7 7.8 1.0
O A:ASN162 4.7 7.4 1.0
CB A:ASP158 4.7 4.8 1.0
CB A:ASN162 4.9 3.7 1.0

Calcium binding site 2 out of 6 in 1d5j

Go back to Calcium Binding Sites List in 1d5j
Calcium binding site 2 out of 6 in the Crystal Structure of MMP3 Complexed with A Thiazepine 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 Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:8.6
occ:1.00
O A:ASP182 2.1 2.0 1.0
O A:HOH449 2.2 27.8 1.0
OD2 A:ASP107 2.4 8.1 1.0
O A:GLU184 2.6 10.7 1.0
OD1 A:ASP182 2.6 2.3 1.0
OD1 A:ASP107 2.7 15.4 1.0
CG A:ASP107 2.9 8.5 1.0
C A:ASP182 3.2 2.8 1.0
CG A:ASP182 3.6 2.0 1.0
C A:GLU184 3.8 8.8 1.0
CA A:ASP182 3.8 2.0 1.0
CB A:ASP182 3.9 2.0 1.0
N A:GLU184 4.2 10.6 1.0
OG1 A:THR105 4.3 5.6 1.0
N A:ASP183 4.4 6.7 1.0
CB A:ASP107 4.4 5.0 1.0
CA A:GLN185 4.5 10.9 1.0
N A:GLN185 4.6 11.3 1.0
CA A:ASP183 4.6 8.3 1.0
OE1 A:GLN185 4.6 14.7 1.0
C A:ASP183 4.6 10.1 1.0
OD2 A:ASP182 4.6 2.0 1.0
CA A:GLU184 4.8 9.4 1.0
CD1 A:TRP186 4.9 2.0 1.0
CD A:PRO106 5.0 10.0 1.0

Calcium binding site 3 out of 6 in 1d5j

Go back to Calcium Binding Sites List in 1d5j
Calcium binding site 3 out of 6 in the Crystal Structure of MMP3 Complexed with A Thiazepine 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 Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:10.5
occ:1.00
O A:HOH408 2.1 18.6 1.0
O A:GLY173 2.2 15.2 1.0
O A:HOH412 2.3 16.0 1.0
O A:ASP141 2.4 9.1 1.0
O A:ASN175 2.4 12.9 1.0
OD1 A:ASP177 2.6 7.6 1.0
C A:GLY173 3.4 14.0 1.0
C A:ASP141 3.5 8.3 1.0
CG A:ASP177 3.5 4.0 1.0
C A:ASN175 3.5 7.1 1.0
O A:ALA140 3.6 4.7 1.0
OD2 A:ASP177 3.8 3.2 1.0
CA A:ASP141 4.0 8.1 1.0
N A:GLY173 4.1 15.9 1.0
N A:ASN175 4.1 5.9 1.0
C A:ILE174 4.1 9.8 1.0
CA A:GLY173 4.2 14.1 1.0
O A:GLY171 4.2 11.7 1.0
N A:ASP177 4.2 3.5 1.0
CA A:ASN175 4.4 3.8 1.0
O A:ILE174 4.4 12.6 1.0
N A:ILE174 4.4 11.8 1.0
N A:GLY176 4.4 6.3 1.0
CA A:GLY176 4.5 5.2 1.0
C A:PRO172 4.5 16.3 1.0
C A:GLY176 4.6 5.3 1.0
CA A:ILE174 4.6 12.0 1.0
C A:ALA140 4.6 6.3 1.0
N A:ILE142 4.6 8.6 1.0
CH2 A:TRP92 4.8 2.5 1.0
CB A:ASP177 4.8 2.0 1.0
CG A:MET143 4.8 7.0 1.0
N A:ASP141 4.8 7.1 1.0
N A:MET143 4.9 7.7 1.0
CA A:ASP177 4.9 2.0 1.0
O A:PRO172 4.9 19.3 1.0

Calcium binding site 4 out of 6 in 1d5j

Go back to Calcium Binding Sites List in 1d5j
Calcium binding site 4 out of 6 in the Crystal Structure of MMP3 Complexed with A Thiazepine 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 Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:16.8
occ:1.00
O B:GLY661 2.2 19.0 1.0
O B:GLY659 2.2 23.9 1.0
OE2 B:GLU684 2.3 22.8 1.0
OD1 B:ASP658 2.3 17.2 1.0
O B:VAL663 2.4 19.3 1.0
OD2 B:ASP681 2.5 9.9 1.0
C B:GLY661 3.4 17.6 1.0
CG B:ASP658 3.4 20.4 1.0
CD B:GLU684 3.5 21.1 1.0
C B:GLY659 3.5 22.3 1.0
O B:ASP658 3.5 25.9 1.0
CG B:ASP681 3.6 10.2 1.0
C B:VAL663 3.6 15.6 1.0
C B:ASP658 3.8 21.5 1.0
N B:GLY661 3.9 18.6 1.0
N B:GLY659 4.1 22.4 1.0
OD2 B:ASP658 4.1 24.6 1.0
C B:PRO660 4.1 19.2 1.0
OE1 B:GLU684 4.1 23.9 1.0
C B:ASN662 4.2 17.3 1.0
CA B:GLY661 4.2 16.8 1.0
CB B:ASP681 4.2 8.1 1.0
N B:VAL663 4.2 18.5 1.0
O B:ASN662 4.3 13.8 1.0
CA B:GLY659 4.3 21.9 1.0
N B:ASP658 4.4 14.7 1.0
N B:ASN662 4.4 17.9 1.0
N B:PRO660 4.4 19.6 1.0
CA B:ASP658 4.4 18.9 1.0
CA B:VAL663 4.4 17.3 1.0
CB B:ASP658 4.5 21.6 1.0
OD1 B:ASP681 4.5 14.5 1.0
CG B:GLU684 4.5 15.0 1.0
N B:LEU664 4.5 11.2 1.0
O B:PRO660 4.5 21.7 1.0
CA B:LEU664 4.6 9.8 1.0
CA B:PRO660 4.6 19.0 1.0
CA B:ASN662 4.7 21.0 1.0
CB B:ASN662 4.8 26.4 1.0
CB B:VAL663 4.8 19.0 1.0

Calcium binding site 5 out of 6 in 1d5j

Go back to Calcium Binding Sites List in 1d5j
Calcium binding site 5 out of 6 in the Crystal Structure of MMP3 Complexed with A Thiazepine 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 Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:9.5
occ:1.00
O B:HOH21 2.2 5.6 1.0
O B:HOH14 2.2 22.9 1.0
O B:ASP682 2.2 17.1 1.0
OD1 B:ASP607 2.5 3.1 1.0
OD2 B:ASP607 2.5 4.1 1.0
O B:GLU684 2.6 11.2 1.0
OD1 B:ASP682 2.8 12.7 1.0
CG B:ASP607 2.9 2.1 1.0
C B:ASP682 3.3 17.4 1.0
C B:GLU684 3.6 12.7 1.0
CG B:ASP682 3.8 12.2 1.0
CA B:ASP682 4.0 13.3 1.0
N B:GLU684 4.1 17.5 1.0
CA B:GLN685 4.3 12.4 1.0
CB B:ASP682 4.3 9.6 1.0
N B:GLN685 4.3 10.8 1.0
CB B:ASP607 4.3 5.5 1.0
C B:ASP683 4.3 17.9 1.0
N B:ASP683 4.4 16.9 1.0
CA B:GLU684 4.5 14.4 1.0
OG1 B:THR605 4.5 12.9 1.0
CG B:GLN685 4.6 10.8 1.0
CA B:ASP683 4.6 17.3 1.0
O A:HOH423 4.7 22.9 1.0
CD1 B:TRP686 4.8 2.1 1.0
OD2 B:ASP682 4.9 12.2 1.0
N B:TRP686 5.0 11.7 1.0
O B:ASP683 5.0 20.9 1.0
NE2 B:GLN685 5.0 6.3 1.0

Calcium binding site 6 out of 6 in 1d5j

Go back to Calcium Binding Sites List in 1d5j
Calcium binding site 6 out of 6 in the Crystal Structure of MMP3 Complexed with A Thiazepine 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 Thiazepine Based Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:17.1
occ:1.00
O B:HOH16 2.2 21.4 1.0
O B:ASN675 2.3 10.4 1.0
O B:ASP641 2.4 14.5 1.0
O B:GLY673 2.4 17.6 1.0
OD1 B:ASP677 2.5 18.1 1.0
C B:ASN675 3.5 13.3 1.0
C B:ASP641 3.5 14.3 1.0
C B:GLY673 3.6 15.1 1.0
CG B:ASP677 3.6 14.1 1.0
N B:GLY673 4.1 15.2 1.0
O B:ALA640 4.2 14.2 1.0
N B:ASP677 4.2 7.5 1.0
O B:GLY671 4.2 17.4 1.0
C B:GLY676 4.2 9.7 1.0
N B:ASN675 4.2 13.0 1.0
C B:ILE674 4.3 14.1 1.0
OD2 B:ASP677 4.3 14.4 1.0
CA B:GLY673 4.3 12.0 1.0
CA B:GLY676 4.3 10.4 1.0
N B:GLY676 4.3 13.3 1.0
CA B:ASP641 4.3 13.9 1.0
O B:ILE674 4.4 16.2 1.0
CA B:ASN675 4.4 13.8 1.0
N B:ILE642 4.5 12.6 1.0
C B:PRO672 4.5 17.7 1.0
N B:ILE674 4.6 13.9 1.0
CA B:ILE642 4.6 9.3 1.0
N B:MET643 4.6 8.0 1.0
CB B:ASP677 4.7 13.0 1.0
CA B:ILE674 4.8 11.5 1.0
O B:GLY676 4.8 12.0 1.0
CA B:ASP677 4.8 9.6 1.0
CH2 B:TRP592 4.8 16.8 1.0
O B:PRO672 4.9 19.8 1.0

Reference:

N.G.Almstead, R.S.Bradley, S.Pikul, B.De, M.G.Natchus, Y.O.Taiwo, F.Gu, L.E.Williams, B.A.Hynd, M.J.Janusz, C.M.Dunaway, G.E.Mieling. Design, Synthesis, and Biological Evaluation of Potent Thiazine- and Thiazepine-Based Matrix Metalloproteinase Inhibitors. J.Med.Chem. V. 42 4547 1999.
ISSN: ISSN 0022-2623
PubMed: 10579818
DOI: 10.1021/JM990330Y
Page generated: Sat Dec 12 02:52:26 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy