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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

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