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Calcium in PDB 1bqo: Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors

Enzymatic activity of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors

All present enzymatic activity of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors:
3.4.24.17;

Protein crystallography data

The structure of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors, PDB code: 1bqo was solved by S.Pikul, K.L.M.Dunham, N.G.Almstead, B.De, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, T.J.Rydel, C.M.Dunaway, F.Gu, G.E.Mieling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.900, 79.000, 106.100, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 29.4

Other elements in 1bqo:

The structure of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors (pdb code 1bqo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors, PDB code: 1bqo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1bqo

Go back to Calcium Binding Sites List in 1bqo
Calcium binding site 1 out of 6 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:12.1
occ:1.00
 O A:GLY159 2.2 15.5 1.0
O A:VAL163 2.3 8.4 1.0
OD2 A:ASP181 2.3 6.1 1.0
OE2 A:GLU184 2.3 9.3 1.0
O A:GLY161 2.4 6.8 1.0
OD1 A:ASP158 2.4 5.2 1.0
CG A:ASP181 3.3 8.7 1.0
C A:VAL163 3.4 9.3 1.0
C A:GLY159 3.5 11.5 1.0
CD A:GLU184 3.5 9.1 1.0
C A:GLY161 3.6 7.1 1.0
CG A:ASP158 3.6 4.8 1.0
N A:GLY161 4.0 3.5 1.0
CB A:ASP181 4.0 8.4 1.0
N A:GLY159 4.0 11.7 1.0
N A:VAL163 4.1 9.7 1.0
C A:PRO160 4.1 8.6 1.0
OD1 A:ASP181 4.2 10.2 1.0
CA A:VAL163 4.3 10.0 1.0
CA A:GLY161 4.3 5.1 1.0
C A:ASP158 4.3 13.4 1.0
OD2 A:ASP158 4.3 4.0 1.0
CG A:GLU184 4.3 5.2 1.0
CA A:GLY159 4.4 10.5 1.0
N A:ASP158 4.4 12.9 1.0
N A:PRO160 4.4 9.8 1.0
CA A:PRO160 4.4 10.6 1.0
N A:LEU164 4.4 5.4 1.0
C A:ASN162 4.4 8.3 1.0
OE1 A:GLU184 4.4 9.2 1.0
O A:HOH328 4.5 15.3 1.0
CA A:LEU164 4.6 3.6 1.0
CA A:ASP158 4.6 12.9 1.0
N A:ASN162 4.6 6.6 1.0
O A:PRO160 4.6 9.4 1.0
CB A:VAL163 4.7 9.7 1.0
CB A:ASP158 4.7 6.7 1.0
O A:ASP158 4.8 14.3 1.0
O A:ASN162 4.8 11.1 1.0
CA A:ASN162 4.9 5.9 1.0
O A:HOH306 5.0 9.5 1.0

Calcium binding site 2 out of 6 in 1bqo

Go back to Calcium Binding Sites List in 1bqo
Calcium binding site 2 out of 6 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:7.4
occ:1.00
 O A:ASP182 2.2 5.9 1.0
OD2 A:ASP107 2.3 2.9 1.0
O A:GLU184 2.4 5.2 1.0
OD1 A:ASP182 2.6 5.1 1.0
OD1 A:ASP107 2.7 9.8 1.0
O A:HOH342 2.7 43.4 1.0
CG A:ASP107 2.9 2.0 1.0
C A:ASP182 3.3 5.0 1.0
C A:GLU184 3.6 6.5 1.0
CG A:ASP182 3.7 2.0 1.0
CA A:ASP182 3.9 2.1 1.0
OG1 A:THR105 4.1 7.0 1.0
CB A:ASP182 4.2 2.0 1.0
CA A:GLN185 4.2 5.3 1.0
N A:GLU184 4.2 11.8 1.0
CD1 A:TRP186 4.2 2.0 1.0
CB A:ASP107 4.3 2.0 1.0
N A:GLN185 4.3 9.7 1.0
N A:ASP183 4.4 8.9 1.0
OE1 A:GLN185 4.6 22.5 1.0
C A:ASP183 4.6 11.1 1.0
N A:TRP186 4.6 9.6 1.0
CA A:GLU184 4.6 6.3 1.0
OD2 A:ASP182 4.7 5.7 1.0
CA A:ASP183 4.7 8.1 1.0
NE1 A:TRP186 4.8 2.0 1.0
CG A:PRO106 4.9 14.1 1.0
CD A:GLN185 4.9 18.5 1.0

Calcium binding site 3 out of 6 in 1bqo

Go back to Calcium Binding Sites List in 1bqo
Calcium binding site 3 out of 6 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:9.2
occ:1.00
 O A:ASN175 2.2 17.8 1.0
O A:GLY173 2.3 11.9 1.0
OD1 A:ASP177 2.4 4.9 1.0
O A:ASP141 2.5 7.4 1.0
O A:HOH314 2.7 15.5 1.0
CG A:ASP177 3.3 4.7 1.0
C A:ASN175 3.5 12.9 1.0
C A:GLY173 3.5 12.0 1.0
OD2 A:ASP177 3.7 3.2 1.0
C A:ASP141 3.7 7.0 1.0
O A:ALA140 4.0 3.0 1.0
N A:ASN175 4.1 12.4 1.0
N A:ASP177 4.1 3.8 1.0
C A:ILE174 4.1 14.4 1.0
N A:GLY173 4.2 12.6 1.0
O A:GLY171 4.3 9.7 1.0
CA A:ASP141 4.3 6.5 1.0
CA A:ASN175 4.3 12.2 1.0
O A:ILE174 4.4 16.7 1.0
CA A:GLY173 4.4 13.6 1.0
N A:GLY176 4.4 9.0 1.0
CA A:GLY176 4.4 2.0 1.0
N A:ILE174 4.4 14.8 1.0
C A:PRO172 4.5 9.7 1.0
C A:GLY176 4.5 4.8 1.0
CB A:ASP177 4.5 4.0 1.0
CA A:ILE174 4.6 13.4 1.0
O A:PRO172 4.6 11.7 1.0
N A:ILE142 4.7 9.7 1.0
CA A:ASP177 4.8 2.4 1.0
N A:MET143 4.8 2.7 1.0
CG A:MET143 4.9 2.0 1.0
CH2 A:TRP92 5.0 9.9 1.0
CA A:ILE142 5.0 5.4 1.0
C A:ALA140 5.0 3.8 1.0

Calcium binding site 4 out of 6 in 1bqo

Go back to Calcium Binding Sites List in 1bqo
Calcium binding site 4 out of 6 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:19.9
occ:1.00
 O B:GLY159 2.1 25.5 1.0
OE2 B:GLU184 2.3 6.8 1.0
OD2 B:ASP181 2.3 16.9 1.0
O B:GLY161 2.3 22.1 1.0
OD1 B:ASP158 2.4 28.8 1.0
O B:VAL163 2.4 8.7 1.0
C B:GLY159 3.3 25.9 1.0
N B:GLY161 3.4 25.1 1.0
C B:GLY161 3.4 20.9 1.0
CG B:ASP181 3.4 11.4 1.0
N B:GLY159 3.5 27.1 1.0
CD B:GLU184 3.5 11.9 1.0
C B:VAL163 3.5 9.6 1.0
CG B:ASP158 3.6 28.7 1.0
CA B:GLY161 3.9 21.7 1.0
CA B:GLY159 4.0 26.8 1.0
N B:VAL163 4.1 15.6 1.0
CB B:ASP181 4.2 7.5 1.0
OE1 B:GLU184 4.3 12.8 1.0
N B:PRO160 4.3 24.1 1.0
CA B:VAL163 4.3 14.7 1.0
OD1 B:ASP181 4.3 12.4 1.0
OD2 B:ASP158 4.3 29.8 1.0
C B:ASN162 4.4 14.4 1.0
C B:PRO160 4.4 25.9 1.0
O B:HOH427 4.5 4.1 1.0
N B:ASN162 4.5 17.7 1.0
CG B:GLU184 4.5 7.4 1.0
C B:ASP158 4.5 28.4 1.0
N B:LEU164 4.5 7.4 1.0
N B:ASP158 4.5 24.7 1.0
CB B:ASP158 4.6 28.9 1.0
CA B:PRO160 4.6 25.0 1.0
CB B:VAL163 4.7 15.5 1.0
O B:ASN162 4.7 12.6 1.0
CA B:LEU164 4.7 8.3 1.0
CA B:ASP158 4.7 26.6 1.0
CA B:ASN162 4.9 17.4 1.0

Calcium binding site 5 out of 6 in 1bqo

Go back to Calcium Binding Sites List in 1bqo
Calcium binding site 5 out of 6 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:18.4
occ:1.00
 O B:ASP182 2.3 11.6 1.0
OD1 B:ASP107 2.4 11.0 1.0
OD2 B:ASP107 2.4 6.9 1.0
O B:HOH409 2.5 11.3 1.0
O B:GLU184 2.6 14.8 1.0
OD1 B:ASP182 2.6 14.8 1.0
CG B:ASP107 2.7 6.3 1.0
C B:ASP182 3.4 12.1 1.0
CG B:ASP182 3.7 6.3 1.0
C B:GLU184 3.7 12.9 1.0
OG1 B:THR105 4.1 10.4 1.0
CA B:ASP182 4.1 10.3 1.0
CB B:ASP107 4.2 7.8 1.0
N B:GLU184 4.3 16.8 1.0
CB B:ASP182 4.3 8.1 1.0
O A:HOH346 4.4 22.3 1.0
CA B:GLN185 4.4 11.2 1.0
N B:GLN185 4.5 14.7 1.0
N B:ASP183 4.5 13.3 1.0
C B:ASP183 4.5 16.7 1.0
OE1 B:GLN185 4.6 17.8 1.0
OD2 B:ASP182 4.6 9.7 1.0
CD1 B:TRP186 4.6 2.0 1.0
CG B:PRO106 4.6 12.3 1.0
CD B:PRO106 4.7 10.4 1.0
CA B:GLU184 4.7 14.0 1.0
CA B:ASP183 4.8 16.0 1.0
N B:TRP186 4.8 12.6 1.0
N B:ASP107 4.9 13.4 1.0

Calcium binding site 6 out of 6 in 1bqo

Go back to Calcium Binding Sites List in 1bqo
Calcium binding site 6 out of 6 in the Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca305

b:8.9
occ:1.00
 OD1 B:ASP177 2.3 15.0 1.0
O B:GLY173 2.3 16.3 1.0
O B:ASP141 2.3 5.4 1.0
O B:ASN175 2.3 13.1 1.0
O B:HOH402 2.4 17.1 1.0
CG B:ASP177 3.2 8.6 1.0
OD2 B:ASP177 3.5 12.5 1.0
C B:ASP141 3.5 7.4 1.0
C B:ASN175 3.5 12.6 1.0
C B:GLY173 3.6 12.2 1.0
N B:ASN175 4.1 13.9 1.0
O B:ALA140 4.1 13.0 1.0
C B:ILE174 4.2 11.9 1.0
CA B:ASP141 4.2 8.5 1.0
N B:ASP177 4.3 7.5 1.0
C B:GLY176 4.3 8.8 1.0
N B:GLY173 4.3 8.7 1.0
N B:GLY176 4.4 13.3 1.0
N B:ILE174 4.4 12.6 1.0
CA B:ILE174 4.4 12.9 1.0
CA B:GLY176 4.5 9.5 1.0
CA B:ASN175 4.5 12.3 1.0
O B:GLY171 4.5 12.9 1.0
CA B:GLY173 4.5 7.9 1.0
N B:ILE142 4.5 9.2 1.0
CB B:ASP177 4.6 9.4 1.0
O B:ILE174 4.6 13.8 1.0
C B:PRO172 4.7 9.9 1.0
CA B:ILE142 4.8 8.0 1.0
CG B:MET143 4.8 2.0 1.0
N B:MET143 4.8 8.8 1.0
O B:GLY176 4.8 11.6 1.0
CA B:ASP177 4.8 9.1 1.0
O B:PRO172 4.9 15.9 1.0

Reference:

S.Pikul, K.L.Mcdow Dunham, N.G.Almstead, B.De, M.G.Natchus, M.V.Anastasio, S.J.Mcphail, C.E.Snider, Y.O.Taiwo, T.Rydel, C.M.Dunaway, F.Gu, G.E.Mieling. Discovery of Potent, Achiral Matrix Metalloproteinase Inhibitors. J.Med.Chem. V. 41 3568 1998.
ISSN: ISSN 0022-2623
PubMed: 9733482
DOI: 10.1021/JM980253R
Page generated: Thu Jul 11 06:31:09 2024

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