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Calcium in PDB 1biw: Design and Synthesis of Conformationally-Constrained Mmp Inhibitors

Enzymatic activity of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors

All present enzymatic activity of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors:
3.4.24.17;

Protein crystallography data

The structure of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors, PDB code: 1biw was solved by M.G.Natchus, M.Cheng, C.T.Wahl, S.Pikul, N.G.Almstead, R.S.Bradley, Y.O.Taiwo, G.E.Mieling, C.M.Dunaway, C.E.Snider, J.M.Mciver, B.L.Barnett, S.J.Mcphail, M.B.Anastasio, B.De, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 38.060, 77.280, 106.400, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 27.5

Other elements in 1biw:

The structure of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors (pdb code 1biw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors, PDB code: 1biw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1biw

Go back to Calcium Binding Sites List in 1biw
Calcium binding site 1 out of 6 in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:2.0
occ:1.00
 O A:GLY159 2.3 7.2 1.0
OE2 A:GLU184 2.3 1.5 1.0
OD2 A:ASP181 2.3 14.9 1.0
O A:VAL163 2.3 4.1 1.0
OD1 A:ASP158 2.3 9.7 1.0
O A:GLY161 2.4 3.9 1.0
CG A:ASP181 2.8 12.7 1.0
OD1 A:ASP181 3.2 16.6 1.0
C A:VAL163 3.4 5.5 1.0
C A:GLY159 3.5 4.8 1.0
CD A:GLU184 3.5 2.6 1.0
C A:GLY161 3.5 3.4 1.0
CG A:ASP158 3.5 8.2 1.0
CB A:ASP181 3.7 9.0 1.0
N A:GLY161 3.9 4.5 1.0
C A:PRO160 4.1 5.8 1.0
N A:GLY159 4.1 3.4 1.0
OD2 A:ASP158 4.2 12.5 1.0
CA A:GLY161 4.2 1.5 1.0
CA A:VAL163 4.2 4.2 1.0
OE1 A:GLU184 4.3 4.2 1.0
N A:VAL163 4.3 5.0 1.0
N A:ASP158 4.3 4.8 1.0
N A:PRO160 4.4 5.1 1.0
CA A:GLY159 4.4 3.8 1.0
N A:LEU164 4.4 5.8 1.0
CG A:GLU184 4.4 1.5 1.0
CA A:PRO160 4.4 4.2 1.0
C A:ASP158 4.5 5.4 1.0
O A:PRO160 4.5 11.3 1.0
CA A:LEU164 4.5 3.0 1.0
C A:ASN162 4.6 6.6 1.0
CA A:ASP158 4.6 6.5 1.0
CB A:ASP158 4.7 1.5 1.0
N A:ASN162 4.7 5.6 1.0
CB A:VAL163 4.9 2.8 1.0
O A:ASN162 4.9 6.9 1.0

Calcium binding site 2 out of 6 in 1biw

Go back to Calcium Binding Sites List in 1biw
Calcium binding site 2 out of 6 in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:7.2
occ:1.00
 O A:ASP182 2.3 6.6 1.0
O A:GLU184 2.3 1.8 1.0
OD2 A:ASP107 2.3 9.6 1.0
OD1 A:ASP107 2.3 2.1 1.0
OD1 A:ASP182 2.4 5.0 1.0
CG A:ASP107 2.7 5.0 1.0
O A:HOH315 2.9 30.8 1.0
O B:HOH808 3.1 12.8 1.0
C A:ASP182 3.4 4.8 1.0
C A:GLU184 3.5 1.5 1.0
CG A:ASP182 3.5 1.7 1.0
CA A:ASP182 4.1 2.1 1.0
CA A:GLN185 4.3 3.6 1.0
CB A:ASP182 4.3 1.5 1.0
CB A:ASP107 4.3 1.5 1.0
N A:GLN185 4.3 1.5 1.0
OE1 A:GLN185 4.4 1.5 1.0
OD2 A:ASP182 4.4 1.5 1.0
OG1 A:THR105 4.4 5.5 1.0
N A:ASP183 4.5 4.3 1.0
N A:GLU184 4.5 4.2 1.0
CA A:GLU184 4.6 1.7 1.0
CA A:ASP183 4.6 5.2 1.0
C A:ASP183 4.7 5.4 1.0
CD1 A:TRP186 4.7 1.5 1.0
N A:TRP186 4.9 4.3 1.0
CD A:GLN185 5.0 1.5 1.0

Calcium binding site 3 out of 6 in 1biw

Go back to Calcium Binding Sites List in 1biw
Calcium binding site 3 out of 6 in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:5.7
occ:1.00
 O A:ASN175 2.2 2.0 1.0
O A:ASP141 2.3 3.7 1.0
OD1 A:ASP177 2.3 6.5 1.0
O A:GLY173 2.3 1.5 1.0
O A:HOH326 2.4 1.5 1.0
O A:HOH314 2.6 14.7 1.0
CG A:ASP177 3.2 1.6 1.0
OD2 A:ASP177 3.3 1.5 1.0
C A:ASP141 3.4 3.9 1.0
C A:ASN175 3.4 1.5 1.0
C A:GLY173 3.5 2.3 1.0
O A:ALA140 3.9 6.4 1.0
CA A:ASP141 4.2 5.2 1.0
C A:ILE174 4.2 4.7 1.0
O A:GLY171 4.2 13.8 1.0
N A:ASN175 4.2 1.8 1.0
CA A:GLY176 4.2 2.1 1.0
N A:GLY173 4.3 11.8 1.0
N A:GLY176 4.3 1.5 1.0
N A:ASP177 4.3 1.8 1.0
CA A:ASN175 4.4 1.5 1.0
O A:ILE174 4.4 5.8 1.0
CA A:GLY173 4.4 3.7 1.0
C A:GLY176 4.4 1.5 1.0
N A:ILE142 4.5 5.1 1.0
N A:ILE174 4.5 3.5 1.0
CB A:ASP177 4.5 1.5 1.0
CA A:ILE174 4.5 6.0 1.0
C A:PRO172 4.6 14.6 1.0
N A:MET143 4.7 4.9 1.0
CH2 A:TRP92 4.7 2.4 1.0
CA A:ILE142 4.7 3.0 1.0
CG A:MET143 4.9 1.5 1.0
CA A:ASP177 4.9 1.5 1.0
C A:ALA140 4.9 7.4 1.0
O A:PRO172 4.9 17.6 1.0

Calcium binding site 4 out of 6 in 1biw

Go back to Calcium Binding Sites List in 1biw
Calcium binding site 4 out of 6 in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:5.2
occ:1.00
 OE2 B:GLU184 2.3 1.5 1.0
OD2 B:ASP181 2.3 1.5 1.0
O B:VAL163 2.3 5.9 1.0
O B:ASP158 2.3 23.4 1.0
O B:GLY159 2.3 14.1 1.0
O B:GLY161 2.4 6.4 1.0
OD1 B:ASP158 2.4 1.5 1.0
CG B:ASP181 3.3 4.8 1.0
C B:ASP158 3.4 18.5 1.0
C B:VAL163 3.5 5.6 1.0
CD B:GLU184 3.5 4.3 1.0
C B:GLY159 3.5 12.7 1.0
C B:GLY161 3.5 3.5 1.0
CG B:ASP158 3.6 1.5 1.0
N B:GLY161 3.9 7.9 1.0
N B:VAL163 4.1 5.3 1.0
OD1 B:ASP181 4.1 4.5 1.0
CB B:ASP181 4.1 2.6 1.0
CA B:GLY159 4.2 14.0 1.0
CA B:VAL163 4.3 7.0 1.0
OE1 B:GLU184 4.3 5.8 1.0
CA B:GLY161 4.3 2.4 1.0
N B:GLY159 4.3 17.6 1.0
CA B:ASP158 4.3 13.2 1.0
N B:ASP158 4.4 14.2 1.0
CB B:ASP158 4.4 6.5 1.0
CG B:GLU184 4.4 1.5 1.0
C B:PRO160 4.4 12.0 1.0
OD2 B:ASP158 4.5 3.2 1.0
N B:LEU164 4.5 2.2 1.0
N B:PRO160 4.6 10.5 1.0
C B:ASN162 4.6 4.5 1.0
N B:ASN162 4.6 3.5 1.0
CA B:LEU164 4.7 1.5 1.0
CA B:PRO160 4.7 11.0 1.0
CA B:ASN162 4.9 5.2 1.0
O B:HOH822 4.9 1.5 1.0
CB B:VAL163 5.0 9.1 1.0

Calcium binding site 5 out of 6 in 1biw

Go back to Calcium Binding Sites List in 1biw
Calcium binding site 5 out of 6 in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca804

b:15.1
occ:1.00
 OD2 B:ASP107 2.3 3.0 1.0
O B:ASP182 2.3 7.5 1.0
OD1 B:ASP182 2.3 3.6 1.0
OD1 B:ASP107 2.3 1.5 1.0
O B:GLU184 2.4 2.1 1.0
O B:HOH823 2.5 18.6 1.0
CG B:ASP107 2.7 2.8 1.0
C B:ASP182 3.4 7.2 1.0
CG B:ASP182 3.4 1.5 1.0
C B:GLU184 3.6 2.7 1.0
CA B:ASP182 4.0 3.4 1.0
CB B:ASP182 4.1 4.4 1.0
OG1 B:THR105 4.2 6.9 1.0
CB B:ASP107 4.2 3.2 1.0
CA B:GLN185 4.3 1.7 1.0
OD2 B:ASP182 4.3 1.5 1.0
CD1 B:TRP186 4.4 1.8 1.0
N B:GLN185 4.4 1.7 1.0
N B:ASP183 4.5 7.9 1.0
N B:GLU184 4.6 2.6 1.0
N B:TRP186 4.7 2.1 1.0
CA B:GLU184 4.7 4.2 1.0
C B:ASP183 4.7 3.7 1.0
CA B:ASP183 4.8 4.9 1.0
NE1 B:TRP186 4.9 1.5 1.0
O B:HOH818 4.9 22.4 1.0
OE1 B:GLN185 4.9 25.4 1.0
N B:ASP107 5.0 5.2 1.0

Calcium binding site 6 out of 6 in 1biw

Go back to Calcium Binding Sites List in 1biw
Calcium binding site 6 out of 6 in the Design and Synthesis of Conformationally-Constrained Mmp Inhibitors


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Design and Synthesis of Conformationally-Constrained Mmp Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca805

b:2.0
occ:1.00
 OD1 B:ASP177 2.2 12.2 1.0
O B:GLY173 2.3 3.1 1.0
O B:ASN175 2.3 6.4 1.0
O B:ASP141 2.3 1.5 1.0
O B:HOH819 2.4 29.8 1.0
O B:HOH807 2.5 1.5 1.0
CG B:ASP177 3.0 7.9 1.0
OD2 B:ASP177 3.1 9.6 1.0
C B:ASP141 3.4 3.2 1.0
C B:GLY173 3.5 2.1 1.0
C B:ASN175 3.5 5.2 1.0
O B:ALA140 3.7 5.6 1.0
CA B:GLY176 4.2 1.8 1.0
CA B:ASP141 4.2 1.5 1.0
N B:ASP177 4.3 3.3 1.0
N B:GLY173 4.3 3.6 1.0
CA B:GLY173 4.3 1.5 1.0
CB B:ASP177 4.3 2.4 1.0
C B:ILE174 4.3 6.4 1.0
N B:GLY176 4.3 2.4 1.0
N B:ASN175 4.3 4.8 1.0
C B:GLY176 4.4 1.5 1.0
O B:GLY171 4.4 1.5 1.0
N B:ILE142 4.4 6.6 1.0
N B:ILE174 4.5 6.6 1.0
O B:ILE174 4.5 4.8 1.0
CA B:ASN175 4.5 5.6 1.0
N B:MET143 4.6 4.2 1.0
CA B:ILE174 4.6 5.4 1.0
C B:PRO172 4.7 4.3 1.0
C B:ALA140 4.7 5.2 1.0
CG B:MET143 4.7 4.0 1.0
CA B:ILE142 4.7 3.2 1.0
CA B:ASP177 4.7 1.5 1.0
O B:PRO172 4.9 1.5 1.0

Reference:

M.G.Natchus, M.Cheng, C.T.Wahl, S.Pikul, N.G.Almstead, R.S.Bradley, Y.O.Taiwo, G.E.Mieling, C.M.Dunaway, C.E.Snider, J.M.Mciver, B.L.Barnett, S.J.Mcphail, M.B.Anastasio, B.De. Design and Synthesis of Conformationally-Constrained Mmp Inhibitors. Bioorg.Med.Chem.Lett. V. 8 2077 1998.
ISSN: ISSN 0960-894X
PubMed: 9873489
DOI: 10.1016/S0960-894X(98)00370-9
Page generated: Thu Jul 11 06:25:52 2024

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