Calcium in PDB 8fg8: Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One

Enzymatic activity of Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One

All present enzymatic activity of Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One:
2.4.1.5;

Protein crystallography data

The structure of Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One, PDB code: 8fg8 was solved by N.Schormann, C.Deivanayagam, S.Velu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.04 / 2.35
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 150.455, 150.455, 304.948, 90, 90, 90
R / Rfree (%) 20.5 / 23.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One (pdb code 8fg8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One, PDB code: 8fg8:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 8fg8

Go back to Calcium Binding Sites List in 8fg8
Calcium binding site 1 out of 3 in the Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1201

b:40.0
occ:1.00
 OE2 A:GLU405 2.2 40.0 1.0
O A:GLU405 2.3 46.2 1.0
O A:ASN455 2.4 41.6 1.0
OD1 A:ASP933 2.4 35.5 1.0
OD1 A:ASP411 2.4 51.4 1.0
O A:HOH1308 2.5 37.2 1.0
OD2 A:ASP411 2.6 41.7 1.0
CG A:ASP411 2.8 46.5 1.0
CD A:GLU405 3.3 44.4 1.0
C A:GLU405 3.4 43.3 1.0
C A:ASN455 3.6 41.4 1.0
CG A:ASP933 3.6 39.1 1.0
CG A:GLU405 3.8 43.7 1.0
CA A:GLU405 3.9 39.8 1.0
O A:ASP933 4.1 43.0 1.0
OD2 A:ASP933 4.3 40.0 1.0
CB A:ASP411 4.3 46.4 1.0
OE1 A:GLU405 4.3 41.9 1.0
CB A:ASN455 4.4 37.3 1.0
O A:VAL412 4.4 43.4 1.0
O A:HOH1456 4.4 37.7 1.0
N A:VAL456 4.5 41.7 1.0
CA A:VAL456 4.5 38.7 1.0
CB A:GLU405 4.5 42.2 1.0
CA A:ASN455 4.5 40.6 1.0
N A:PHE406 4.5 44.2 1.0
CG1 A:VAL456 4.6 39.3 1.0
CB A:ASP933 4.6 37.6 1.0
ND2 A:ASN1023 4.7 43.1 1.0
CA A:ASP933 4.7 40.7 1.0
C A:ASP933 4.8 39.8 1.0
CA A:PHE406 4.9 42.2 1.0
CA A:ASP411 5.0 44.0 1.0

Calcium binding site 2 out of 3 in 8fg8

Go back to Calcium Binding Sites List in 8fg8
Calcium binding site 2 out of 3 in the Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1201

b:42.4
occ:1.00
 OE2 B:GLU405 2.2 40.8 1.0
O B:GLU405 2.3 43.8 1.0
O B:ASN455 2.4 39.6 1.0
OD1 B:ASP411 2.4 43.3 1.0
OD1 B:ASP933 2.4 34.5 1.0
O B:HOH1377 2.4 35.8 1.0
OD2 B:ASP411 2.6 42.1 1.0
CG B:ASP411 2.8 45.2 1.0
CD B:GLU405 3.3 48.2 1.0
C B:GLU405 3.4 44.5 1.0
C B:ASN455 3.6 38.6 1.0
CG B:ASP933 3.6 36.7 1.0
CG B:GLU405 3.7 46.3 1.0
CA B:GLU405 3.9 43.9 1.0
O B:ASP933 4.1 46.5 1.0
OD2 B:ASP933 4.3 36.2 1.0
CB B:ASP411 4.3 46.2 1.0
OE1 B:GLU405 4.3 45.9 1.0
CB B:ASN455 4.4 38.3 1.0
O B:VAL412 4.4 42.5 1.0
CB B:GLU405 4.5 46.5 1.0
N B:VAL456 4.5 40.1 1.0
CA B:VAL456 4.5 39.6 1.0
CA B:ASN455 4.5 37.5 1.0
N B:PHE406 4.5 42.0 1.0
O B:HOH1467 4.6 44.3 1.0
O B:HOH1310 4.6 37.5 1.0
CG1 B:VAL456 4.6 46.0 1.0
CB B:ASP933 4.7 35.9 1.0
ND2 B:ASN1023 4.7 45.5 1.0
CA B:ASP933 4.8 40.2 1.0
C B:ASP933 4.9 42.9 1.0
CA B:PHE406 4.9 41.0 1.0
CA B:ASP411 5.0 45.8 1.0

Calcium binding site 3 out of 3 in 8fg8

Go back to Calcium Binding Sites List in 8fg8
Calcium binding site 3 out of 3 in the Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Gtfb in Complex with Inhibitor 2-[(2,4,5- Trihydroxyphenyl)Methylidene]-1-Benzofuran-3-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1218

b:85.3
occ:1.00
 O B:HOH1301 2.6 40.2 1.0
O3 B:BTB1203 2.7 75.5 1.0
O5 B:XV51202 2.7 62.4 1.0
O4 B:XV51202 3.1 88.3 1.0
OE2 B:GLU489 3.2 45.5 1.0
C12 B:XV51202 3.3 81.5 1.0
OE1 B:GLU489 3.4 48.4 1.0
C13 B:XV51202 3.6 83.5 1.0
CD B:GLU489 3.6 50.4 1.0
C3 B:BTB1203 3.7 66.0 1.0
O8 B:BTB1203 3.8 82.9 1.0
NE1 B:TRP491 4.1 40.9 1.0
OD1 B:ASN455 4.3 36.0 1.0
CA B:ALA452 4.3 39.3 1.0
C11 B:XV51202 4.3 80.5 1.0
CD1 B:TRP491 4.4 39.9 1.0
CB B:ALA452 4.5 38.4 1.0
O B:HOH1404 4.5 39.5 1.0
CD2 B:LEU407 4.6 36.5 1.0
N B:ALA452 4.8 38.5 1.0
C14 B:XV51202 4.8 76.1 1.0
C2 B:BTB1203 4.9 64.3 1.0
CG B:GLU489 4.9 47.9 1.0
OD2 B:ASP562 5.0 53.4 1.0

Reference:

P.Ahirwar, V.Kozlovskaya, B.Nijampatnam, E.M.Rojas, P.Pukkanasut, D.Inman, M.Dolmat, A.C.Law, N.Schormann, C.Deivanayagam, G.J.Harber, S.M.Michalek, H.Wu, E.Kharlampieva, S.E.Velu. Hydrogel-Encapsulated Biofilm Inhibitors Abrogate the Cariogenic Activity of Streptococcus Mutans. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37285134
DOI: 10.1021/ACS.JMEDCHEM.3C00272
Page generated: Wed Jul 26 13:19:03 2023

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