Calcium in PDB 8a9t: Tubulin-[1,2]Oxazoloisoindole-1 Complex

The structure of Tubulin-[1,2]Oxazoloisoindole-1 Complex, PDB code: 8a9t was solved by A.E.Prota, A.-C.Abel, M.O.Steinmetz, P.Barraja, A.Montalbano, V.Spano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.91 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.212, 158.054, 180.717, 90, 90, 90
R / Rfree (%)	19.4 / 23.7

The structure of Tubulin-[1,2]Oxazoloisoindole-1 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Tubulin-[1,2]Oxazoloisoindole-1 Complex (pdb code 8a9t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tubulin-[1,2]Oxazoloisoindole-1 Complex, PDB code: 8a9t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:93.1 occ:1.00 O A:HOH618 2.2 89.1 1.0 O A:GLY44 2.3 85.9 1.0 OG1 A:THR41 2.4 93.4 1.0 OD2 A:ASP39 2.4 80.8 1.0 O A:THR41 2.4 106.0 1.0 OD1 A:ASP39 2.5 75.5 1.0 OE2 A:GLU55 2.5 86.8 1.0 OE1 A:GLU55 2.7 96.6 1.0 CG A:ASP39 2.8 82.1 1.0 CD A:GLU55 3.0 87.7 1.0 CB A:THR41 3.4 92.2 1.0 C A:THR41 3.4 97.7 1.0 C A:GLY44 3.5 94.6 1.0 CA A:THR41 3.8 90.9 1.0 N A:THR41 4.1 94.9 1.0 CB A:ASP39 4.3 82.3 1.0 CZ A:PHE49 4.3 70.6 1.0 CA A:GLY45 4.3 100.8 1.0 N A:GLY44 4.3 93.9 1.0 N A:GLY45 4.4 100.1 1.0 CG A:GLU55 4.5 85.8 1.0 CA A:GLY44 4.5 94.4 1.0 N A:ILE42 4.6 99.6 1.0 OD1 A:ASN50 4.6 91.9 1.0 CG2 A:THR41 4.7 89.7 1.0 CE2 A:PHE49 4.7 75.6 1.0 OD2 A:ASP47 4.8 92.9 1.0 NE2 A:HIS61 4.8 84.0 1.0 ND2 A:ASN50 4.9 71.3 1.0

Calcium binding site 2 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:108.0 occ:1.00 OD2 E:ASP44 3.8 116.9 1.0 O A:HOH636 3.9 74.2 1.0 NZ A:LYS166 4.2 80.2 1.0 OG A:SER158 4.3 70.1 1.0 O A:GLY162 4.4 81.8 1.0 OD1 A:ASP199 4.4 79.5 1.0 O A:HIS197 4.7 61.0 1.0 O A:GLU196 4.8 80.6 1.0 CB A:SER158 4.8 61.4 1.0 O A:LYS164 4.8 80.0 1.0 CG E:ASP44 4.8 118.7 1.0 CE A:LYS166 5.0 59.3 1.0

Calcium binding site 3 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:99.0 occ:1.00 OE1 B:GLU113 2.6 93.6 1.0 CD B:GLU113 3.3 82.5 1.0 OE2 B:GLU113 3.3 84.2 1.0 OE1 B:GLU110 4.6 56.7 1.0 CG B:GLU113 4.8 66.4 1.0

Calcium binding site 4 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:68.5 occ:1.00 O C:GLY44 2.3 74.3 1.0 OE1 C:GLU55 2.4 55.5 1.0 O C:THR41 2.4 77.5 1.0 OE2 C:GLU55 2.4 73.4 1.0 O C:HOH620 2.5 62.8 1.0 OD2 C:ASP39 2.5 61.0 1.0 OG1 C:THR41 2.6 79.5 1.0 OD1 C:ASP39 2.7 66.5 1.0 CD C:GLU55 2.7 66.0 1.0 CG C:ASP39 3.0 68.8 1.0 C C:GLY44 3.4 75.6 1.0 C C:THR41 3.4 80.5 1.0 CB C:THR41 3.5 74.9 1.0 CA C:THR41 3.9 70.6 1.0 O C:HOH608 4.1 60.8 1.0 N C:THR41 4.2 63.0 1.0 N C:GLY45 4.2 84.5 1.0 CA C:GLY45 4.2 78.1 1.0 CG C:GLU55 4.3 59.1 1.0 N C:GLY44 4.3 88.7 1.0 CA C:GLY44 4.3 79.9 1.0 CB C:ASP39 4.5 68.1 1.0 OD1 C:ASN50 4.5 64.2 1.0 OD2 C:ASP47 4.6 80.9 1.0 N C:ILE42 4.6 81.5 1.0 CZ C:PHE49 4.7 59.6 1.0 NE2 C:HIS61 4.7 60.8 1.0 CG2 C:THR41 4.9 64.2 1.0 O C:HOH666 4.9 57.6 1.0 ND2 C:ASN50 4.9 50.2 1.0 CE1 C:PHE49 5.0 64.6 1.0

Calcium binding site 5 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-1 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-[1,2]Oxazoloisoindole-1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:103.0 occ:1.00 OG1 C:THR381 2.6 49.7 1.0 O C:PRO307 2.8 56.5 1.0 CD1 C:TYR312 3.3 48.4 1.0 CE1 C:TYR312 3.3 53.7 1.0 C C:LYS311 3.3 48.8 1.0 C C:GLY310 3.4 58.9 1.0 CB C:THR381 3.4 38.3 1.0 N C:LYS311 3.4 45.4 1.0 O C:LYS311 3.4 50.6 1.0 O C:GLY310 3.5 60.5 1.0 C C:PRO307 3.6 65.5 1.0 CA C:LYS311 3.7 42.4 1.0 N C:TYR312 3.7 50.8 1.0 CA C:PRO307 3.8 50.3 1.0 CZ C:TYR312 3.8 43.3 1.0 CG C:TYR312 3.8 49.7 1.0 CB C:PRO307 3.9 46.8 1.0 CA C:GLY310 4.0 51.7 1.0 CD2 C:TYR312 4.2 48.1 1.0 CE2 C:TYR312 4.2 41.9 1.0 CA C:TYR312 4.3 48.5 1.0 CA C:THR381 4.3 37.2 1.0 N C:GLY310 4.3 52.9 1.0 OH C:TYR312 4.5 55.9 1.0 CG2 C:THR381 4.6 45.9 1.0 CB C:TYR312 4.6 49.4 1.0 O C:GLN342 4.8 54.6 1.0 N C:THR382 4.8 40.5 1.0 N C:ARG308 4.9 64.2 1.0 CB C:ALA383 4.9 42.0 1.0 C C:THR381 4.9 43.2 1.0

M.Barreca, V.Spano, R.Rocca, R.Bivacqua, A.C.Abel, A.Maruca, A.Montalbano, M.V.Raimondi, C.Tarantelli, E.Gaudio, L.Cascione, A.Rinaldi, R.Bai, M.O.Steinmetz, A.E.Prota, S.Alcaro, E.Hamel, F.Bertoni, P.Barraja. Development of [1,2]Oxazoloisoindoles Tubulin Polymerization Inhibitors: Further Chemical Modifications and Potential Therapeutic Effects Against Lymphomas. Eur.J.Med.Chem. V. 243 14744 2022.
ISSN: ISSN 0223-5234
PubMed: 36242921
DOI: 10.1016/J.EJMECH.2022.114744