Calcium in PDB 8a9z: Tubulin-[1,2]Oxazoloisoindole-2E Complex

The structure of Tubulin-[1,2]Oxazoloisoindole-2E Complex, PDB code: 8a9z 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)	49.89 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.5, 155.847, 178.855, 90, 90, 90
R / Rfree (%)	19.9 / 24

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

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Tubulin-[1,2]Oxazoloisoindole-2E Complex (pdb code 8a9z). 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-2E Complex, PDB code: 8a9z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-2E 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-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:91.4 occ:1.00 OD2 A:ASP39 2.3 88.0 1.0 O A:GLY44 2.3 93.8 1.0 OE2 A:GLU55 2.4 78.2 1.0 OG1 A:THR41 2.4 91.2 1.0 O A:THR41 2.4 95.9 1.0 OD1 A:ASP39 2.5 88.4 1.0 OE1 A:GLU55 2.5 90.1 1.0 CG A:ASP39 2.7 84.4 1.0 CD A:GLU55 2.8 86.2 1.0 CB A:THR41 3.4 91.8 1.0 C A:THR41 3.5 98.1 1.0 C A:GLY44 3.5 92.4 1.0 CA A:THR41 3.8 101.0 1.0 N A:THR41 4.1 96.4 1.0 CZ A:PHE49 4.1 84.5 1.0 CA A:GLY45 4.2 92.0 1.0 CB A:ASP39 4.2 80.1 1.0 N A:GLY45 4.3 91.1 1.0 CG A:GLU55 4.3 84.7 1.0 N A:GLY44 4.3 94.3 1.0 OD2 A:ASP47 4.4 89.4 1.0 OD1 A:ASN50 4.5 77.5 1.0 CA A:GLY44 4.5 89.5 1.0 NE2 A:HIS61 4.6 78.2 1.0 N A:ILE42 4.7 98.8 1.0 CE1 A:PHE49 4.7 75.9 1.0 CG2 A:THR41 4.7 86.9 1.0 ND2 A:ASN50 4.7 71.9 1.0

Calcium binding site 2 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-2E 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-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:99.0 occ:1.00 OE1 B:GLU113 2.6 102.2 1.0 OE2 B:GLU113 3.1 97.4 1.0 CD B:GLU113 3.2 98.9 1.0 OE1 B:GLU110 4.2 56.7 1.0 CG B:GLU113 4.7 79.7 1.0 OG B:SER97 4.7 94.7 1.0

Calcium binding site 3 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-2E 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-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:70.6 occ:1.00 O C:THR41 2.3 74.1 1.0 OE2 C:GLU55 2.4 66.5 1.0 OE1 C:GLU55 2.5 66.6 1.0 OD2 C:ASP39 2.5 62.4 1.0 OG1 C:THR41 2.5 65.5 1.0 O C:GLY44 2.6 75.3 1.0 O C:HOH604 2.7 63.9 1.0 OD1 C:ASP39 2.7 71.0 1.0 CD C:GLU55 2.8 64.5 1.0 CG C:ASP39 2.9 67.9 1.0 C C:THR41 3.4 72.6 1.0 C C:GLY44 3.4 74.5 1.0 CB C:THR41 3.6 70.5 1.0 CA C:THR41 3.9 74.1 1.0 O C:HOH609 4.1 60.9 1.0 N C:GLY45 4.2 77.7 1.0 N C:GLY44 4.2 80.9 1.0 CA C:GLY44 4.2 76.0 1.0 N C:THR41 4.2 70.0 1.0 CG C:GLU55 4.3 57.5 1.0 CA C:GLY45 4.3 70.1 1.0 CB C:ASP39 4.4 63.1 1.0 N C:ILE42 4.5 71.3 1.0 OD2 C:ASP47 4.5 76.8 1.0 OD1 C:ASN50 4.6 57.8 1.0 NE2 C:HIS61 4.7 59.6 1.0 CZ C:PHE49 4.8 62.2 1.0 CG2 C:THR41 4.9 63.2 1.0 CA C:ILE42 4.9 69.1 1.0 ND2 C:ASN50 4.9 57.5 1.0

Calcium binding site 4 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-2E 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-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:81.8 occ:1.00 O C:PRO307 2.7 63.3 1.0 OG1 C:THR381 2.8 42.2 1.0 C C:LYS311 3.2 49.8 1.0 N C:LYS311 3.2 41.4 1.0 CD1 C:TYR312 3.3 45.7 1.0 C C:GLY310 3.3 56.9 1.0 CE1 C:TYR312 3.3 61.9 1.0 CA C:LYS311 3.4 51.0 1.0 O C:GLY310 3.4 59.1 1.0 O C:LYS311 3.5 46.8 1.0 CB C:THR381 3.5 38.1 1.0 N C:TYR312 3.5 54.8 1.0 C C:PRO307 3.7 61.8 1.0 CG C:TYR312 3.8 51.4 1.0 CA C:PRO307 3.8 55.4 1.0 CZ C:TYR312 3.9 59.0 1.0 CB C:PRO307 3.9 49.3 1.0 CA C:GLY310 4.0 53.0 1.0 CA C:TYR312 4.2 47.9 1.0 CD2 C:TYR312 4.3 49.5 1.0 CA C:THR381 4.3 40.4 1.0 CE2 C:TYR312 4.3 50.0 1.0 N C:GLY310 4.3 62.2 1.0 O C:GLN342 4.5 59.0 1.0 CB C:TYR312 4.5 46.9 1.0 OH C:TYR312 4.6 55.6 1.0 CG2 C:THR381 4.7 39.0 1.0 N C:THR382 4.8 45.3 1.0 N C:ARG308 4.9 61.2 1.0 CB C:ALA383 4.9 44.9 1.0 CB C:LYS311 4.9 54.8 1.0 C C:THR381 5.0 42.8 1.0

Calcium binding site 5 out of 5 in the Tubulin-[1,2]Oxazoloisoindole-2E 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-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:104.0 occ:1.00 O A:HOH630 2.5 70.5 1.0 OD2 E:ASP44 3.2 114.6 1.0 OG A:SER158 3.7 71.6 1.0 NZ A:LYS166 3.9 73.1 1.0 CB A:SER158 4.2 65.0 1.0 O A:GLY162 4.4 80.4 1.0 CG E:ASP44 4.4 112.5 1.0 O A:GLU196 4.5 68.3 1.0 O A:HIS197 4.6 64.5 1.0 O A:HOH665 4.7 73.3 1.0 CA A:HIS197 4.8 62.5 1.0 OD1 A:ASP199 4.8 75.2 1.0 CA A:SER158 4.8 59.9 1.0 OD1 E:ASP44 4.9 96.2 1.0 C A:HIS197 5.0 62.1 1.0 CE A:LYS166 5.0 62.1 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