Calcium in PDB 8r6o: Tubulin-4AZA2996 Complex

The structure of Tubulin-4AZA2996 Complex, PDB code: 8r6o was solved by J.Herman, E.Vanstreels, D.Bardiot, A.E.Prota, N.Olieric, L.-J.Gao, T.Vercruysse, T.Daems, M.Waer, P.Herdewijn, T.Louat, M.O.Steinmetz, S.Dejonghe, B.Sprangers, D.Daelemans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.20 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.327, 158.182, 182.681, 90, 90, 90
R / Rfree (%)	20.8 / 23.3

The structure of Tubulin-4AZA2996 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-4AZA2996 Complex (pdb code 8r6o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Tubulin-4AZA2996 Complex, PDB code: 8r6o:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:96.6 occ:1.00 OE2 A:GLU55 2.4 97.3 1.0 O A:GLY44 2.4 101.3 1.0 O A:HOH621 2.4 95.0 1.0 O A:THR41 2.5 100.8 1.0 OD1 A:ASP39 2.5 91.7 1.0 OD2 A:ASP39 2.6 93.4 1.0 OG1 A:THR41 2.6 97.3 1.0 OE1 A:GLU55 2.7 96.8 1.0 CD A:GLU55 2.9 94.7 1.0 CG A:ASP39 2.9 90.1 1.0 C A:GLY44 3.4 105.1 1.0 CB A:THR41 3.5 96.5 1.0 C A:THR41 3.5 102.5 1.0 CA A:GLY45 3.9 116.4 1.0 CA A:THR41 3.9 97.9 1.0 N A:GLY45 4.1 118.8 1.0 CZ A:PHE49 4.2 85.3 1.0 N A:THR41 4.3 94.7 1.0 CG A:GLU55 4.4 89.5 1.0 CB A:ASP39 4.4 89.4 1.0 N A:GLY44 4.4 107.0 1.0 CA A:GLY44 4.5 107.5 1.0 ND2 A:ASN50 4.6 88.8 1.0 N A:ILE42 4.6 99.7 1.0 OD1 A:ASN50 4.7 95.1 1.0 NE2 A:HIS61 4.8 90.6 1.0 CG2 A:THR41 4.8 88.8 1.0 OD2 A:ASP47 4.9 95.3 1.0 CE1 A:PHE49 5.0 80.2 1.0

Calcium binding site 2 out of 3 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:92.8 occ:1.00 OE1 B:GLU113 2.5 88.6 1.0 CD B:GLU113 3.4 86.4 1.0 OE2 B:GLU113 3.6 86.7 1.0 OE1 B:GLU110 4.1 59.6 1.0 OE2 B:GLU110 4.7 62.9 1.0 CD B:GLU110 4.8 55.9 1.0 CG B:GLU113 4.8 74.0 1.0

Calcium binding site 3 out of 3 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:74.5 occ:1.00 OG1 C:THR41 2.2 94.1 1.0 O C:THR41 2.3 91.8 1.0 OE2 C:GLU55 2.4 75.0 1.0 OD2 C:ASP39 2.4 71.2 1.0 O C:GLY44 2.5 78.0 1.0 OE1 C:GLU55 2.5 74.3 1.0 OD1 C:ASP39 2.6 79.3 1.0 CD C:GLU55 2.8 71.8 1.0 CG C:ASP39 2.9 75.9 1.0 C C:THR41 3.4 92.3 1.0 C C:GLY44 3.5 78.0 1.0 CB C:THR41 3.6 93.7 1.0 CA C:THR41 3.9 91.1 1.0 OD2 C:ASP47 4.1 77.0 1.0 N C:THR41 4.2 89.5 1.0 CG C:GLU55 4.3 64.4 1.0 N C:GLY45 4.3 79.7 1.0 CA C:GLY45 4.4 83.3 1.0 CG2 C:THR41 4.4 90.6 1.0 CB C:ASP39 4.4 73.4 1.0 N C:GLY44 4.4 80.3 1.0 CA C:GLY44 4.4 78.7 1.0 N C:ILE42 4.5 88.9 1.0 OD1 C:ASN50 4.6 69.5 1.0 NE2 C:HIS61 4.6 61.0 1.0 CZ C:PHE49 4.6 59.9 1.0 ND2 C:ASN50 4.7 57.8 1.0 O C:HOH692 4.9 80.7 1.0 CE1 C:PHE49 4.9 60.8 1.0 CA C:ILE42 4.9 86.4 1.0

J.Herman, E.Vanstreels, D.Bardiot, A.E.Prota, N.Gaillard, L.J.Gao, T.Vercruysse, L.Persoons, T.Daems, M.Waer, P.Herdewijn, T.Louat, M.O.Steinmetz, S.De Jonghe, B.Sprangers, D.Daelemans. 3-Nitropyridine Analogues As Novel Microtubule-Targeting Agents. Plos One V. 19 07153 2024.
ISSN: ESSN 1932-6203
PubMed: 39509402
DOI: 10.1371/JOURNAL.PONE.0307153