Calcium in PDB 6fkj: Tubulin-TUB075 Complex

The structure of Tubulin-TUB075 Complex, PDB code: 6fkj was solved by A.E.Prota, M.O.Steinmetz, E.-M.Priego, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.670, 157.562, 180.100, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.6

The structure of Tubulin-TUB075 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-TUB075 Complex (pdb code 6fkj). 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-TUB075 Complex, PDB code: 6fkj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:67.2 occ:1.00 O A:GLY44 2.2 68.1 1.0 OD1 A:ASP39 2.4 67.6 1.0 O A:HOH615 2.4 80.8 1.0 O A:THR41 2.5 84.0 1.0 OD2 A:ASP39 2.5 68.0 1.0 OG1 A:THR41 2.6 69.6 1.0 OE2 A:GLU55 2.6 62.3 1.0 OE1 A:GLU55 2.6 73.1 1.0 CG A:ASP39 2.8 67.3 1.0 CD A:GLU55 2.9 73.6 1.0 C A:GLY44 3.4 88.1 1.0 CB A:THR41 3.4 84.9 1.0 C A:THR41 3.5 82.4 1.0 CA A:THR41 3.9 85.1 1.0 N A:GLY44 4.2 89.4 1.0 N A:THR41 4.2 82.5 1.0 O A:HOH624 4.2 58.9 1.0 CA A:GLY45 4.2 82.5 1.0 N A:GLY45 4.3 85.0 1.0 CB A:ASP39 4.3 65.8 1.0 CA A:GLY44 4.4 92.4 1.0 CG A:GLU55 4.4 71.3 1.0 OD2 A:ASP47 4.5 78.0 1.0 CZ A:PHE49 4.5 68.8 1.0 OD1 A:ASN50 4.6 67.2 1.0 N A:ILE42 4.7 80.8 1.0 NE2 A:HIS61 4.7 70.0 1.0 CG2 A:THR41 4.8 74.7 1.0 CE1 A:PHE49 4.9 64.0 1.0 ND2 A:ASN50 4.9 59.5 1.0

Calcium binding site 2 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:98.4 occ:1.00 O B:HOH639 2.4 52.5 1.0 OE2 B:GLU113 2.6 82.6 1.0 O B:HOH720 2.7 83.4 1.0 OE1 B:GLU110 3.4 46.2 1.0 CD B:GLU113 3.7 77.5 1.0 OE1 B:GLU113 4.1 84.3 1.0 CD B:GLU110 4.2 46.5 1.0 OE2 B:GLU110 4.4 60.5 1.0 O B:HOH689 4.5 55.4 1.0 CG B:GLU113 4.9 60.1 1.0

Calcium binding site 3 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:0.2 occ:1.00 O B:HOH604 2.5 0.9 1.0 O B:HOH714 2.7 72.1 1.0 O B:HOH705 2.7 75.1 1.0 O B:HOH732 2.9 81.4 1.0 OD2 B:ASP116 4.4 77.1 1.0 O B:HOH659 4.9 58.2 1.0

Calcium binding site 4 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:54.3 occ:1.00 OE1 C:GLU55 2.3 49.6 1.0 O C:THR41 2.3 65.4 1.0 O C:GLY44 2.4 66.7 1.0 O C:HOH605 2.4 44.3 1.0 OE2 C:GLU55 2.5 55.4 1.0 OD2 C:ASP39 2.5 57.3 1.0 OD1 C:ASP39 2.6 55.1 1.0 OG1 C:THR41 2.6 53.0 1.0 CD C:GLU55 2.7 49.1 1.0 CG C:ASP39 2.9 55.7 1.0 C C:THR41 3.4 66.4 1.0 C C:GLY44 3.5 69.9 1.0 CB C:THR41 3.6 56.0 1.0 CA C:THR41 3.9 62.9 1.0 O C:HOH612 4.0 50.5 1.0 N C:THR41 4.2 65.5 1.0 CG C:GLU55 4.2 43.0 1.0 N C:GLY45 4.3 70.0 1.0 OD2 C:ASP47 4.3 69.7 1.0 CA C:GLY45 4.3 67.7 1.0 N C:GLY44 4.4 66.7 1.0 CB C:ASP39 4.4 57.5 1.0 CA C:GLY44 4.5 69.7 1.0 N C:ILE42 4.5 68.8 1.0 OD1 C:ASN50 4.6 43.7 1.0 NE2 C:HIS61 4.7 41.4 1.0 CZ C:PHE49 4.7 54.9 1.0 ND2 C:ASN50 4.9 38.5 1.0 CE1 C:PHE49 4.9 52.3 1.0 CG2 C:THR41 4.9 48.9 1.0 CA C:ILE42 5.0 65.0 1.0

Calcium binding site 5 out of 5 in the Tubulin-TUB075 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-TUB075 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:99.5 occ:1.00 O A:HOH660 2.4 79.1 1.0 OD2 E:ASP44 3.5 0.9 1.0 OG A:SER158 3.8 59.4 1.0 O A:GLY162 4.3 78.7 1.0 NZ A:LYS166 4.4 47.9 1.0 CB A:SER158 4.4 54.9 1.0 O A:GLU196 4.5 62.2 1.0 CG E:ASP44 4.7 1.0 1.0 CA A:HIS197 5.0 51.5 1.0

O.Bueno, J.Estevez Gallego, S.Martins, A.E.Prota, F.Gago, A.Gomez-Sanjuan, M.J.Camarasa, I.Barasoain, M.O.Steinmetz, J.F.Diaz, M.J.Perez-Perez, S.Liekens, E.M.Priego. High-Affinity Ligands of the Colchicine Domain in Tubulin Based on A Structure-Guided Design. Sci Rep V. 8 4242 2018.
ISSN: ESSN 2045-2322
PubMed: 29523799
DOI: 10.1038/S41598-018-22382-X