Calcium in PDB 6fkl: Tubulin-TUB015 Complex

The structure of Tubulin-TUB015 Complex, PDB code: 6fkl 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)	49.44 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.748, 157.764, 179.971, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.7

The structure of Tubulin-TUB015 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-TUB015 Complex (pdb code 6fkl). 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-TUB015 Complex, PDB code: 6fkl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:64.0 occ:1.00 O A:GLY44 2.3 67.2 1.0 O A:HOH617 2.3 58.9 1.0 OD2 A:ASP39 2.5 63.9 1.0 OD1 A:ASP39 2.5 66.8 1.0 O A:THR41 2.5 77.6 1.0 OE2 A:GLU55 2.5 57.7 1.0 OG1 A:THR41 2.6 64.3 1.0 OE1 A:GLU55 2.6 67.0 1.0 CG A:ASP39 2.8 66.9 1.0 CD A:GLU55 2.9 71.2 1.0 C A:GLY44 3.5 76.1 1.0 C A:THR41 3.5 73.4 1.0 CB A:THR41 3.5 71.7 1.0 CA A:THR41 4.0 77.0 1.0 N A:THR41 4.2 81.2 1.0 CA A:GLY45 4.3 79.8 1.0 N A:GLY45 4.3 79.0 1.0 N A:GLY44 4.3 79.4 1.0 CB A:ASP39 4.3 65.8 1.0 OD2 A:ASP47 4.4 69.1 1.0 O A:HOH682 4.4 58.5 1.0 CG A:GLU55 4.4 65.6 1.0 OD1 A:ASN50 4.5 69.2 1.0 CA A:GLY44 4.5 79.3 1.0 CZ A:PHE49 4.5 63.1 1.0 N A:ILE42 4.7 79.1 1.0 NE2 A:HIS61 4.8 66.4 1.0 CG2 A:THR41 4.9 68.6 1.0 ND2 A:ASN50 4.9 59.0 1.0 CE1 A:PHE49 5.0 61.4 1.0

Calcium binding site 2 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.3 occ:1.00 O E:HOH207 2.9 84.1 1.0 O A:HOH701 3.0 81.6 1.0 O A:HOH636 3.2 53.6 1.0 OD2 E:ASP44 3.6 0.2 1.0 OG A:SER158 3.8 50.2 1.0 O A:GLY162 4.0 76.4 1.0 O A:HOH619 4.1 57.5 1.0 NZ A:LYS166 4.2 43.3 1.0 CB A:SER158 4.3 49.6 1.0 CG E:ASP44 4.8 0.2 1.0 O A:GLU196 4.8 57.1 1.0 CA A:SER158 4.9 53.3 1.0 O A:LYS164 4.9 58.8 1.0 O A:HIS197 4.9 52.8 1.0 C A:GLY162 5.0 72.8 1.0

Calcium binding site 3 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:94.7 occ:1.00 O B:HOH616 2.4 59.9 1.0 OE2 B:GLU113 2.8 82.0 1.0 OE1 B:GLU113 3.3 84.8 1.0 CD B:GLU113 3.4 75.4 1.0 OE1 B:GLU110 4.8 46.0 1.0 CG B:GLU113 4.9 59.3 1.0

Calcium binding site 4 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:0.7 occ:1.00 O B:HOH707 2.5 74.1 1.0 O B:HOH691 2.5 74.0 1.0 O B:HOH719 3.1 81.5 1.0 OD2 B:ASP116 3.9 71.3 1.0 CG B:ASP116 4.5 57.4 1.0 CB B:ASP116 4.5 44.5 1.0 O B:HOH696 4.7 54.1 1.0

Calcium binding site 5 out of 5 in the Tubulin-TUB015 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-TUB015 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:49.6 occ:1.00 O C:THR41 2.4 59.3 1.0 O C:GLY44 2.4 61.8 1.0 OE1 C:GLU55 2.4 48.2 1.0 OE2 C:GLU55 2.4 49.7 1.0 O C:HOH603 2.5 42.0 1.0 OD2 C:ASP39 2.5 52.5 1.0 OG1 C:THR41 2.6 51.3 1.0 OD1 C:ASP39 2.6 50.2 1.0 CD C:GLU55 2.8 49.3 1.0 CG C:ASP39 2.9 51.6 1.0 C C:THR41 3.4 62.4 1.0 C C:GLY44 3.5 66.1 1.0 CB C:THR41 3.6 54.5 1.0 CA C:THR41 3.9 61.1 1.0 O C:HOH604 4.1 51.0 1.0 N C:THR41 4.2 61.0 1.0 CG C:GLU55 4.3 46.0 1.0 OD2 C:ASP47 4.3 70.0 1.0 N C:GLY45 4.3 66.0 1.0 CA C:GLY45 4.4 61.3 1.0 N C:GLY44 4.4 65.3 1.0 CB C:ASP39 4.4 56.6 1.0 CA C:GLY44 4.5 69.4 1.0 N C:ILE42 4.6 68.0 1.0 OD1 C:ASN50 4.6 45.6 1.0 NE2 C:HIS61 4.6 40.1 1.0 CZ C:PHE49 4.6 46.5 1.0 ND2 C:ASN50 4.9 38.2 1.0 CE1 C:PHE49 4.9 45.9 1.0 CG2 C:THR41 4.9 46.5 1.0 CA C:ILE42 5.0 62.6 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