Calcium in PDB 6s9e: Tubulin-Gdp.Alf Complex

The structure of Tubulin-Gdp.Alf Complex, PDB code: 6s9e was solved by M.A.Oliva, J.Estevez-Gallego, J.F.Diaz, A.E.Prota, M.O.Steinmetz, F.A.Balaguer, D.Lucena-Agell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.999, 157.357, 180.261, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.8

The structure of Tubulin-Gdp.Alf Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Magnesium	(Mg)	5 atoms
Aluminium	(Al)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Tubulin-Gdp.Alf Complex (pdb code 6s9e). 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-Gdp.Alf Complex, PDB code: 6s9e:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tubulin-Gdp.Alf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Gdp.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:71.9 occ:1.00 O A:GLY44 2.2 76.3 1.0 OD2 A:ASP39 2.3 77.1 1.0 O A:THR41 2.4 71.6 1.0 OE2 A:GLU55 2.4 74.5 1.0 O A:HOH609 2.4 65.6 1.0 OD1 A:ASP39 2.4 77.5 1.0 OG1 A:THR41 2.4 71.8 1.0 OE1 A:GLU55 2.5 78.1 1.0 CG A:ASP39 2.7 77.5 1.0 CD A:GLU55 2.8 76.3 1.0 C A:THR41 3.3 74.8 1.0 HA3 A:GLY45 3.4 96.1 1.0 CB A:THR41 3.4 75.6 1.0 C A:GLY44 3.5 76.8 1.0 HB A:THR41 3.5 87.5 1.0 HZ A:PHE49 3.6 94.3 1.0 H A:THR41 3.6 82.4 1.0 H A:GLY44 3.7 96.2 1.0 CA A:THR41 3.8 76.8 1.0 HE2 A:HIS61 3.9 89.4 1.0 HD21 A:ASN50 3.9 88.2 1.0 N A:THR41 4.0 76.0 1.0 CA A:GLY45 4.2 82.8 1.0 CB A:ASP39 4.2 78.0 1.0 CG A:GLU55 4.3 76.1 1.0 N A:GLY45 4.3 83.5 1.0 N A:GLY44 4.3 79.4 1.0 CZ A:PHE49 4.4 72.0 1.0 HE1 A:PHE49 4.5 85.8 1.0 CA A:GLY44 4.5 78.1 1.0 N A:ILE42 4.5 96.8 1.0 HA A:ILE42 4.6 99.5 1.0 NE2 A:HIS61 4.6 66.1 1.0 OD2 A:ASP47 4.6 78.2 1.0 HB2 A:ASP39 4.6 87.8 1.0 HB3 A:ASP39 4.6 87.8 1.0 HG2 A:GLU55 4.6 99.5 1.0 HG3 A:GLU55 4.7 99.5 1.0 HA A:THR41 4.7 90.1 1.0 OD1 A:ASN50 4.7 68.3 1.0 ND2 A:ASN50 4.7 68.3 1.0 CG2 A:THR41 4.7 78.8 1.0 HA2 A:GLY45 4.8 96.1 1.0 CE1 A:PHE49 4.9 71.1 1.0 H A:GLY43 4.9 90.6 1.0 HG21 A:THR41 4.9 84.6 1.0 HA2 A:GLY44 5.0 89.1 1.0 HA A:ASP39 5.0 89.0 1.0 HB3 A:GLU55 5.0 90.1 1.0 CA A:ILE42 5.0 96.7 1.0

Calcium binding site 2 out of 3 in the Tubulin-Gdp.Alf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Gdp.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:79.8 occ:1.00 OE2 B:GLU113 2.3 60.8 1.0 O B:HOH602 2.4 60.4 1.0 OE1 B:GLU113 2.4 64.5 1.0 CD B:GLU113 2.7 62.0 1.0 CG B:GLU113 4.2 60.4 1.0 HG3 B:GLU113 4.6 69.2 1.0 HG2 B:GLU113 4.7 69.2 1.0 HB2 B:GLU113 4.8 50.0 1.0 HB3 B:GLU113 4.9 50.0 1.0 CB B:GLU113 5.0 57.6 1.0

Calcium binding site 3 out of 3 in the Tubulin-Gdp.Alf Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Gdp.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:58.7 occ:1.00 OD2 C:ASP39 2.3 65.8 1.0 OE2 C:GLU55 2.4 55.0 1.0 OG1 C:THR41 2.4 58.6 1.0 O C:THR41 2.4 58.3 1.0 OE1 C:GLU55 2.4 55.5 1.0 O C:HOH603 2.4 41.6 1.0 OD1 C:ASP39 2.4 66.8 1.0 O C:GLY44 2.5 69.3 1.0 CG C:ASP39 2.7 66.6 1.0 CD C:GLU55 2.7 54.8 1.0 HA3 C:GLY45 3.4 83.9 1.0 C C:THR41 3.4 58.9 1.0 CB C:THR41 3.5 58.9 1.0 C C:GLY44 3.6 68.5 1.0 H C:THR41 3.6 74.5 1.0 HB C:THR41 3.7 77.8 1.0 HZ C:PHE49 3.8 67.5 1.0 HE2 C:HIS61 3.9 64.5 1.0 CA C:THR41 3.9 59.5 1.0 H C:GLY44 4.0 77.4 1.0 HD21 C:ASN50 4.1 51.0 1.0 N C:THR41 4.1 60.1 1.0 O C:HOH626 4.2 51.3 1.0 CB C:ASP39 4.2 67.5 1.0 CG C:GLU55 4.2 53.5 1.0 CA C:GLY45 4.3 67.4 1.0 OD2 C:ASP47 4.3 63.8 1.0 N C:GLY45 4.3 66.6 1.0 HE1 C:PHE49 4.4 58.3 1.0 OD1 C:ASN50 4.4 47.3 1.0 HB3 C:ASP39 4.5 76.2 1.0 N C:GLY44 4.5 68.2 1.0 CZ C:PHE49 4.5 50.9 1.0 CA C:GLY44 4.6 67.6 1.0 NE2 C:HIS61 4.6 49.3 1.0 N C:ILE42 4.6 70.8 1.0 HG2 C:GLU55 4.6 60.8 1.0 HG3 C:GLU55 4.6 60.8 1.0 HA C:ILE42 4.6 76.7 1.0 HB2 C:ASP39 4.7 76.2 1.0 HA2 C:GLY45 4.7 83.9 1.0 HA2 C:GLY44 4.8 80.6 1.0 CG2 C:THR41 4.8 59.3 1.0 HA C:THR41 4.8 80.7 1.0 ND2 C:ASN50 4.8 45.9 1.0 CE1 C:PHE49 4.8 50.1 1.0 HG21 C:THR41 4.9 68.1 1.0 HB3 C:GLU55 4.9 52.8 1.0 HG23 C:THR41 4.9 68.1 1.0 HA C:ASP39 4.9 79.7 1.0

J.Estevez-Gallego, F.Josa-Prado, R.M.Buey, F.A.Balaguer, A.E.Prota, D.Lucenal-Agell, C.Kamma-Lorger, M.O.Steinmetz, I.Barasoain, S.Kamimura, J.F.Diaz, M.A.Oliva. Structural Model For Differential Cap Maturation at Growing Microtubule Ends Elife 2020.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.50155