Calcium in PDB 6gze: Tubulin-Gdp.Bef Complex

The structure of Tubulin-Gdp.Bef Complex, PDB code: 6gze was solved by M.A.Oliva, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.176, 156.744, 180.587, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.7

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

Fluorine	(F)	3 atoms
Magnesium	(Mg)	5 atoms

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

Calcium binding site 1 out of 3 in the Tubulin-Gdp.Bef 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.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:95.1 occ:1.00 HG22 A:THR41 1.7 95.1 1.0 OD2 A:ASP39 2.4 96.8 1.0 O A:HOH603 2.4 97.2 1.0 OE2 A:GLU55 2.4 0.3 1.0 O A:THR41 2.4 99.0 1.0 O A:GLY44 2.4 90.5 1.0 OD1 A:ASP39 2.4 96.2 1.0 OE1 A:GLU55 2.4 0.5 1.0 CG2 A:THR41 2.5 95.3 1.0 HG21 A:THR41 2.7 95.1 1.0 CD A:GLU55 2.7 0.5 1.0 CG A:ASP39 2.7 96.1 1.0 HG23 A:THR41 2.9 95.1 1.0 HZ A:PHE49 3.4 85.3 1.0 HA3 A:GLY45 3.5 0.3 1.0 C A:THR41 3.5 99.7 1.0 C A:GLY44 3.6 91.3 1.0 CB A:THR41 3.7 97.7 1.0 H A:THR41 3.7 99.1 1.0 HE2 A:HIS61 4.0 84.5 1.0 H A:GLY44 4.0 94.2 1.0 CA A:THR41 4.0 98.9 1.0 HD21 A:ASN50 4.0 87.0 1.0 OG1 A:THR41 4.2 99.1 1.0 CG A:GLU55 4.2 0.7 1.0 CZ A:PHE49 4.2 82.6 1.0 CB A:ASP39 4.2 95.6 1.0 N A:THR41 4.2 97.9 1.0 CA A:GLY45 4.3 0.1 1.0 HG1 A:THR41 4.3 99.8 1.0 HE1 A:PHE49 4.4 84.2 1.0 N A:GLY45 4.4 0.0 1.0 OD1 A:ASN50 4.4 83.1 1.0 HG2 A:GLU55 4.5 0.2 1.0 HB A:THR41 4.5 98.4 1.0 HA A:ILE42 4.5 0.9 1.0 HG3 A:GLU55 4.5 0.2 1.0 HB2 A:ASP39 4.6 98.9 1.0 N A:GLY44 4.6 92.9 1.0 N A:ILE42 4.6 0.1 1.0 NE2 A:HIS61 4.7 84.2 1.0 HB3 A:ASP39 4.7 98.9 1.0 CA A:GLY44 4.7 92.3 1.0 CE1 A:PHE49 4.7 81.9 1.0 ND2 A:ASN50 4.8 85.4 1.0 OD1 A:ASP47 4.9 95.6 1.0 HA2 A:GLY45 4.9 0.3 1.0 HA A:THR41 4.9 100.0 1.0 HA A:ASP39 4.9 99.8 1.0 HA2 A:GLY44 5.0 93.7 1.0 CA A:ILE42 5.0 0.3 1.0

Calcium binding site 2 out of 3 in the Tubulin-Gdp.Bef 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.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:0.8 occ:1.00 OE1 B:GLU113 2.4 79.5 1.0 OE2 B:GLU113 2.4 82.2 1.0 CD B:GLU113 2.7 80.0 1.0 CG B:GLU113 4.2 77.7 1.0 HG3 B:GLU113 4.5 78.0 1.0 HB2 B:GLU113 4.7 75.0 1.0 HG2 B:GLU113 4.7 78.0 1.0 CB B:GLU113 4.9 75.1 1.0 OE1 B:GLU110 5.0 75.5 1.0

Calcium binding site 3 out of 3 in the Tubulin-Gdp.Bef 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.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:85.8 occ:1.00 OD2 C:ASP39 2.4 78.4 1.0 O C:THR41 2.4 79.0 1.0 O C:GLY44 2.4 89.7 1.0 OG1 C:THR41 2.4 78.1 1.0 OE2 C:GLU55 2.4 70.9 1.0 O C:HOH604 2.4 66.3 1.0 OE1 C:GLU55 2.5 69.3 1.0 OD1 C:ASP39 2.5 80.8 1.0 CG C:ASP39 2.7 80.0 1.0 CD C:GLU55 2.8 69.2 1.0 C C:THR41 3.4 80.7 1.0 HA3 C:GLY45 3.4 1.0 1.0 C C:GLY44 3.6 89.8 1.0 CB C:THR41 3.6 80.1 1.0 H C:THR41 3.7 83.7 1.0 HB C:THR41 3.9 82.5 1.0 HE2 C:HIS61 3.9 67.0 1.0 CA C:THR41 3.9 81.5 1.0 H C:GLY44 3.9 91.9 1.0 HZ C:PHE49 4.0 60.9 1.0 HD21 C:ASN50 4.2 61.9 1.0 N C:THR41 4.2 81.8 1.0 CB C:ASP39 4.2 81.1 1.0 OD2 C:ASP47 4.3 79.1 1.0 HE1 C:PHE49 4.3 59.2 1.0 CA C:GLY45 4.3 97.5 1.0 CG C:GLU55 4.3 66.5 1.0 O C:HOH612 4.3 66.4 1.0 N C:GLY45 4.4 97.1 1.0 HA C:ILE42 4.5 99.0 1.0 N C:ILE42 4.5 98.5 1.0 N C:GLY44 4.5 90.3 1.0 HB3 C:ASP39 4.5 82.2 1.0 OD1 C:ASN50 4.6 63.6 1.0 CA C:GLY44 4.6 89.0 1.0 HG2 C:GLU55 4.6 68.3 1.0 CZ C:PHE49 4.7 61.8 1.0 NE2 C:HIS61 4.7 66.7 1.0 HG3 C:GLU55 4.7 68.3 1.0 HB2 C:ASP39 4.7 82.2 1.0 CG2 C:THR41 4.8 81.6 1.0 CE1 C:PHE49 4.8 60.1 1.0 HA2 C:GLY45 4.9 1.0 1.0 HA C:THR41 4.9 83.8 1.0 HG23 C:THR41 4.9 83.5 1.0 ND2 C:ASN50 4.9 61.5 1.0 HA C:ASP39 4.9 84.3 1.0 CA C:ILE42 5.0 97.7 1.0 HG21 C:THR41 5.0 83.5 1.0

F.Josa-Prado, J.Estevez-Gallego, R.M.Buey, F.A.Balaguer, A.E.Prota, M.O.Steinmetz, I.Barasoain, S.Kamimura, J.F.Diaz, M.A.Oliva. Structural Basis For Tubulin Activation Revealed By A Gtp Mimicking State To Be Published.