Calcium in PDB 5jvd: Tubulin-TUB092 Complex

The structure of Tubulin-TUB092 Complex, PDB code: 5jvd was solved by M.-D.Canela, S.Noppen, O.Bueno, A.E.Prota, K.Bargsten, G.Saez-Calvo, M.-L.Jimeno, M.Benkheil, D.Ribatti, S.Velazquez, M.-J.Camarasa, J.F.Diaz, M.O.Steinmetz, E.-M.Priego, M.-J.Perez-Perez, S.Liekens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.251, 156.317, 180.614, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.8

The structure of Tubulin-TUB092 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-TUB092 Complex (pdb code 5jvd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tubulin-TUB092 Complex, PDB code: 5jvd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:89.4 occ:1.00 OE2 A:GLU55 2.4 88.6 1.0 O A:GLY44 2.4 0.3 1.0 O A:THR41 2.6 0.9 1.0 OD1 A:ASP39 2.6 93.2 1.0 OG1 A:THR41 2.6 84.5 1.0 OD2 A:ASP39 2.6 90.6 1.0 OE1 A:GLU55 2.8 92.3 1.0 CG A:ASP39 3.0 93.3 1.0 CD A:GLU55 3.0 89.4 1.0 C A:GLY44 3.4 0.4 1.0 CB A:THR41 3.6 91.0 1.0 C A:THR41 3.6 0.5 1.0 CA A:THR41 4.0 97.9 1.0 OD2 A:ASP47 4.2 96.8 1.0 N A:GLY45 4.2 0.5 1.0 CA A:GLY45 4.2 98.4 1.0 N A:THR41 4.3 0.5 1.0 CZ A:PHE49 4.4 77.1 1.0 CA A:GLY44 4.4 98.1 1.0 N A:GLY44 4.4 95.7 1.0 OD1 A:ASN50 4.4 82.9 1.0 CG A:GLU55 4.5 82.3 1.0 CB A:ASP39 4.5 94.3 1.0 NE2 A:HIS61 4.7 86.7 1.0 CE1 A:PHE49 4.7 76.4 1.0 N A:ILE42 4.8 0.5 1.0 ND2 A:ASN50 4.8 71.6 1.0 CG2 A:THR41 4.9 90.6 1.0

Calcium binding site 2 out of 4 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:0.2 occ:1.00 OD2 B:ASP120 4.0 79.0 1.0 OD1 B:ASP120 4.1 77.5 1.0 CB B:ASP116 4.3 74.5 1.0 OD2 B:ASP116 4.5 94.9 1.0 CG B:ASP120 4.5 75.6 1.0 CG B:ASP116 4.6 83.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:78.1 occ:1.00 O C:THR41 2.2 85.3 1.0 O C:HOH601 2.4 75.2 1.0 OD2 C:ASP39 2.5 77.8 1.0 OE1 C:GLU55 2.5 75.0 1.0 OE2 C:GLU55 2.5 81.0 1.0 OD1 C:ASP39 2.5 77.4 1.0 O C:GLY44 2.5 87.5 1.0 OG1 C:THR41 2.7 76.8 1.0 CD C:GLU55 2.8 73.0 1.0 CG C:ASP39 2.8 77.2 1.0 C C:THR41 3.3 84.0 1.0 CB C:THR41 3.6 75.3 1.0 C C:GLY44 3.6 88.1 1.0 CA C:THR41 3.9 79.3 1.0 O C:HOH607 4.1 67.9 1.0 N C:THR41 4.2 82.2 1.0 OD2 C:ASP47 4.3 90.0 1.0 CG C:GLU55 4.3 60.1 1.0 CB C:ASP39 4.3 76.3 1.0 N C:GLY44 4.4 98.9 1.0 N C:GLY45 4.4 85.7 1.0 CA C:GLY45 4.4 82.7 1.0 N C:ILE42 4.5 86.5 1.0 NE2 C:HIS61 4.5 61.0 1.0 CA C:GLY44 4.5 93.5 1.0 CZ C:PHE49 4.6 60.5 1.0 OD1 C:ASN50 4.6 59.3 1.0 CE1 C:PHE49 4.8 62.2 1.0 CA C:ILE42 4.9 86.8 1.0 CG2 C:THR41 5.0 70.1 1.0

Calcium binding site 4 out of 4 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:0.3 occ:1.00 O A:HOH633 2.8 85.4 1.0 OD2 E:ASP44 3.4 0.2 1.0 OG A:SER158 3.8 73.8 1.0 NZ A:LYS166 4.3 66.5 1.0 CB A:SER158 4.4 70.1 1.0 O A:GLU196 4.4 80.0 1.0 O A:GLY162 4.4 89.0 1.0 CG E:ASP44 4.6 0.3 1.0 CA A:HIS197 4.8 64.9 1.0 CA A:SER158 5.0 63.9 1.0

M.D.Canela, S.Noppen, O.Bueno, A.E.Prota, K.Bargsten, G.Saez-Calvo, M.L.Jimeno, M.Benkheil, D.Ribatti, S.Velazquez, M.J.Camarasa, J.F.Diaz, M.O.Steinmetz, E.M.Priego, M.J.Perez-Perez, S.Liekens. Antivascular and Antitumor Properties of the Tubulin-Binding Chalcone TUB091. Oncotarget V. 8 14325 2017.
ISSN: ESSN 1949-2553
PubMed: 27224920
DOI: 10.18632/ONCOTARGET.9527