Calcium in PDB 6f7c: Tubulin-Compound 12 Complex

The structure of Tubulin-Compound 12 Complex, PDB code: 6f7c was solved by T.Muehlethaler, A.E.Prota, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.54 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.810, 157.900, 180.770, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.3

The structure of Tubulin-Compound 12 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Compound 12 Complex (pdb code 6f7c). 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-Compound 12 Complex, PDB code: 6f7c:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:80.9 occ:1.00 HG23 A:THR41 2.0 95.4 1.0 OD2 A:ASP39 2.4 85.2 1.0 O A:THR41 2.4 98.7 1.0 OE2 A:GLU55 2.4 69.2 1.0 OD1 A:ASP39 2.5 84.8 1.0 O A:GLY44 2.6 88.1 1.0 OE1 A:GLU55 2.7 74.5 1.0 CG A:ASP39 2.8 85.2 1.0 CG2 A:THR41 2.8 96.1 1.0 HG22 A:THR41 2.8 95.4 1.0 O A:HOH601 2.9 79.9 1.0 CD A:GLU55 2.9 71.3 1.0 HG21 A:THR41 3.3 95.4 1.0 HZ A:PHE49 3.4 95.3 1.0 C A:THR41 3.5 0.9 1.0 HA3 A:GLY45 3.7 0.3 1.0 C A:GLY44 3.7 88.5 1.0 H A:GLY44 3.7 0.7 1.0 HG1 A:THR41 3.8 0.1 1.0 H A:THR41 3.8 98.7 1.0 CB A:THR41 3.8 0.4 1.0 HD21 A:ASN50 4.0 88.3 1.0 HE2 A:HIS61 4.0 0.8 1.0 CA A:THR41 4.1 0.2 1.0 CZ A:PHE49 4.2 64.0 1.0 OG1 A:THR41 4.2 0.2 1.0 HE1 A:PHE49 4.3 88.7 1.0 CB A:ASP39 4.3 86.1 1.0 N A:THR41 4.3 0.7 1.0 CG A:GLU55 4.4 70.1 1.0 N A:GLY44 4.4 92.5 1.0 HA A:ILE42 4.4 0.9 1.0 CA A:GLY45 4.5 88.0 1.0 N A:GLY45 4.5 89.9 1.0 O A:HOH703 4.5 38.6 1.0 N A:ILE42 4.5 99.2 1.0 OD1 A:ASN50 4.6 65.2 1.0 OD1 A:ASP47 4.6 75.0 1.0 HB3 A:ASP39 4.6 0.2 1.0 NE2 A:HIS61 4.6 67.9 1.0 CE1 A:PHE49 4.7 64.1 1.0 CA A:GLY44 4.7 90.8 1.0 HB2 A:ASP39 4.7 0.2 1.0 HB A:THR41 4.7 95.2 1.0 O A:HOH649 4.7 38.6 1.0 HG3 A:GLU55 4.8 0.2 1.0 HG2 A:GLU55 4.8 0.2 1.0 ND2 A:ASN50 4.8 66.7 1.0 H A:GLY43 4.9 90.5 1.0 CA A:ILE42 4.9 99.7 1.0 HA2 A:GLY45 5.0 0.3 1.0 HA A:THR41 5.0 100.0 1.0

Calcium binding site 2 out of 3 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:64.7 occ:1.00 O C:GLY44 2.3 70.5 1.0 O C:THR41 2.3 63.4 1.0 OD2 C:ASP39 2.5 59.6 1.0 OG1 C:THR41 2.5 63.4 1.0 OE1 C:GLU55 2.5 57.3 1.0 OE2 C:GLU55 2.6 56.1 1.0 O C:HOH662 2.7 54.6 1.0 OD1 C:ASP39 2.7 60.9 1.0 CD C:GLU55 2.9 56.2 1.0 CG C:ASP39 2.9 60.8 1.0 C C:THR41 3.3 64.0 1.0 C C:GLY44 3.4 69.1 1.0 CB C:THR41 3.4 63.8 1.0 HA3 C:GLY45 3.5 84.5 1.0 HB C:THR41 3.5 93.1 1.0 H C:GLY44 3.6 84.7 1.0 H C:THR41 3.7 89.9 1.0 CA C:THR41 3.8 64.9 1.0 HE2 C:HIS61 4.1 70.8 1.0 HZ C:PHE49 4.1 74.0 1.0 N C:THR41 4.1 66.0 1.0 HD21 C:ASN50 4.2 59.4 1.0 O C:HOH613 4.2 56.3 1.0 N C:GLY45 4.2 68.5 1.0 CA C:GLY45 4.3 69.2 1.0 N C:GLY44 4.3 69.2 1.0 CA C:GLY44 4.4 68.0 1.0 CG C:GLU55 4.4 54.8 1.0 CB C:ASP39 4.4 62.0 1.0 N C:ILE42 4.5 78.2 1.0 HE1 C:PHE49 4.5 78.6 1.0 HA C:ILE42 4.6 81.8 1.0 OD1 C:ASN50 4.6 46.1 1.0 HA2 C:GLY44 4.6 93.8 1.0 HB3 C:ASP39 4.7 69.0 1.0 HA C:THR41 4.7 91.1 1.0 NE2 C:HIS61 4.7 46.4 1.0 HG2 C:GLU55 4.8 72.6 1.0 HG3 C:GLU55 4.8 72.6 1.0 HA2 C:GLY45 4.8 84.5 1.0 CG2 C:THR41 4.8 64.6 1.0 CZ C:PHE49 4.8 48.7 1.0 HB2 C:ASP39 4.8 69.0 1.0 H C:GLY43 4.9 91.6 1.0 OD2 C:ASP47 4.9 64.3 1.0 CA C:ILE42 5.0 77.8 1.0 ND2 C:ASN50 5.0 45.0 1.0 O C:HOH694 5.0 38.6 1.0 HG21 C:THR41 5.0 83.9 1.0

Calcium binding site 3 out of 3 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:38.6 occ:1.00 O C:HOH834 2.2 38.6 1.0 O C:HOH762 2.3 38.6 1.0 OD2 C:ASP218 3.6 78.2 1.0 OE2 C:GLU220 3.8 76.6 1.0 OD1 C:ASP218 3.9 77.2 1.0 CG C:ASP218 4.2 77.6 1.0 HG3 C:GLU220 4.2 0.8 1.0 HG2 C:GLU220 4.4 0.8 1.0 CD C:GLU220 4.6 75.3 1.0 CG C:GLU220 4.6 74.8 1.0

N.M.Cury, T.Muhlethaler, A.B.A.Laranjeira, R.R.Canevarolo, P.P.Zenatti, D.Lucena-Agell, I.Barasoain, C.Song, D.Sun, S.Dovat, R.A.Yunes, A.E.Prota, M.O.Steinmetz, J.F.Diaz, J.A.Yunes. Structural Basis of Colchicine-Site Targeting Acylhydrazones Active Against Multidrug-Resistant Acute Lymphoblastic Leukemia. Iscience V. 21 95 2019.
ISSN: ESSN 2589-0042
PubMed: 31655259
DOI: 10.1016/J.ISCI.2019.10.003