Calcium in PDB 6qqn: Tubulin-TH588 Complex

The structure of Tubulin-TH588 Complex, PDB code: 6qqn was solved by J.C.Patterson, B.A.Joughin, A.E.Prota, T.Muehlethaler, O.H.Jonas, M.A.Whitman, S.Varmeh, S.Chen, S.P.Balk, M.O.Steinmetz, D.A.Lauffenburger, M.B.Yaffe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.832, 156.186, 179.432, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.4

The structure of Tubulin-TH588 Complex also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Tubulin-TH588 Complex (pdb code 6qqn). 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-TH588 Complex, PDB code: 6qqn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:89.3 occ:1.00 O A:GLY44 2.3 96.4 1.0 OD2 A:ASP39 2.4 80.2 1.0 OD1 A:ASP39 2.4 82.0 1.0 O A:THR41 2.4 0.6 1.0 OG1 A:THR41 2.4 98.8 1.0 OE2 A:GLU55 2.4 87.9 1.0 OE1 A:GLU55 2.5 94.2 1.0 CG A:ASP39 2.7 81.6 1.0 CD A:GLU55 2.8 87.5 1.0 C A:THR41 3.3 0.6 1.0 CB A:THR41 3.4 97.5 1.0 C A:GLY44 3.5 0.0 1.0 CA A:THR41 3.8 0.9 1.0 N A:THR41 4.0 98.0 1.0 CB A:ASP39 4.2 82.9 1.0 CA A:GLY45 4.3 0.0 1.0 N A:GLY44 4.3 0.9 1.0 N A:GLY45 4.3 0.4 1.0 CG A:GLU55 4.3 83.8 1.0 OD1 A:ASN50 4.4 84.8 1.0 CZ A:PHE49 4.4 73.9 1.0 O A:HOH647 4.5 69.1 1.0 CA A:GLY44 4.5 0.3 1.0 N A:ILE42 4.5 0.6 1.0 CG2 A:THR41 4.7 94.3 1.0 NE2 A:HIS61 4.8 92.6 1.0 ND2 A:ASN50 4.9 85.8 1.0 CA A:ILE42 4.9 0.0 1.0 CE1 A:PHE49 5.0 72.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:96.9 occ:1.00 OE1 B:GLU113 2.4 97.6 1.0 OE2 B:GLU113 2.5 0.2 1.0 CD B:GLU113 2.8 90.8 1.0 CG B:GLU113 4.3 70.8 1.0 OE1 B:GLU110 4.5 60.1 1.0 CB B:GLU113 5.0 64.3 1.0

Calcium binding site 3 out of 4 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:0.3 occ:1.00 O B:HOH636 2.4 71.1 1.0 O B:HOH626 2.4 87.9 1.0 CB B:ASP116 4.4 60.5 1.0 OD2 B:ASP120 4.5 81.8 1.0 CG B:ASP116 4.7 65.1 1.0 OD2 B:ASP116 4.7 70.6 1.0 OD1 B:ASP120 4.8 80.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-TH588 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-TH588 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:72.0 occ:1.00 OG1 C:THR41 2.3 85.1 1.0 OD2 C:ASP39 2.4 66.7 1.0 OE1 C:GLU55 2.4 57.1 1.0 O C:THR41 2.4 80.0 1.0 OE2 C:GLU55 2.4 64.1 1.0 O C:GLY44 2.4 71.5 1.0 OD1 C:ASP39 2.5 66.0 1.0 CD C:GLU55 2.7 63.8 1.0 CG C:ASP39 2.8 65.7 1.0 CB C:THR41 3.3 81.8 1.0 C C:THR41 3.4 79.5 1.0 C C:GLY44 3.6 77.2 1.0 CA C:THR41 3.8 77.1 1.0 OD2 C:ASP47 4.1 66.6 1.0 N C:THR41 4.2 74.1 1.0 CG C:GLU55 4.3 59.7 1.0 CB C:ASP39 4.3 68.7 1.0 O C:HOH638 4.3 49.8 1.0 N C:GLY44 4.4 81.5 1.0 CA C:GLY45 4.4 82.7 1.0 N C:GLY45 4.4 82.1 1.0 N C:ILE42 4.5 84.0 1.0 CA C:GLY44 4.5 78.7 1.0 OD1 C:ASN50 4.6 63.9 1.0 CZ C:PHE49 4.6 57.5 1.0 CG2 C:THR41 4.6 78.5 1.0 NE2 C:HIS61 4.7 60.3 1.0 ND2 C:ASN50 4.9 58.8 1.0 CE1 C:PHE49 4.9 59.3 1.0

J.C.Patterson, B.A.Joughin, A.E.Prota, T.Muhlethaler, O.H.Jonas, M.A.Whitman, S.Varmeh, S.Chen, S.P.Balk, M.O.Steinmetz, D.A.Lauffenburger, M.B.Yaffe. Visage Reveals A Targetable Mitotic Spindle Vulnerability in Cancer Cells. Cell Syst V. 9 74 2019.
ISSN: ISSN 2405-4720
PubMed: 31302152
DOI: 10.1016/J.CELS.2019.05.009