Calcium in PDB 6gf3: Tubulin-Jerantinine B Acetate Complex

The structure of Tubulin-Jerantinine B Acetate Complex, PDB code: 6gf3 was solved by C.J.Smedley, P.A.Stanley, M.E.Qazzaz, A.E.Prota, N.Olieric, H.Collins, H.Eastman, A.S.Barrow, K.-H.Lim, T.-S.Kam, B.J.Smith, H.M.Duivenvoorden, B.S.Parker, T.D.Bradshaw, M.O.Steinmetz, J.E.Moses, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.720, 158.150, 180.950, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.1

The structure of Tubulin-Jerantinine B Acetate Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Tubulin-Jerantinine B Acetate Complex (pdb code 6gf3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Tubulin-Jerantinine B Acetate Complex, PDB code: 6gf3:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Tubulin-Jerantinine B Acetate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Jerantinine B Acetate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.5 occ:1.00 OE2 A:GLU55 2.4 0.4 1.0 OD1 A:ASP39 2.4 0.4 1.0 O A:GLY44 2.5 0.7 1.0 OG1 A:THR41 2.6 91.5 1.0 O A:THR41 2.6 0.4 1.0 OD2 A:ASP39 2.9 0.9 1.0 OE1 A:GLU55 2.9 0.9 1.0 CD A:GLU55 3.0 0.5 1.0 CG A:ASP39 3.0 0.7 1.0 C A:GLY44 3.4 0.1 1.0 CB A:THR41 3.5 97.6 1.0 C A:THR41 3.6 1.0 1.0 CA A:GLY45 4.0 0.6 1.0 CA A:THR41 4.0 0.2 1.0 N A:GLY45 4.1 0.5 1.0 OD1 A:ASN50 4.2 96.8 1.0 N A:THR41 4.3 0.5 1.0 CZ A:PHE49 4.3 96.4 1.0 CB A:ASP39 4.5 0.7 1.0 CG A:GLU55 4.5 0.7 1.0 OD2 A:ASP47 4.5 0.2 1.0 CA A:GLY44 4.5 0.5 1.0 N A:GLY44 4.5 0.9 1.0 ND2 A:ASN50 4.8 88.4 1.0 N A:ILE42 4.8 0.9 1.0 CG2 A:THR41 4.8 98.9 1.0 C A:GLY45 4.9 0.7 1.0 CE1 A:PHE49 4.9 90.7 1.0 CG A:ASP47 4.9 0.2 1.0 CG A:ASN50 4.9 83.9 1.0

Calcium binding site 2 out of 2 in the Tubulin-Jerantinine B Acetate Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Jerantinine B Acetate Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:81.9 occ:1.00 O C:GLY44 2.3 95.5 1.0 OD2 C:ASP39 2.4 88.2 1.0 OD1 C:ASP39 2.4 93.9 1.0 OE2 C:GLU55 2.4 74.2 1.0 OG1 C:THR41 2.4 74.5 1.0 O C:THR41 2.5 86.5 1.0 CG C:ASP39 2.7 86.3 1.0 OE1 C:GLU55 2.8 78.1 1.0 CD C:GLU55 3.0 74.4 1.0 CB C:THR41 3.4 74.5 1.0 C C:GLY44 3.5 96.0 1.0 C C:THR41 3.5 85.0 1.0 CA C:THR41 3.9 76.4 1.0 N C:THR41 4.1 80.2 1.0 OD2 C:ASP47 4.2 86.6 1.0 CB C:ASP39 4.2 76.4 1.0 CA C:GLY45 4.3 86.6 1.0 N C:GLY45 4.3 89.6 1.0 N C:GLY44 4.4 0.6 1.0 CG C:GLU55 4.5 69.5 1.0 CA C:GLY44 4.5 0.7 1.0 NE2 C:HIS61 4.6 65.6 1.0 OD1 C:ASN50 4.7 69.0 1.0 O C:HOH661 4.7 81.5 1.0 CZ C:PHE49 4.7 69.9 1.0 N C:ILE42 4.7 97.8 1.0 CG2 C:THR41 4.8 69.7 1.0 ND2 C:ASN50 4.9 69.4 1.0 CE1 C:PHE49 4.9 63.5 1.0 CA C:ASP39 5.0 79.2 1.0 C C:ASP39 5.0 75.7 1.0

C.J.Smedley, P.A.Stanley, M.E.Qazzaz, A.E.Prota, N.Olieric, H.Collins, H.Eastman, A.S.Barrow, K.H.Lim, T.S.Kam, B.J.Smith, H.M.Duivenvoorden, B.S.Parker, T.D.Bradshaw, M.O.Steinmetz, J.E.Moses. Sustainable Syntheses of (-)-Jerantinines A & E and Structural Characterisation of the Jerantinine-Tubulin Complex at the Colchicine Binding Site. Sci Rep V. 8 10617 2018.
ISSN: ESSN 2045-2322
PubMed: 30006510
DOI: 10.1038/S41598-018-28880-2