Calcium in PDB 8ahm: Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z

The structure of Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z, PDB code: 8ahm was solved by M.A.Oliva, J.F.Diaz, K.H.Altmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.84 / 2.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.047, 157.8, 181.894, 90, 90, 90
R / Rfree (%)	20 / 24.1

The structure of Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z (pdb code 8ahm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z, PDB code: 8ahm:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:72.0 occ:1.00 OD2 A:ASP39 2.3 70.8 1.0 OD1 A:ASP39 2.4 73.5 1.0 O A:THR41 2.4 85.7 1.0 OE2 A:GLU55 2.4 72.3 1.0 OG1 A:THR41 2.4 93.5 1.0 O A:GLY44 2.4 74.9 1.0 OE1 A:GLU55 2.5 83.0 1.0 O A:HOH612 2.5 71.8 1.0 CG A:ASP39 2.6 75.1 1.0 CD A:GLU55 2.8 80.7 1.0 C A:THR41 3.3 104.9 1.0 HZ A:PHE49 3.4 93.7 1.0 CB A:THR41 3.5 87.6 1.0 C A:GLY44 3.5 85.6 1.0 HA3 A:GLY45 3.6 95.2 1.0 H A:THR41 3.6 80.8 1.0 HB A:THR41 3.7 87.7 1.0 H A:GLY44 3.7 96.7 1.0 HE2 A:HIS61 3.7 92.8 1.0 CA A:THR41 3.8 95.4 1.0 HD21 A:ASN50 4.0 94.3 1.0 N A:THR41 4.1 80.6 1.0 CB A:ASP39 4.1 75.0 1.0 CZ A:PHE49 4.2 95.3 1.0 CG A:GLU55 4.3 84.5 1.0 N A:GLY44 4.4 97.0 1.0 CA A:GLY45 4.4 94.9 1.0 N A:GLY45 4.4 90.4 1.0 HA A:ILE42 4.4 97.7 1.0 HE1 A:PHE49 4.5 89.3 1.0 HB3 A:ASP39 4.5 75.2 1.0 CA A:GLY44 4.5 96.3 1.0 N A:ILE42 4.5 91.3 1.0 NE2 A:HIS61 4.5 93.4 1.0 HB2 A:ASP39 4.6 75.2 1.0 HG2 A:GLU55 4.6 83.8 1.0 HG3 A:GLU55 4.7 83.8 1.0 OD1 A:ASN50 4.7 86.2 1.0 HA A:THR41 4.7 95.2 1.0 HA2 A:GLY44 4.8 96.4 1.0 CG2 A:THR41 4.8 84.9 1.0 CE1 A:PHE49 4.8 90.7 1.0 ND2 A:ASN50 4.8 95.1 1.0 HA A:ASP39 4.8 78.3 1.0 OD2 A:ASP47 4.9 88.5 1.0 H A:GLY43 4.9 77.7 1.0 CA A:ILE42 4.9 97.1 1.0 HA2 A:GLY45 4.9 95.2 1.0 HB3 A:GLU55 4.9 84.2 1.0 HG23 A:THR41 5.0 84.8 1.0 CA A:ASP39 5.0 78.2 1.0 HG21 A:THR41 5.0 84.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:102.7 occ:1.00 O B:HOH629 2.4 80.5 1.0 O B:HOH630 2.4 80.8 1.0 OD1 B:ASP120 3.6 63.8 1.0 OD2 B:ASP120 3.8 71.8 1.0 HB3 B:ASP116 3.8 64.3 1.0 CG B:ASP120 4.1 76.2 1.0 CB B:ASP116 4.7 65.4 1.0 HH12 B:ARG123 4.8 59.9 1.0 O B:ASP116 4.9 57.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:87.5 occ:1.00 O B:HOH614 2.4 73.8 1.0 OE1 B:GLU113 2.5 78.9 1.0 CD B:GLU113 3.2 87.0 1.0 OE2 B:GLU113 3.3 100.8 1.0 OE1 B:GLU110 4.6 55.3 1.0 CG B:GLU113 4.7 70.4 1.0 HB2 B:GLU113 4.9 55.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:61.3 occ:1.00 OG1 C:THR41 2.4 65.3 1.0 OE2 C:GLU55 2.4 61.0 1.0 OD2 C:ASP39 2.4 55.4 1.0 O C:HOH645 2.4 51.0 1.0 OD1 C:ASP39 2.4 59.5 1.0 OE1 C:GLU55 2.4 59.0 1.0 O C:THR41 2.4 67.2 1.0 O C:GLY44 2.5 70.3 1.0 CD C:GLU55 2.7 62.5 1.0 CG C:ASP39 2.7 55.1 1.0 HA3 C:GLY45 3.1 84.2 1.0 CB C:THR41 3.4 70.2 1.0 C C:THR41 3.4 69.5 1.0 C C:GLY44 3.5 73.3 1.0 HB C:THR41 3.5 70.1 1.0 H C:THR41 3.7 64.2 1.0 CA C:THR41 3.8 70.8 1.0 HZ C:PHE49 3.9 64.3 1.0 CA C:GLY45 3.9 83.9 1.0 HE2 C:HIS61 4.0 60.8 1.0 HD21 C:ASN50 4.0 58.9 1.0 H C:GLY44 4.0 68.9 1.0 N C:GLY45 4.1 61.2 1.0 N C:THR41 4.1 64.7 1.0 HA2 C:GLY45 4.1 84.2 1.0 HE1 C:PHE49 4.2 58.8 1.0 CG C:GLU55 4.2 54.9 1.0 CB C:ASP39 4.2 60.3 1.0 O C:HOH607 4.4 56.0 1.0 CA C:GLY44 4.6 70.6 1.0 CZ C:PHE49 4.6 65.6 1.0 HB3 C:ASP39 4.6 60.9 1.0 N C:GLY44 4.6 68.0 1.0 HG2 C:GLU55 4.6 55.1 1.0 HG3 C:GLU55 4.6 55.1 1.0 NE2 C:HIS61 4.6 61.5 1.0 OD1 C:ASN50 4.6 61.9 1.0 N C:ILE42 4.6 74.1 1.0 HB2 C:ASP39 4.7 60.9 1.0 CG2 C:THR41 4.7 71.4 1.0 HA C:ILE42 4.7 70.0 1.0 CE1 C:PHE49 4.8 59.8 1.0 HA C:THR41 4.8 70.3 1.0 HA2 C:GLY44 4.8 71.9 1.0 OD2 C:ASP47 4.8 88.1 1.0 ND2 C:ASN50 4.8 59.7 1.0 H C:GLY45 4.8 61.5 1.0 HG21 C:THR41 4.8 71.0 1.0 HA C:ASP39 4.9 75.4 1.0 HG23 C:THR41 5.0 71.0 1.0 HB3 C:GLU55 5.0 54.9 1.0

C.P.Bold, D.Lucena-Agell, M.A.Oliva, J.F.Diaz, K.H.Altmann. Synthesis and Biological Evaluation of C(13)/C(13')-Bis(Desmethyl)Disorazole Z. Angew.Chem.Int.Ed.Engl. 12190 2022.
ISSN: ESSN 1521-3773
PubMed: 36281761
DOI: 10.1002/ANIE.202212190