Magnesium 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:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Tubulin in Complex with C(13)/C(13')-Bis- Desmethyl-Disorazole Z, PDB code: 8ahm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 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 Magnesium with other atoms in the Mg 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:Mg502 b:40.4 occ:1.00 O1G A:GTP501 2.0 34.2 1.0 O1B A:GTP501 2.0 33.7 1.0 O A:HOH611 2.1 40.8 1.0 O A:HOH616 2.1 36.4 1.0 O A:HOH615 2.1 41.1 1.0 O A:HOH606 2.1 43.0 1.0 PG A:GTP501 3.2 46.3 1.0 PB A:GTP501 3.2 41.9 1.0 HZ1 B:LYS254 3.2 65.2 1.0 HB2 A:GLN11 3.5 45.7 1.0 O3B A:GTP501 3.5 56.5 1.0 HG2 A:GLU71 3.7 76.2 1.0 O3A A:GTP501 3.7 49.5 1.0 H A:GLN11 3.8 47.6 1.0 O2G A:GTP501 3.8 41.1 1.0 HB2 A:ASP98 3.9 43.2 1.0 HG3 A:GLU71 4.0 76.2 1.0 NZ B:LYS254 4.0 67.0 1.0 OD1 A:ASP69 4.1 43.2 1.0 OE2 A:GLU71 4.1 80.0 1.0 HB3 A:GLN11 4.1 45.7 1.0 CB A:GLN11 4.2 46.1 1.0 CG A:GLU71 4.2 76.3 1.0 HZ2 B:LYS254 4.2 65.2 1.0 OD2 A:ASP98 4.3 37.8 1.0 HZ3 B:LYS254 4.3 65.2 1.0 HB3 A:ASP98 4.3 43.2 1.0 OD2 A:ASP69 4.4 50.7 1.0 O3G A:GTP501 4.4 39.4 1.0 O2B A:GTP501 4.5 50.5 1.0 CB A:ASP98 4.5 42.8 1.0 N A:GLN11 4.5 47.9 1.0 OE1 A:GLN11 4.6 59.8 1.0 O1A A:GTP501 4.7 43.6 1.0 CD A:GLU71 4.7 79.8 1.0 CG A:ASP69 4.7 52.8 1.0 PA A:GTP501 4.8 43.6 1.0 CG A:ASP98 4.8 39.3 1.0 HA2 A:GLY10 4.8 37.8 1.0 HB A:THR145 4.8 40.4 1.0 HG1 A:THR145 4.9 45.2 1.0 CA A:GLN11 5.0 53.1 1.0

Magnesium binding site 2 out of 5 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 Magnesium with other atoms in the Mg 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:Mg502 b:44.2 occ:1.00 O B:HOH602 2.1 53.8 1.0 O B:HOH619 2.1 45.1 1.0 O C:HOH654 2.1 45.4 1.0 O B:HOH625 2.1 49.2 1.0 OE1 B:GLN11 2.1 53.6 1.0 O1A B:GDP501 2.4 43.7 1.0 HD21 B:ASN101 3.1 46.6 1.0 CD B:GLN11 3.3 67.9 1.0 PA B:GDP501 3.6 35.9 1.0 HB3 B:GLN11 3.7 45.1 1.0 O3A B:GDP501 3.8 39.1 1.0 HB2 B:GLN11 3.9 45.1 1.0 ND2 B:ASN101 3.9 47.1 1.0 OD2 B:ASP179 4.0 54.5 1.0 H8 B:GDP501 4.1 48.3 1.0 HE22 B:GLN11 4.1 68.0 1.0 CB B:GLN11 4.1 45.2 1.0 NE2 B:GLN11 4.2 68.9 1.0 CG B:GLN11 4.3 62.0 1.0 HD22 B:ASN101 4.3 46.6 1.0 C5' B:GDP501 4.4 36.6 1.0 O1B B:GDP501 4.5 39.8 1.0 O5' B:GDP501 4.5 30.6 1.0 OE1 C:GLU254 4.6 80.8 1.0 O2A B:GDP501 4.7 33.2 1.0 HG2 B:GLN11 4.7 61.6 1.0 PB B:GDP501 4.8 39.0 1.0 CG B:ASN101 4.8 52.8 1.0 OD1 B:ASN101 4.8 58.7 1.0 HB3 B:ASP179 5.0 46.2 1.0 CG B:ASP179 5.0 50.9 1.0

Magnesium binding site 3 out of 5 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 Magnesium with other atoms in the Mg 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 C:Mg502 b:33.9 occ:1.00 O C:HOH630 2.1 34.4 1.0 O C:HOH647 2.1 39.1 1.0 O C:HOH604 2.1 31.5 1.0 O C:HOH633 2.1 39.1 1.0 O1B C:GTP501 2.1 32.1 1.0 O1G C:GTP501 2.1 33.2 1.0 PB C:GTP501 3.3 33.6 1.0 HZ1 D:LYS254 3.3 38.8 1.0 PG C:GTP501 3.3 41.1 1.0 HG2 C:GLU71 3.5 58.9 1.0 HB2 C:GLN11 3.5 38.1 1.0 O3B C:GTP501 3.7 41.9 1.0 O3A C:GTP501 3.7 45.5 1.0 H C:GLN11 3.8 32.3 1.0 O2G C:GTP501 3.8 40.2 1.0 OE2 C:GLU71 3.9 51.7 1.0 HB2 C:ASP98 3.9 43.6 1.0 OD1 C:ASP69 4.0 35.7 1.0 NZ D:LYS254 4.0 38.5 1.0 HG3 C:GLU71 4.0 58.9 1.0 HZ2 D:LYS254 4.1 38.8 1.0 OD2 C:ASP69 4.1 43.1 1.0 CG C:GLU71 4.1 58.9 1.0 HB3 C:GLN11 4.3 38.1 1.0 CB C:GLN11 4.3 38.4 1.0 OD2 C:ASP98 4.3 45.6 1.0 HB3 C:ASP98 4.3 43.6 1.0 HZ3 D:LYS254 4.3 38.8 1.0 N C:GLN11 4.5 32.4 1.0 CG C:ASP69 4.5 40.0 1.0 CD C:GLU71 4.5 51.5 1.0 CB C:ASP98 4.5 43.6 1.0 O2B C:GTP501 4.5 39.5 1.0 O3G C:GTP501 4.5 33.2 1.0 O1A C:GTP501 4.6 46.7 1.0 OE1 C:GLN11 4.7 56.4 1.0 PA C:GTP501 4.8 38.4 1.0 HG1 C:THR145 4.8 48.5 1.0 HA2 C:GLY10 4.8 38.4 1.0 HB C:THR145 4.9 39.0 1.0 CG C:ASP98 4.9 45.4 1.0 HG21 C:VAL74 4.9 45.3 1.0 CA C:GLN11 5.0 42.8 1.0

Magnesium binding site 4 out of 5 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 Magnesium with other atoms in the Mg 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 D:Mg502 b:59.0 occ:1.00 O D:HOH604 2.1 61.3 1.0 OE1 D:GLN11 2.1 98.7 1.0 O D:HOH606 2.1 66.6 1.0 O D:HOH603 2.1 55.8 1.0 O1A D:GDP501 2.3 84.7 1.0 CD D:GLN11 3.3 115.3 1.0 PA D:GDP501 3.7 67.6 1.0 H8 D:GDP501 3.7 63.8 1.0 HB3 D:GLN11 3.8 94.6 1.0 HE22 D:GLN11 3.9 114.6 1.0 NE2 D:GLN11 4.0 117.4 1.0 O3A D:GDP501 4.1 68.3 1.0 HB2 D:GLN11 4.2 94.6 1.0 C5' D:GDP501 4.3 70.0 1.0 HD21 D:ASN101 4.3 92.5 1.0 CB D:GLN11 4.3 95.1 1.0 CG D:GLN11 4.3 110.7 1.0 O5' D:GDP501 4.5 50.2 1.0 OD1 D:ASN101 4.5 79.5 1.0 O2A D:GDP501 4.7 54.9 1.0 HG2 D:GLN11 4.7 109.4 1.0 C8 D:GDP501 4.7 63.8 1.0 HE21 D:GLN11 4.9 114.6 1.0 O1B D:GDP501 4.9 68.8 1.0

Magnesium binding site 5 out of 5 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 Magnesium with other atoms in the Mg binding site number 5 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 F:Mg402 b:80.2 occ:1.00 OE2 F:GLU331 2.1 113.9 1.0 OD1 F:ASN333 2.1 100.4 1.0 O1G F:ACP401 2.4 97.6 1.0 O1B F:ACP401 2.5 116.1 1.0 CD F:GLU331 3.0 103.1 1.0 OE1 F:GLU331 3.2 105.2 1.0 CG F:ASN333 3.3 86.8 1.0 HD21 F:ASN333 3.5 102.4 1.0 PG F:ACP401 3.6 127.4 1.0 ND2 F:ASN333 3.8 103.8 1.0 O2G F:ACP401 3.9 96.7 1.0 PB F:ACP401 3.9 112.6 1.0 HZ2 F:LYS74 3.9 86.9 1.0 HZ1 F:LYS74 4.1 86.9 1.0 CG F:GLU331 4.3 82.8 1.0 HG3 F:GLU331 4.4 82.2 1.0 NZ F:LYS74 4.4 86.1 1.0 O2B F:ACP401 4.5 99.8 1.0 C3B F:ACP401 4.5 101.9 1.0 CB F:ASN333 4.5 81.4 1.0 HA F:ASN333 4.5 65.0 1.0 HB3 F:ASN333 4.6 80.4 1.0 HD22 F:ASN333 4.7 102.4 1.0 HZ3 F:LYS74 4.7 86.9 1.0 O3G F:ACP401 4.8 100.7 1.0 HG2 F:GLU331 4.8 82.2 1.0 O2A F:ACP401 5.0 100.5 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