Magnesium in PDB 8a9z: Tubulin-[1,2]Oxazoloisoindole-2E Complex

The structure of Tubulin-[1,2]Oxazoloisoindole-2E Complex, PDB code: 8a9z was solved by A.E.Prota, A.-C.Abel, M.O.Steinmetz, P.Barraja, A.Montalbano, V.Spano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.89 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.5, 155.847, 178.855, 90, 90, 90
R / Rfree (%)	19.9 / 24

The structure of Tubulin-[1,2]Oxazoloisoindole-2E Complex also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-[1,2]Oxazoloisoindole-2E Complex (pdb code 8a9z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-[1,2]Oxazoloisoindole-2E Complex, PDB code: 8a9z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-2E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-[1,2]Oxazoloisoindole-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.9 occ:1.00 O2G A:GTP501 1.9 50.5 1.0 O A:HOH625 2.1 50.8 1.0 O A:HOH622 2.1 49.2 1.0 O A:HOH620 2.2 47.0 1.0 O1B A:GTP501 2.2 46.0 1.0 O A:HOH610 2.2 43.3 1.0 PG A:GTP501 3.1 57.7 1.0 PB A:GTP501 3.2 49.0 1.0 O3B A:GTP501 3.4 60.3 1.0 O3A A:GTP501 3.8 54.4 1.0 OE2 A:GLU71 3.8 58.1 1.0 O3G A:GTP501 3.9 55.6 1.0 NZ B:LYS254 3.9 59.3 1.0 OD1 A:ASP69 4.2 57.1 1.0 CB A:GLN11 4.3 45.9 1.0 CG A:GLU71 4.3 60.8 1.0 O1G A:GTP501 4.3 54.3 1.0 CB A:ASP98 4.5 47.5 1.0 NE2 A:GLN11 4.5 46.6 1.0 OD2 A:ASP69 4.5 57.7 1.0 CD A:GLU71 4.5 60.5 1.0 N A:GLN11 4.5 42.5 1.0 O2B A:GTP501 4.5 53.6 1.0 CG A:ASP98 4.8 68.2 1.0 O1A A:GTP501 4.8 49.5 1.0 OG1 A:THR145 4.8 53.8 1.0 CG A:ASP69 4.8 58.1 1.0 PA A:GTP501 4.9 44.2 1.0 CE B:LYS254 4.9 46.4 1.0 OD2 A:ASP98 4.9 79.3 1.0

Magnesium binding site 2 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-2E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-[1,2]Oxazoloisoindole-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:41.3 occ:1.00 O B:HOH616 2.0 58.5 1.0 O1A B:GDP501 2.2 40.6 1.0 OE1 B:GLN11 2.3 57.2 1.0 O C:HOH603 2.4 51.6 1.0 O B:HOH653 2.5 49.2 1.0 O B:HOH615 2.6 61.5 1.0 O C:HOH693 3.0 55.7 1.0 CD B:GLN11 3.5 59.0 1.0 OD2 B:ASP179 3.5 55.9 1.0 PA B:GDP501 3.6 40.3 1.0 O3A B:GDP501 4.0 46.9 1.0 OE2 C:GLU254 4.1 60.4 1.0 CB B:GLN11 4.2 41.1 1.0 OD1 B:ASN101 4.2 47.9 1.0 C5' B:GDP501 4.3 44.0 1.0 CG B:GLN11 4.3 50.5 1.0 O5' B:GDP501 4.4 45.2 1.0 NE2 B:GLN11 4.4 61.9 1.0 O2A B:GDP501 4.6 41.0 1.0 CG B:ASP179 4.6 54.2 1.0 O1B B:GDP501 4.7 44.2 1.0 C8 B:GDP501 4.9 45.2 1.0

Magnesium binding site 3 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-2E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-[1,2]Oxazoloisoindole-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:47.2 occ:1.00 O3G C:GTP501 2.0 47.6 1.0 O C:HOH620 2.0 44.6 1.0 O C:HOH640 2.1 54.7 1.0 O C:HOH632 2.1 45.5 1.0 O1B C:GTP501 2.2 46.7 1.0 O C:HOH619 2.2 46.6 1.0 PG C:GTP501 3.1 57.3 1.0 PB C:GTP501 3.4 44.0 1.0 O1G C:GTP501 3.6 61.9 1.0 O3B C:GTP501 3.7 48.4 1.0 O3A C:GTP501 3.8 41.6 1.0 OE2 C:GLU71 3.9 58.6 1.0 NZ D:LYS254 3.9 54.3 1.0 CG C:GLU71 4.2 46.6 1.0 CB C:GLN11 4.2 38.3 1.0 OD1 C:ASP69 4.3 46.2 1.0 OD2 C:ASP69 4.4 45.5 1.0 O2G C:GTP501 4.4 48.5 1.0 OE1 C:GLN11 4.4 49.3 1.0 OD2 C:ASP98 4.5 66.0 1.0 CD C:GLU71 4.5 52.2 1.0 N C:GLN11 4.5 38.2 1.0 O2B C:GTP501 4.7 43.2 1.0 CB C:ASP98 4.7 54.5 1.0 CG C:ASP69 4.8 46.2 1.0 OG1 C:THR145 4.9 43.2 1.0 O1A C:GTP501 4.9 43.4 1.0 PA C:GTP501 5.0 40.2 1.0 CE D:LYS254 5.0 59.5 1.0 CA C:GLN11 5.0 38.4 1.0

Magnesium binding site 4 out of 4 in the Tubulin-[1,2]Oxazoloisoindole-2E Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-[1,2]Oxazoloisoindole-2E Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:86.3 occ:1.00 O D:HOH602 2.0 89.8 1.0 OE1 D:GLN11 2.1 103.6 1.0 O D:HOH604 2.1 84.4 1.0 O D:HOH626 2.3 76.2 1.0 O1A D:GDP501 2.3 96.5 1.0 CD D:GLN11 3.2 105.7 1.0 PA D:GDP501 3.8 76.5 1.0 NE2 D:GLN11 3.9 106.2 1.0 O D:HOH617 3.9 72.7 1.0 CB D:GLN11 4.2 88.3 1.0 CG D:GLN11 4.3 94.4 1.0 C5' D:GDP501 4.5 79.9 1.0 O2A D:GDP501 4.5 78.8 1.0 O5' D:GDP501 4.7 76.6 1.0 O3A D:GDP501 4.8 88.8 1.0 O1B D:GDP501 4.8 74.8 1.0 OD1 D:ASN101 4.9 106.3 1.0 C8 D:GDP501 4.9 80.7 1.0 ND2 D:ASN101 4.9 102.4 1.0

M.Barreca, V.Spano, R.Rocca, R.Bivacqua, A.C.Abel, A.Maruca, A.Montalbano, M.V.Raimondi, C.Tarantelli, E.Gaudio, L.Cascione, A.Rinaldi, R.Bai, M.O.Steinmetz, A.E.Prota, S.Alcaro, E.Hamel, F.Bertoni, P.Barraja. Development of [1,2]Oxazoloisoindoles Tubulin Polymerization Inhibitors: Further Chemical Modifications and Potential Therapeutic Effects Against Lymphomas. Eur.J.Med.Chem. V. 243 14744 2022.
ISSN: ISSN 0223-5234
PubMed: 36242921
DOI: 10.1016/J.EJMECH.2022.114744