Magnesium in PDB 8r6o: Tubulin-4AZA2996 Complex

The structure of Tubulin-4AZA2996 Complex, PDB code: 8r6o was solved by J.Herman, E.Vanstreels, D.Bardiot, A.E.Prota, N.Olieric, L.-J.Gao, T.Vercruysse, T.Daems, M.Waer, P.Herdewijn, T.Louat, M.O.Steinmetz, S.Dejonghe, B.Sprangers, D.Daelemans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.20 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.327, 158.182, 182.681, 90, 90, 90
R / Rfree (%)	20.8 / 23.3

The structure of Tubulin-4AZA2996 Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-4AZA2996 Complex (pdb code 8r6o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-4AZA2996 Complex, PDB code: 8r6o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.2 occ:1.00 O1G A:GTP501 2.0 44.4 1.0 O A:HOH627 2.1 54.7 1.0 O A:HOH605 2.1 45.4 1.0 O1B A:GTP501 2.1 39.3 1.0 O A:HOH614 2.2 49.7 1.0 O A:HOH626 2.3 47.4 1.0 PG A:GTP501 3.2 45.7 1.0 PB A:GTP501 3.3 39.1 1.0 O3B A:GTP501 3.6 56.2 1.0 OE1 A:GLU71 3.8 66.5 1.0 O3A A:GTP501 3.8 48.4 1.0 O2G A:GTP501 3.9 53.1 1.0 CB A:GLN11 4.0 45.9 1.0 OD1 A:ASP69 4.2 56.7 1.0 OD2 A:ASP69 4.3 56.0 1.0 O3G A:GTP501 4.4 43.3 1.0 CB A:ASP98 4.4 57.0 1.0 N A:GLN11 4.4 47.2 1.0 OE1 A:GLN11 4.5 51.8 1.0 NZ B:LYS254 4.5 62.9 1.0 OD2 A:ASP98 4.5 61.8 1.0 O2B A:GTP501 4.6 49.0 1.0 O1A A:GTP501 4.7 45.3 1.0 CG A:ASP69 4.7 57.6 1.0 PA A:GTP501 4.8 42.8 1.0 CD A:GLU71 4.8 65.6 1.0 CG A:ASP98 4.8 60.6 1.0 CA A:GLN11 4.8 49.4 1.0 CD A:GLN11 5.0 48.4 1.0

Magnesium binding site 2 out of 5 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:57.6 occ:1.00 O B:HOH606 2.1 48.9 1.0 O B:HOH668 2.2 61.6 1.0 O B:HOH604 2.2 59.6 1.0 O1B B:GDP501 3.0 43.8 1.0 OE1 B:GLN11 3.3 55.4 1.0 O C:HOH619 3.4 60.5 1.0 O B:HOH601 3.5 46.5 1.0 O3A B:GDP501 3.6 47.1 1.0 O1A B:GDP501 3.6 47.5 1.0 OE2 B:GLU71 3.7 76.8 1.0 PB B:GDP501 3.8 38.5 1.0 CB B:GLN11 3.9 49.7 1.0 O B:HOH641 3.9 42.9 1.0 O B:HOH609 4.0 43.3 1.0 O B:HOH623 4.2 54.5 1.0 O B:HOH652 4.2 52.5 1.0 PA B:GDP501 4.2 41.7 1.0 CD B:GLN11 4.2 56.5 1.0 O3B B:GDP501 4.3 41.5 1.0 OD1 B:ASN101 4.5 50.1 1.0 CG B:GLN11 4.7 52.6 1.0 CD B:GLU71 4.7 69.5 1.0 O C:HOH735 4.8 57.0 1.0 N B:GLN11 4.9 48.8 1.0 O2A B:GDP501 5.0 40.9 1.0 CA B:GLN11 5.0 47.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.6 occ:1.00 O C:HOH651 1.9 39.0 1.0 O1G C:GTP501 1.9 35.7 1.0 O C:HOH617 2.0 41.5 1.0 O C:HOH649 2.0 40.5 1.0 O C:HOH650 2.1 40.6 1.0 O1B C:GTP501 2.3 35.4 1.0 PG C:GTP501 3.2 38.3 1.0 PB C:GTP501 3.4 34.5 1.0 O3B C:GTP501 3.6 43.4 1.0 O2G C:GTP501 3.7 40.0 1.0 O3A C:GTP501 3.8 41.5 1.0 OE2 C:GLU71 3.9 49.4 1.0 OD1 C:ASP69 4.1 43.8 1.0 CG C:GLU71 4.1 46.9 1.0 OD2 C:ASP69 4.2 43.4 1.0 OD2 C:ASP98 4.2 47.2 1.0 CB C:GLN11 4.2 38.9 1.0 CB C:ASP98 4.3 46.8 1.0 O3G C:GTP501 4.4 37.8 1.0 N C:GLN11 4.5 36.6 1.0 CD C:GLU71 4.5 46.0 1.0 CG C:ASP69 4.6 42.7 1.0 O2B C:GTP501 4.7 40.0 1.0 CG C:ASP98 4.7 48.7 1.0 OE1 C:GLN11 4.7 45.0 1.0 NZ D:LYS254 4.9 52.5 1.0 O1A C:GTP501 4.9 38.4 1.0 PA C:GTP501 5.0 37.1 1.0 CA C:GLN11 5.0 38.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:80.4 occ:1.00 OE1 D:GLN11 2.3 89.2 1.0 O1A D:GDP501 2.4 80.9 1.0 O D:HOH611 2.6 75.4 1.0 CD D:GLN11 3.6 89.0 1.0 PA D:GDP501 3.7 76.9 1.0 C5' D:GDP501 4.0 77.4 1.0 OD1 D:ASN101 4.1 94.6 1.0 O3A D:GDP501 4.1 78.7 1.0 NE2 D:GLN11 4.3 92.7 1.0 O5' D:GDP501 4.4 76.0 1.0 CB D:GLN11 4.6 82.0 1.0 ND2 D:ASN101 4.6 101.1 1.0 CG D:GLN11 4.6 84.9 1.0 CG D:ASN101 4.8 97.5 1.0 O2A D:GDP501 4.9 75.7 1.0 O1B D:GDP501 5.0 77.5 1.0

Magnesium binding site 5 out of 5 in the Tubulin-4AZA2996 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-4AZA2996 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:93.8 occ:1.00 OE2 F:GLU331 2.3 105.2 1.0 O1B F:ACP701 2.4 109.5 1.0 ND2 F:ASN333 2.5 89.5 1.0 O3G F:ACP701 2.6 101.5 1.0 CD F:GLU331 3.1 97.0 1.0 OE1 F:GLU331 3.1 97.5 1.0 PB F:ACP701 3.5 115.2 1.0 PG F:ACP701 3.6 116.0 1.0 CG F:ASN333 3.6 87.7 1.0 C3B F:ACP701 3.7 117.1 1.0 NZ F:LYS74 3.8 107.2 1.0 OD1 F:ASN333 4.0 87.6 1.0 O1G F:ACP701 4.2 102.4 1.0 O3A F:ACP701 4.4 109.5 1.0 CG F:GLU331 4.5 88.2 1.0 O2B F:ACP701 4.8 115.0 1.0 CE F:LYS74 4.9 105.6 1.0 CB F:ASN333 4.9 79.4 1.0 O2A F:ACP701 5.0 111.8 1.0 O2G F:ACP701 5.0 110.0 1.0

J.Herman, E.Vanstreels, D.Bardiot, A.E.Prota, N.Gaillard, L.J.Gao, T.Vercruysse, L.Persoons, T.Daems, M.Waer, P.Herdewijn, T.Louat, M.O.Steinmetz, S.De Jonghe, B.Sprangers, D.Daelemans. 3-Nitropyridine Analogues As Novel Microtubule-Targeting Agents. Plos One V. 19 07153 2024.
ISSN: ESSN 1932-6203
PubMed: 39509402
DOI: 10.1371/JOURNAL.PONE.0307153