Magnesium in PDB 6y6d: Tubulin-7-Aminonoscapine Complex

The structure of Tubulin-7-Aminonoscapine Complex, PDB code: 6y6d was solved by M.A.Oliva, A.E.Prota, J.Rodriguez-Salarichs, W.Gu, Y.L.Bennani, J.Jimenez-Barbero, A.Canales, M.O.Steinmetz, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.34 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.360, 157.150, 180.370, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.4

The structure of Tubulin-7-Aminonoscapine Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Tubulin-7-Aminonoscapine Complex (pdb code 6y6d). 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-7-Aminonoscapine Complex, PDB code: 6y6d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-7-Aminonoscapine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-7-Aminonoscapine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.4 occ:1.00 O1G A:GTP501 2.1 35.5 1.0 O A:HOH619 2.1 43.3 1.0 O A:HOH622 2.1 47.9 1.0 O A:HOH649 2.1 42.7 1.0 O A:HOH651 2.1 51.7 1.0 O1B A:GTP501 2.2 38.7 1.0 PG A:GTP501 3.3 48.7 1.0 PB A:GTP501 3.4 47.1 1.0 O3B A:GTP501 3.7 58.4 1.0 O2G A:GTP501 3.8 46.2 1.0 O3A A:GTP501 3.9 48.2 1.0 NZ B:LYS254 4.0 61.5 1.0 OE1 A:GLU71 4.0 71.0 1.0 CB A:GLN11 4.0 43.8 1.0 OD1 A:ASP69 4.1 55.7 1.0 OD2 A:ASP69 4.2 49.0 1.0 N A:GLN11 4.3 45.9 1.0 CG A:GLU71 4.4 67.2 1.0 CB A:ASP98 4.4 52.6 1.0 OD2 A:ASP98 4.5 57.4 1.0 OE1 A:GLN11 4.5 63.1 1.0 O3G A:GTP501 4.5 37.4 1.0 ND2 B:ASN249 4.6 0.3 1.0 O1A A:GTP501 4.6 47.6 1.0 CG A:ASP69 4.6 58.5 1.0 O2B A:GTP501 4.6 54.2 1.0 CD A:GLU71 4.6 68.0 1.0 CG A:ASP98 4.7 60.0 1.0 CA A:GLN11 4.7 47.1 1.0 PA A:GTP501 4.8 46.0 1.0 OD1 B:ASN249 4.9 0.9 1.0

Magnesium binding site 2 out of 5 in the Tubulin-7-Aminonoscapine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-7-Aminonoscapine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:40.8 occ:1.00 O B:HOH625 2.1 46.2 1.0 O C:HOH735 2.1 55.9 1.0 O B:HOH615 2.1 57.5 1.0 O B:HOH668 2.1 51.6 1.0 OE1 B:GLN11 2.1 58.6 1.0 O1A B:GDP501 2.2 46.7 1.0 CD B:GLN11 3.3 57.8 1.0 PA B:GDP501 3.5 43.0 1.0 O3A B:GDP501 3.8 48.3 1.0 OD2 B:ASP179 3.8 55.2 1.0 CB B:GLN11 4.0 46.7 1.0 CG B:GLN11 4.1 54.4 1.0 OD1 B:ASN101 4.3 49.6 1.0 C5' B:GDP501 4.3 43.8 1.0 NE2 B:GLN11 4.3 61.1 1.0 O5' B:GDP501 4.4 43.0 1.0 O C:HOH682 4.4 65.4 1.0 O2A B:GDP501 4.6 44.5 1.0 O1B B:GDP501 4.6 35.8 1.0 C8 B:GDP501 4.8 46.0 1.0 OE1 C:GLU254 4.8 74.3 1.0 CG B:ASP179 4.9 58.1 1.0 PB B:GDP501 4.9 43.0 1.0

Magnesium binding site 3 out of 5 in the Tubulin-7-Aminonoscapine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-7-Aminonoscapine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:38.5 occ:1.00 O1G C:GTP501 2.0 34.4 1.0 O1B C:GTP501 2.0 39.4 1.0 O C:HOH637 2.1 41.4 1.0 O C:HOH670 2.1 38.9 1.0 O C:HOH632 2.1 42.5 1.0 O C:HOH690 2.1 38.5 1.0 PG C:GTP501 3.1 42.5 1.0 PB C:GTP501 3.2 40.9 1.0 O3B C:GTP501 3.5 49.4 1.0 O2G C:GTP501 3.6 41.3 1.0 O3A C:GTP501 3.7 45.5 1.0 NZ D:LYS254 3.9 54.1 1.0 OD1 C:ASP69 4.1 48.5 1.0 OE1 C:GLU71 4.1 54.4 1.0 OD2 C:ASP69 4.2 42.1 1.0 CB C:GLN11 4.2 31.6 1.0 O3G C:GTP501 4.4 38.9 1.0 CG C:GLU71 4.4 53.5 1.0 CB C:ASP98 4.4 48.4 1.0 OD2 C:ASP98 4.4 56.5 1.0 N C:GLN11 4.4 32.7 1.0 O2B C:GTP501 4.4 46.5 1.0 O1A C:GTP501 4.6 39.0 1.0 CG C:ASP69 4.6 50.3 1.0 PA C:GTP501 4.7 39.7 1.0 OE1 C:GLN11 4.7 61.6 1.0 ND2 D:ASN249 4.8 0.2 1.0 CD C:GLU71 4.8 55.2 1.0 OD1 D:ASN249 4.8 0.3 1.0 CG C:ASP98 4.8 53.5 1.0 CA C:GLN11 4.9 36.9 1.0 CE D:LYS254 4.9 51.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-7-Aminonoscapine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-7-Aminonoscapine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:79.3 occ:1.00 O D:HOH642 2.1 68.2 1.0 O D:HOH603 2.1 76.0 1.0 OE1 D:GLN11 2.3 74.8 1.0 OD2 D:ASP179 2.3 91.0 1.0 O1A D:GDP501 2.8 62.7 1.0 CD D:GLN11 3.4 76.7 1.0 CG D:ASP179 3.6 0.5 1.0 C5' D:GDP501 4.1 64.7 1.0 NE2 D:GLN11 4.1 77.0 1.0 PA D:GDP501 4.2 64.8 1.0 OD1 D:ASP179 4.3 0.9 1.0 C8 D:GDP501 4.3 56.7 1.0 CG D:GLN11 4.5 74.5 1.0 CB D:ASP179 4.5 0.3 1.0 O5' D:GDP501 4.6 66.4 1.0 O3A D:GDP501 4.8 55.9 1.0 CB D:GLN11 4.8 72.6 1.0 N7 D:GDP501 5.0 53.4 1.0

Magnesium binding site 5 out of 5 in the Tubulin-7-Aminonoscapine Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-7-Aminonoscapine Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:92.8 occ:1.00 ND2 F:ASN333 1.9 1.0 1.0 O F:HOH802 2.0 86.3 1.0 OE2 F:GLU331 2.1 0.3 1.0 OE1 F:GLU331 2.2 0.4 1.0 OD1 F:ASN333 2.2 0.1 1.0 O3G F:ACP701 2.3 0.4 1.0 CG F:ASN333 2.3 0.7 1.0 CD F:GLU331 2.4 0.1 1.0 O1B F:ACP701 3.2 0.3 1.0 PG F:ACP701 3.5 0.7 1.0 O1G F:ACP701 3.6 0.3 1.0 CB F:ASN333 3.8 0.2 1.0 CG F:GLU331 3.9 0.2 1.0 PB F:ACP701 4.3 0.7 1.0 C3B F:ACP701 4.3 0.8 1.0 CA F:ASN333 4.4 91.7 1.0 N F:ASN333 4.7 82.4 1.0 CB F:GLU331 4.8 91.2 1.0 O2G F:ACP701 4.8 0.8 1.0 OD2 F:ASP318 4.8 94.8 1.0 CE F:LYS74 4.8 94.3 1.0 O3A F:ACP701 4.9 0.6 1.0 O F:VAL332 4.9 69.3 1.0 C F:VAL332 5.0 70.7 1.0 NZ F:LYS74 5.0 0.9 1.0

M.A.Oliva, A.E.Prota, J.Rodriguez-Salarichs, Y.L.Bennani, J.Jimenez-Barbero, K.Bargsten, A.Canales, M.O.Steinmetz, J.F.Diaz. Structural Basis of Noscapine Activation For Tubulin Binding. J.Med.Chem. V. 63 8495 2020.
ISSN: ISSN 0022-2623
PubMed: 32657585
DOI: 10.1021/ACS.JMEDCHEM.0C00855