Magnesium in PDB 5jvd: Tubulin-TUB092 Complex

The structure of Tubulin-TUB092 Complex, PDB code: 5jvd was solved by M.-D.Canela, S.Noppen, O.Bueno, A.E.Prota, K.Bargsten, G.Saez-Calvo, M.-L.Jimeno, M.Benkheil, D.Ribatti, S.Velazquez, M.-J.Camarasa, J.F.Diaz, M.O.Steinmetz, E.-M.Priego, M.-J.Perez-Perez, S.Liekens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.251, 156.317, 180.614, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.8

The structure of Tubulin-TUB092 Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-TUB092 Complex (pdb code 5jvd). 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-TUB092 Complex, PDB code: 5jvd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:75.0 occ:1.00 O A:HOH601 1.6 53.1 1.0 O2G A:GTP501 1.7 51.9 1.0 O A:HOH625 1.8 64.4 1.0 O1B A:GTP501 2.4 46.0 1.0 O A:HOH606 2.9 51.5 1.0 PG A:GTP501 3.0 51.6 1.0 O A:HOH634 3.0 50.6 1.0 O A:HOH616 3.1 49.0 1.0 PB A:GTP501 3.1 46.9 1.0 O3A A:GTP501 3.2 66.0 1.0 O3B A:GTP501 3.5 73.0 1.0 O1G A:GTP501 3.8 53.9 1.0 O1A A:GTP501 3.9 48.1 1.0 O3G A:GTP501 4.1 43.3 1.0 PA A:GTP501 4.2 48.6 1.0 CB A:GLN11 4.2 54.9 1.0 OE2 A:GLU71 4.4 82.5 1.0 OE1 A:GLN11 4.5 59.0 1.0 O A:HOH610 4.5 53.1 1.0 O2B A:GTP501 4.6 50.5 1.0 OD2 A:ASP98 4.6 62.8 1.0 N A:GLN11 4.7 48.1 1.0 CB A:ASP98 4.7 55.8 1.0 CG A:ASP98 4.8 60.4 1.0 O2A A:GTP501 4.9 42.4 1.0 OD1 A:ASP69 4.9 57.5 1.0 CD A:GLN11 5.0 52.7 1.0

Magnesium binding site 2 out of 5 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:45.9 occ:1.00 O1A B:GDP502 2.1 43.2 1.0 O C:HOH653 2.1 71.8 1.0 O B:HOH606 2.2 63.9 1.0 OE1 B:GLN11 2.4 68.3 1.0 O B:HOH627 2.7 65.5 1.0 O B:HOH603 2.7 70.7 1.0 O B:HOH635 3.0 59.8 1.0 PA B:GDP502 3.4 46.2 1.0 O B:HOH643 3.5 80.0 1.0 CD B:GLN11 3.6 67.7 1.0 OD2 B:ASP179 3.6 67.2 1.0 O3A B:GDP502 3.6 61.8 1.0 ND2 B:ASN101 4.1 46.5 1.0 CB B:GLN11 4.2 43.1 1.0 C5' B:GDP502 4.2 42.7 1.0 O5' B:GDP502 4.3 39.8 1.0 CG B:GLN11 4.3 59.4 1.0 O2A B:GDP502 4.5 46.6 1.0 NE2 B:GLN11 4.6 71.2 1.0 CG B:ASP179 4.6 69.2 1.0 OE1 C:GLU254 4.6 87.8 1.0 C8 B:GDP502 4.7 41.1 1.0 O1B B:GDP502 4.8 35.8 1.0 PB B:GDP502 4.9 47.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.9 occ:1.00 O C:HOH622 2.0 44.4 1.0 O C:HOH610 2.0 49.4 1.0 O C:HOH643 2.1 55.9 1.0 O1G C:GTP501 2.2 34.0 1.0 O1B C:GTP501 2.2 31.6 1.0 O C:HOH618 2.3 40.1 1.0 PB C:GTP501 3.4 40.1 1.0 PG C:GTP501 3.5 45.6 1.0 OE1 C:GLU71 3.8 72.0 1.0 O3A C:GTP501 3.8 68.5 1.0 O3B C:GTP501 3.9 57.1 1.0 CB C:GLN11 4.0 42.9 1.0 O2G C:GTP501 4.1 53.9 1.0 OD1 C:ASP69 4.2 42.8 1.0 OD2 C:ASP69 4.2 46.8 1.0 CG C:GLU71 4.2 57.9 1.0 N C:GLN11 4.4 46.5 1.0 O1A C:GTP501 4.4 40.5 1.0 OE1 C:GLN11 4.5 51.8 1.0 CD C:GLU71 4.5 65.4 1.0 CB C:ASP98 4.5 47.1 1.0 OD2 C:ASP98 4.6 59.5 1.0 O3G C:GTP501 4.6 37.3 1.0 CG C:ASP69 4.6 47.2 1.0 O2B C:GTP501 4.7 38.2 1.0 PA C:GTP501 4.7 43.0 1.0 CA C:GLN11 4.8 44.7 1.0 CG C:ASP98 5.0 56.3 1.0

Magnesium binding site 4 out of 5 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:75.3 occ:1.00 O D:HOH617 2.4 63.0 1.0 OE1 D:GLN11 2.7 84.3 1.0 O1A D:GDP501 2.7 83.6 1.0 OD2 D:ASP179 3.1 0.8 1.0 O3A D:GDP501 3.7 92.2 1.0 PA D:GDP501 3.7 82.6 1.0 ND2 D:ASN101 3.9 85.3 1.0 CD D:GLN11 3.9 87.7 1.0 C5' D:GDP501 4.0 69.5 1.0 CG D:ASP179 4.2 0.5 1.0 O5' D:GDP501 4.3 76.9 1.0 CB D:GLN11 4.7 81.6 1.0 O1B D:GDP501 4.7 68.9 1.0 CB D:ASP179 4.7 0.4 1.0 CG D:ASN101 4.8 90.2 1.0 CG D:GLN11 4.8 84.2 1.0 OD1 D:ASN101 4.8 93.0 1.0 NE2 D:GLN11 4.8 89.3 1.0 PB D:GDP501 4.8 73.8 1.0

Magnesium binding site 5 out of 5 in the Tubulin-TUB092 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-TUB092 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:0.7 occ:1.00 O1B F:ACP402 2.7 0.6 1.0 OE2 F:GLU331 2.7 0.9 1.0 OD1 F:ASN333 2.7 0.1 1.0 O1G F:ACP402 2.7 0.2 1.0 OE1 F:GLU331 2.9 0.7 1.0 CD F:GLU331 3.2 0.6 1.0 NZ F:LYS74 3.5 0.9 1.0 CG F:ASN333 3.8 0.9 1.0 PB F:ACP402 3.9 0.3 1.0 PG F:ACP402 4.1 0.4 1.0 ND2 F:ASN333 4.3 0.6 1.0 O2B F:ACP402 4.3 0.2 1.0 O2G F:ACP402 4.5 0.1 1.0 CE F:LYS74 4.5 0.1 1.0 C3B F:ACP402 4.6 0.2 1.0 O F:HOH503 4.6 79.6 1.0 CG F:GLU331 4.7 0.0 1.0

M.D.Canela, S.Noppen, O.Bueno, A.E.Prota, K.Bargsten, G.Saez-Calvo, M.L.Jimeno, M.Benkheil, D.Ribatti, S.Velazquez, M.J.Camarasa, J.F.Diaz, M.O.Steinmetz, E.M.Priego, M.J.Perez-Perez, S.Liekens. Antivascular and Antitumor Properties of the Tubulin-Binding Chalcone TUB091. Oncotarget V. 8 14325 2017.
ISSN: ESSN 1949-2553
PubMed: 27224920
DOI: 10.18632/ONCOTARGET.9527