Magnesium in PDB 6f7c: Tubulin-Compound 12 Complex

The structure of Tubulin-Compound 12 Complex, PDB code: 6f7c was solved by T.Muehlethaler, A.E.Prota, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.54 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.810, 157.900, 180.770, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 24.3

The structure of Tubulin-Compound 12 Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-Compound 12 Complex (pdb code 6f7c). 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-Compound 12 Complex, PDB code: 6f7c:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:47.1 occ:1.00 O A:HOH646 2.0 45.3 1.0 O2G A:GTP501 2.0 40.9 1.0 O A:HOH654 2.2 45.6 1.0 O A:HOH618 2.3 49.5 1.0 O A:HOH678 2.3 47.1 1.0 O1B A:GTP501 2.3 36.8 1.0 PG A:GTP501 3.2 48.5 1.0 PB A:GTP501 3.3 46.8 1.0 HB2 A:GLN11 3.4 58.4 1.0 O3B A:GTP501 3.6 60.0 1.0 H A:GLN11 3.6 54.3 1.0 HG2 A:GLU71 3.7 91.3 1.0 O1G A:GTP501 3.7 49.2 1.0 HB2 A:ASP98 3.8 67.9 1.0 O3A A:GTP501 3.8 52.4 1.0 O B:HOH690 3.9 67.8 1.0 OE2 A:GLU71 4.0 62.5 1.0 OD1 A:ASP69 4.1 49.5 1.0 HB3 A:GLN11 4.2 58.4 1.0 HG3 A:GLU71 4.2 91.3 1.0 OD2 A:ASP69 4.2 52.9 1.0 HZ3 B:LYS254 4.2 95.0 1.0 CB A:GLN11 4.2 41.9 1.0 HB3 A:ASP98 4.3 67.9 1.0 OD2 A:ASP98 4.3 54.7 1.0 CG A:GLU71 4.3 60.3 1.0 N A:GLN11 4.4 39.0 1.0 CB A:ASP98 4.4 53.1 1.0 O3G A:GTP501 4.4 43.8 1.0 O1A A:GTP501 4.6 48.0 1.0 CG A:ASP69 4.6 51.4 1.0 O2B A:GTP501 4.6 50.4 1.0 CD A:GLU71 4.6 62.5 1.0 HZ1 B:LYS254 4.7 95.0 1.0 HA2 A:GLY10 4.7 61.9 1.0 CG A:ASP98 4.7 53.4 1.0 HG1 A:THR145 4.7 59.7 1.0 PA A:GTP501 4.8 45.5 1.0 HB A:THR145 4.8 59.8 1.0 HG21 A:VAL74 4.9 79.6 1.0 NZ B:LYS254 4.9 50.0 1.0 OE1 A:GLN11 4.9 46.1 1.0 CA A:GLN11 4.9 41.3 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:41.1 occ:1.00 O B:HOH661 2.2 45.0 1.0 OE1 B:GLN11 2.3 40.9 1.0 O1A B:GDP501 2.3 43.1 1.0 O C:HOH617 2.4 57.9 1.0 O B:HOH688 2.4 51.0 1.0 O B:HOH652 2.7 52.0 1.0 O B:HOH741 3.2 70.5 1.0 CD B:GLN11 3.4 42.6 1.0 HB3 B:GLN11 3.5 53.7 1.0 PA B:GDP501 3.6 43.0 1.0 H8 B:GDP501 3.7 59.8 1.0 O3A B:GDP501 3.8 45.1 1.0 OD2 B:ASP179 4.0 45.4 1.0 HB2 B:GLN11 4.0 53.7 1.0 CB B:GLN11 4.1 41.8 1.0 CG B:GLN11 4.2 43.4 1.0 HG2 B:GLN11 4.3 63.8 1.0 C5' B:GDP501 4.4 46.5 1.0 HD21 B:ASN101 4.4 55.3 1.0 O5' B:GDP501 4.4 46.2 1.0 OD1 B:ASN101 4.5 39.2 1.0 O C:HOH620 4.5 59.5 1.0 NE2 B:GLN11 4.5 44.0 1.0 OE1 C:GLU254 4.5 44.3 1.0 HE22 B:GLN11 4.5 62.2 1.0 O1B B:GDP501 4.7 39.9 1.0 C8 B:GDP501 4.7 51.1 1.0 O2A B:GDP501 4.7 40.0 1.0 CG B:ASP179 4.9 45.2 1.0 PB B:GDP501 4.9 43.0 1.0 O B:HOH744 4.9 67.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:43.7 occ:1.00 O C:HOH643 2.0 39.0 1.0 O1G C:GTP501 2.0 41.2 1.0 O C:HOH671 2.1 48.8 1.0 O C:HOH790 2.2 40.9 1.0 O1B C:GTP501 2.2 40.5 1.0 O C:HOH614 2.3 45.0 1.0 PG C:GTP501 3.1 47.0 1.0 HZ3 D:LYS254 3.1 66.4 1.0 PB C:GTP501 3.2 47.3 1.0 O3B C:GTP501 3.5 50.4 1.0 HB2 C:GLN11 3.5 45.7 1.0 O2G C:GTP501 3.5 47.0 1.0 O3A C:GTP501 3.7 50.8 1.0 H C:GLN11 3.7 44.9 1.0 HG2 C:GLU71 3.7 56.8 1.0 HB2 C:ASP98 3.7 59.4 1.0 NZ D:LYS254 3.9 50.5 1.0 HZ1 D:LYS254 3.9 66.4 1.0 HB3 C:GLN11 4.0 45.7 1.0 HG3 C:GLU71 4.1 56.8 1.0 OD1 C:ASP69 4.1 41.2 1.0 OD2 C:ASP69 4.1 42.8 1.0 OE2 C:GLU71 4.1 48.9 1.0 HZ2 D:LYS254 4.2 66.4 1.0 CB C:GLN11 4.2 36.6 1.0 HE21 C:GLN11 4.3 59.7 1.0 OD2 C:ASP98 4.3 47.6 1.0 CG C:GLU71 4.3 48.0 1.0 HB3 C:ASP98 4.3 59.4 1.0 CB C:ASP98 4.4 46.1 1.0 N C:GLN11 4.4 35.8 1.0 O3G C:GTP501 4.4 42.9 1.0 O2B C:GTP501 4.5 47.0 1.0 CG C:ASP69 4.6 41.9 1.0 O1A C:GTP501 4.6 44.0 1.0 HG1 C:THR145 4.7 51.4 1.0 CG C:ASP98 4.7 47.1 1.0 CD C:GLU71 4.7 49.0 1.0 PA C:GTP501 4.7 40.6 1.0 HA2 C:GLY10 4.8 51.3 1.0 HB C:THR145 4.8 55.5 1.0 O C:HOH786 4.8 75.1 1.0 NE2 C:GLN11 4.8 38.2 1.0 CA C:GLN11 4.9 36.2 1.0 HG21 C:VAL74 5.0 55.1 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:68.8 occ:1.00 OE1 D:GLN11 2.0 84.1 1.0 O D:HOH657 2.3 66.0 1.0 O D:HOH608 2.4 65.1 1.0 O1A D:GDP501 2.4 84.5 1.0 CD D:GLN11 3.1 83.6 1.0 H8 D:GDP501 3.2 93.4 1.0 HB3 D:GLN11 3.8 0.5 1.0 HE22 D:GLN11 3.8 0.5 1.0 O D:HOH621 3.9 71.9 1.0 PA D:GDP501 3.9 72.2 1.0 NE2 D:GLN11 3.9 86.2 1.0 CG D:GLN11 4.1 80.1 1.0 HG2 D:GLN11 4.2 1.0 1.0 C8 D:GDP501 4.2 79.1 1.0 CB D:GLN11 4.3 78.5 1.0 HB2 D:GLN11 4.4 0.5 1.0 C5' D:GDP501 4.4 76.7 1.0 O3A D:GDP501 4.5 69.8 1.0 H2' D:GDP501 4.6 91.6 1.0 N7 D:GDP501 4.7 84.3 1.0 O5' D:GDP501 4.7 72.8 1.0 HE21 D:GLN11 4.7 0.5 1.0 O2A D:GDP501 4.8 70.5 1.0 HG3 D:GLN11 4.9 1.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Compound 12 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Compound 12 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:0.1 occ:1.00 HD21 F:ASN333 2.0 0.8 1.0 O1B F:ACP401 2.2 1.0 1.0 OE2 F:GLU331 2.6 96.3 1.0 O1G F:ACP401 2.6 0.4 1.0 ND2 F:ASN333 2.7 76.1 1.0 HD22 F:ASN333 2.7 0.8 1.0 HZ3 F:LYS74 3.2 0.5 1.0 OE1 F:GLU331 3.2 95.7 1.0 CD F:GLU331 3.3 96.1 1.0 PB F:ACP401 3.4 0.3 1.0 PG F:ACP401 3.8 0.8 1.0 C3B F:ACP401 3.9 0.4 1.0 CG F:ASN333 3.9 75.8 1.0 NZ F:LYS74 3.9 78.9 1.0 HZ2 F:LYS74 4.0 0.5 1.0 O2B F:ACP401 4.0 1.0 1.0 H3B2 F:ACP401 4.0 0.2 1.0 OD1 F:ASN333 4.4 75.9 1.0 HZ1 F:LYS74 4.4 0.5 1.0 HE3 F:LYS74 4.7 0.6 1.0 CG F:GLU331 4.7 96.3 1.0 O3G F:ACP401 4.7 0.7 1.0 O3A F:ACP401 4.8 0.7 1.0 O2G F:ACP401 4.8 0.4 1.0 H3B1 F:ACP401 4.8 0.2 1.0 CE F:LYS74 4.9 79.2 1.0 HB3 F:ASN333 5.0 99.2 1.0 HG2 F:GLU331 5.0 0.7 1.0

N.M.Cury, T.Muhlethaler, A.B.A.Laranjeira, R.R.Canevarolo, P.P.Zenatti, D.Lucena-Agell, I.Barasoain, C.Song, D.Sun, S.Dovat, R.A.Yunes, A.E.Prota, M.O.Steinmetz, J.F.Diaz, J.A.Yunes. Structural Basis of Colchicine-Site Targeting Acylhydrazones Active Against Multidrug-Resistant Acute Lymphoblastic Leukemia. Iscience V. 21 95 2019.
ISSN: ESSN 2589-0042
PubMed: 31655259
DOI: 10.1016/J.ISCI.2019.10.003