Magnesium in PDB 4yj2: Crystal Structure of Tubulin Bound to Mi-181

The structure of Crystal Structure of Tubulin Bound to Mi-181, PDB code: 4yj2 was solved by D.E.Mcnamara, J.Z.Torres, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	90.72 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.830, 157.650, 181.030, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 23.1

The structure of Crystal Structure of Tubulin Bound to Mi-181 also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin Bound to Mi-181 (pdb code 4yj2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Tubulin Bound to Mi-181, PDB code: 4yj2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Tubulin Bound to Mi-181


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin Bound to Mi-181 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:56.9 occ:1.00 O2G A:GTP501 2.0 54.4 1.0 O A:HOH618 2.1 45.1 1.0 O A:HOH615 2.1 45.5 1.0 O A:HOH611 2.1 55.0 1.0 O A:HOH604 2.1 45.0 1.0 O2B A:GTP501 2.2 52.2 1.0 PG A:GTP501 3.3 51.3 1.0 PB A:GTP501 3.4 51.4 1.0 OE1 A:GLU71 3.6 77.9 1.0 O3B A:GTP501 3.8 70.4 1.0 O3G A:GTP501 3.9 51.7 1.0 NZ B:LYS254 4.0 64.4 1.0 CG A:GLU71 4.0 69.5 1.0 OD2 A:ASP98 4.0 53.4 1.0 OD1 A:ASP69 4.1 56.9 1.0 O2A A:GTP501 4.1 76.8 1.0 O3A A:GTP501 4.2 63.8 1.0 CB A:GLN11 4.2 53.6 1.0 CB A:ASP98 4.2 52.1 1.0 CD A:GLU71 4.3 70.1 1.0 OD2 A:ASP69 4.3 49.0 1.0 OE1 A:GLN11 4.5 62.8 1.0 O1G A:GTP501 4.5 60.3 1.0 N A:GLN11 4.5 54.7 1.0 CG A:ASP98 4.5 52.4 1.0 O1B A:GTP501 4.6 57.5 1.0 CG A:ASP69 4.7 56.4 1.0 PA A:GTP501 4.8 58.8 1.0 ND2 B:ASN249 4.9 0.1 1.0 CA A:GLN11 5.0 56.6 1.0 OG1 A:THR145 5.0 50.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tubulin Bound to Mi-181


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin Bound to Mi-181 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:42.6 occ:1.00 O B:HOH621 2.1 41.5 1.0 OE1 B:GLN11 2.1 51.3 1.0 O B:HOH605 2.1 66.4 1.0 O B:HOH626 2.1 50.5 1.0 O C:HOH632 2.1 42.0 1.0 O2A B:GDP501 2.3 52.5 1.0 CD B:GLN11 3.2 56.8 1.0 PA B:GDP501 3.5 47.0 1.0 OD2 B:ASP179 3.7 57.4 1.0 O3A B:GDP501 3.8 54.9 1.0 CB B:GLN11 4.0 46.2 1.0 NE2 B:GLN11 4.1 64.2 1.0 CG B:GLN11 4.2 55.1 1.0 OD1 B:ASN101 4.3 51.7 1.0 O C:HOH605 4.3 57.1 1.0 C5' B:GDP501 4.4 41.6 1.0 O5' B:GDP501 4.4 39.6 1.0 O2B B:GDP501 4.6 43.4 1.0 OE1 C:GLU254 4.6 59.8 1.0 O1A B:GDP501 4.6 49.6 1.0 CG B:ASP179 4.8 56.5 1.0 PB B:GDP501 4.8 45.1 1.0 C8 B:GDP501 5.0 43.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tubulin Bound to Mi-181


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin Bound to Mi-181 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg505 b:46.1 occ:1.00 O2G C:GTP501 2.0 46.1 1.0 O C:HOH629 2.1 37.2 1.0 O C:HOH620 2.1 51.3 1.0 O C:HOH611 2.1 32.2 1.0 O C:HOH637 2.1 37.8 1.0 O2B C:GTP501 2.1 45.6 1.0 PB C:GTP501 3.1 42.1 1.0 PG C:GTP501 3.1 77.0 1.0 O3A C:GTP501 3.4 67.6 1.0 O3G C:GTP501 3.5 49.0 1.0 O3B C:GTP501 3.5 75.8 1.0 NZ D:LYS254 3.8 58.9 1.0 OE1 C:GLU71 4.1 72.9 1.0 CB C:GLN11 4.2 47.8 1.0 CG C:GLU71 4.3 60.6 1.0 OD1 C:ASP69 4.3 58.9 1.0 O1G C:GTP501 4.4 54.5 1.0 OD2 C:ASP69 4.4 51.5 1.0 OE1 C:GLN11 4.4 75.7 1.0 OD2 C:ASP98 4.4 64.7 1.0 O1B C:GTP501 4.4 45.4 1.0 CB C:ASP98 4.5 50.8 1.0 N C:GLN11 4.5 41.0 1.0 PA C:GTP501 4.6 42.5 1.0 CD C:GLU71 4.7 65.9 1.0 O2A C:GTP501 4.7 50.2 1.0 ND2 D:ASN249 4.7 69.4 0.6 CG C:ASP69 4.8 53.6 1.0 CG C:ASP98 5.0 61.3 1.0 CA C:GLN11 5.0 47.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tubulin Bound to Mi-181


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin Bound to Mi-181 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:87.1 occ:1.00 O D:HOH608 2.1 75.8 1.0 OE1 D:GLN11 2.1 0.7 1.0 O2A D:GDP501 2.3 95.4 1.0 O D:HOH602 3.1 67.7 1.0 CD D:GLN11 3.3 0.8 1.0 PA D:GDP501 3.5 76.0 1.0 OD2 D:ASP179 3.7 0.1 1.0 O1A D:GDP501 3.7 66.8 1.0 ND2 D:ASN101 4.0 84.2 1.0 CB D:GLN11 4.0 94.7 1.0 O2B D:GDP501 4.1 65.0 1.0 NE2 D:GLN11 4.2 0.9 1.0 CG D:GLN11 4.2 99.8 1.0 O3B D:GDP501 4.6 64.6 1.0 O3A D:GDP501 4.6 0.1 1.0 O5' D:GDP501 4.6 79.5 1.0 C5' D:GDP501 4.6 76.1 1.0 PB D:GDP501 4.7 69.2 1.0 CG D:ASP179 4.9 0.2 1.0 CG D:ASN101 4.9 0.9 1.0 OD1 D:ASN101 4.9 0.2 1.0

D.E.Mcnamara, S.Senese, T.O.Yeates, J.Z.Torres. Structures of Potent Anticancer Compounds Bound to Tubulin. Protein Sci. 2015.
ISSN: ESSN 1469-896X
PubMed: 25970265
DOI: 10.1002/PRO.2704