Magnesium in PDB 4yj3: Crystal Structure of Tubulin Bound to Compound 2

The structure of Crystal Structure of Tubulin Bound to Compound 2, PDB code: 4yj3 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)	91.07 / 3.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.200, 157.690, 181.920, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 27.9

The structure of Crystal Structure of Tubulin Bound to Compound 2 also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin Bound to Compound 2 (pdb code 4yj3). 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 Compound 2, PDB code: 4yj3:
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 Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:0.4 occ:1.00 O1B A:GTP502 2.0 83.5 1.0 O A:HOH602 2.1 84.0 1.0 O A:HOH601 2.1 90.7 1.0 O A:HOH603 2.1 82.2 1.0 OE1 A:GLU71 2.1 90.9 1.0 O2G A:GTP502 2.9 83.5 1.0 CD A:GLU71 3.1 92.5 1.0 PB A:GTP502 3.4 83.5 1.0 CG A:GLU71 3.7 92.4 1.0 OE1 A:GLN11 3.8 88.4 1.0 O3B A:GTP502 3.8 83.5 1.0 PG A:GTP502 3.8 83.5 1.0 OE2 A:GLU71 4.0 94.5 1.0 CB A:GLN11 4.1 86.0 1.0 NZ B:LYS254 4.3 77.7 1.0 O2B A:GTP502 4.3 83.5 1.0 O1G A:GTP502 4.3 83.5 1.0 OD2 A:ASP98 4.4 90.8 1.0 O3A A:GTP502 4.5 83.5 1.0 OD2 A:ASP69 4.5 90.2 1.0 CB A:ASP98 4.6 89.1 1.0 CG2 A:VAL74 4.7 92.5 1.0 CD A:GLN11 4.7 90.1 1.0 OD1 A:ASP69 4.8 86.7 1.0 CB A:GLU71 5.0 94.3 1.0 CG A:ASP98 5.0 89.7 1.0 CG A:GLN11 5.0 89.0 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Tubulin Bound to Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:65.5 occ:1.00 OE1 B:GLN11 2.1 59.9 1.0 O B:HOH602 2.1 63.4 1.0 O B:HOH604 2.1 66.8 1.0 O B:HOH603 2.1 66.2 1.0 O1A B:GDP501 2.5 67.8 1.0 CD B:GLN11 3.3 61.6 1.0 PA B:GDP501 3.8 67.8 1.0 O3A B:GDP501 4.0 67.8 1.0 NE2 B:GLN11 4.1 60.8 1.0 CB B:GLN11 4.2 65.5 1.0 OD1 B:ASN101 4.3 69.4 1.0 CG B:GLN11 4.3 65.0 1.0 O B:HOH601 4.3 66.7 1.0 OE1 C:GLU254 4.4 65.6 1.0 OD2 B:ASP179 4.5 66.6 1.0 O5' B:GDP501 4.6 67.8 1.0 C5' B:GDP501 4.7 67.8 1.0 O1B B:GDP501 4.8 67.8 1.0 ND2 B:ASN101 4.8 70.2 1.0 PB B:GDP501 4.9 67.8 1.0 O2A B:GDP501 4.9 67.8 1.0 CG B:ASN101 4.9 69.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Tubulin Bound to Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg501 b:66.5 occ:1.00 O C:HOH602 2.1 68.9 1.0 O C:HOH607 2.1 74.3 1.0 O C:HOH606 2.1 66.8 1.0 O C:HOH605 2.1 76.2 1.0 O3A C:GTP502 2.5 70.9 1.0 O2G C:GTP502 3.0 70.9 1.0 O1G C:GTP502 3.2 70.9 1.0 O1B C:GTP502 3.3 70.9 1.0 PB C:GTP502 3.3 70.9 1.0 PG C:GTP502 3.4 70.9 1.0 OE1 C:GLU71 3.6 71.9 1.0 O3B C:GTP502 3.6 70.9 1.0 OE1 C:GLN11 3.7 70.9 1.0 CB C:GLN11 3.8 69.3 1.0 PA C:GTP502 3.9 70.9 1.0 O1A C:GTP502 4.0 70.9 1.0 N C:GLN11 4.5 67.4 1.0 CD C:GLU71 4.5 71.8 1.0 NZ D:LYS254 4.6 85.1 1.0 CD C:GLN11 4.6 71.0 1.0 CG C:GLU71 4.7 71.2 1.0 O2B C:GTP502 4.7 70.9 1.0 O2A C:GTP502 4.8 70.9 1.0 CA C:GLN11 4.8 68.5 1.0 CG C:GLN11 4.8 70.3 1.0 O3G C:GTP502 4.9 70.9 1.0 O5' C:GTP502 4.9 70.9 1.0 OD2 C:ASP69 5.0 66.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Tubulin Bound to Compound 2


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 Compound 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:0.6 occ:1.00 O D:HOH602 2.1 0.7 1.0 O D:HOH601 2.1 0.9 1.0 O1A D:GDP501 2.2 0.3 1.0 OE1 D:GLN11 3.0 0.1 1.0 OD2 D:ASP179 3.2 0.7 1.0 ND2 D:ASN101 3.2 0.5 1.0 PA D:GDP501 3.6 0.3 1.0 OD1 D:ASN101 3.9 0.4 1.0 O2A D:GDP501 4.0 0.3 1.0 CG D:ASN101 4.0 0.2 1.0 O1B D:GDP501 4.0 0.3 1.0 CD D:GLN11 4.2 0.9 1.0 CG D:ASP179 4.2 0.4 1.0 C5' D:GDP501 4.5 0.3 1.0 CB D:ASP179 4.5 0.4 1.0 O5' D:GDP501 4.6 0.3 1.0 O3A D:GDP501 4.7 0.3 1.0 NE2 D:GLN11 4.8 0.2 1.0 PB D:GDP501 4.9 0.3 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