Magnesium in PDB 5lyj: Tubulin-Combretastatin A4 Complex

The structure of Tubulin-Combretastatin A4 Complex, PDB code: 5lyj was solved by R.Gaspari, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.43 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.592, 157.170, 180.140, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.7

The structure of Tubulin-Combretastatin A4 Complex also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-Combretastatin A4 Complex (pdb code 5lyj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Tubulin-Combretastatin A4 Complex, PDB code: 5lyj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:69.2 occ:1.00 O2G A:GTP501 1.8 66.3 1.0 O A:HOH607 2.0 52.7 1.0 O A:HOH611 2.1 61.2 1.0 O A:HOH618 2.2 48.4 1.0 O A:HOH620 2.2 53.2 1.0 O1B A:GTP501 2.2 58.1 1.0 PG A:GTP501 2.8 60.9 1.0 PB A:GTP501 3.1 54.8 1.0 O3B A:GTP501 3.1 62.4 1.0 O1G A:GTP501 3.2 60.7 1.0 O3A A:GTP501 3.7 58.3 1.0 OE1 A:GLU71 4.1 82.0 1.0 CB A:ASP98 4.1 70.6 1.0 O3G A:GTP501 4.1 59.9 1.0 OD2 A:ASP98 4.2 75.4 1.0 OD1 A:ASP69 4.2 64.5 1.0 O2B A:GTP501 4.4 56.0 1.0 CB A:GLN11 4.4 54.0 1.0 CG A:ASP98 4.5 74.0 1.0 CG A:GLU71 4.5 78.5 1.0 NZ B:LYS254 4.5 78.5 1.0 O1A A:GTP501 4.6 62.1 1.0 OG1 A:THR145 4.6 57.7 1.0 OD2 A:ASP69 4.6 64.5 1.0 N A:GLN11 4.6 53.6 1.0 PA A:GTP501 4.7 61.1 1.0 OE1 A:GLN11 4.8 55.6 1.0 CD A:GLU71 4.8 82.7 1.0 CG A:ASP69 4.9 63.5 1.0

Magnesium binding site 2 out of 4 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:47.1 occ:1.00 O B:HOH603 2.1 57.9 1.0 OE1 B:GLN11 2.1 61.0 1.0 O1A B:GDP501 2.2 46.0 1.0 O C:HOH650 2.3 58.9 1.0 O B:HOH627 2.5 51.7 1.0 O B:HOH601 2.6 71.4 1.0 CD B:GLN11 3.2 61.4 1.0 OD2 B:ASP179 3.5 64.7 1.0 PA B:GDP501 3.6 50.2 1.0 O3A B:GDP501 3.9 54.0 1.0 NE2 B:GLN11 4.0 65.2 1.0 CG B:GLN11 4.1 57.8 1.0 CB B:GLN11 4.1 52.5 1.0 OD1 B:ASN101 4.4 48.7 1.0 C5' B:GDP501 4.4 39.9 1.0 O5' B:GDP501 4.4 38.0 1.0 O2A B:GDP501 4.6 48.2 1.0 O1B B:GDP501 4.7 47.8 1.0 CG B:ASP179 4.7 62.8 1.0 C8 B:GDP501 4.8 45.1 1.0 OE1 C:GLU254 4.8 76.6 1.0 PB B:GDP501 4.9 45.9 1.0

Magnesium binding site 3 out of 4 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:53.0 occ:1.00 O C:HOH619 2.0 48.1 1.0 O1G C:GTP501 2.0 42.9 1.0 O C:HOH637 2.1 48.1 1.0 O C:HOH609 2.4 44.5 1.0 O1B C:GTP501 2.5 45.5 1.0 PG C:GTP501 3.4 50.6 1.0 OE1 C:GLU71 3.5 77.9 1.0 PB C:GTP501 3.6 50.4 1.0 O2G C:GTP501 3.8 50.5 1.0 O3B C:GTP501 3.9 52.9 1.0 OD2 C:ASP98 4.0 65.4 1.0 CG C:GLU71 4.0 64.1 1.0 CD C:GLU71 4.2 71.5 1.0 O3A C:GTP501 4.2 52.9 1.0 CB C:ASP98 4.2 56.1 1.0 NZ D:LYS254 4.4 74.7 1.0 OD1 C:ASP69 4.4 51.0 1.0 CG C:ASP98 4.4 60.7 1.0 OD2 C:ASP69 4.5 46.9 1.0 O3G C:GTP501 4.5 42.6 1.0 CB C:GLN11 4.6 42.2 1.0 OE1 C:GLN11 4.6 55.7 1.0 O2B C:GTP501 4.9 51.3 1.0 CE D:LYS254 4.9 74.5 1.0 O1A C:GTP501 4.9 48.6 1.0 CG C:ASP69 4.9 49.1 1.0 N C:GLN11 4.9 42.3 1.0

Magnesium binding site 4 out of 4 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:99.6 occ:1.00 O D:HOH602 2.1 61.3 1.0 OE1 D:GLN11 2.5 95.6 1.0 CD D:GLN11 2.8 98.0 1.0 O1A D:GDP501 2.9 87.6 1.0 NE2 D:GLN11 3.3 98.8 1.0 CB D:GLN11 3.5 94.2 1.0 CG D:GLN11 3.7 95.3 1.0 O3A D:GDP501 3.9 78.7 1.0 PA D:GDP501 3.9 82.9 1.0 O1B D:GDP501 4.0 73.5 1.0 OE2 D:GLU71 4.2 0.0 1.0 ND2 D:ASN101 4.5 0.5 1.0 PB D:GDP501 4.6 77.2 1.0 O2A D:GDP501 4.6 85.6 1.0 OD2 D:ASP179 4.8 0.5 1.0 CA D:GLN11 4.9 92.1 1.0

R.Gaspari, A.E.Prota, K.Bargsten, A.Cavalli, M.O.Steinmetz. Structural Basis of Cis- and Trans-Combretastatin Binding to Tubulin Chem 2017.
ISSN: ESSN 2451-9294
DOI: 10.1016/J.CHEMPR.2016.12.005