Magnesium in PDB 5jh7: Tubulin-Eribulin Complex

The structure of Tubulin-Eribulin Complex, PDB code: 5jh7 was solved by H.Doodhi, A.E.Prota, R.Rodriguez-Garcia, H.Xiao, D.W.Custar, K.Bargsten, E.A.Katrukha, M.Hilbert, S.Hua, K.Jiang, I.Grigoriev, C.-P.H.Yang, D.Cox, S.Band Horwitz, L.C.Kapitein, A.Akhmanova, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.18 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.217, 157.134, 182.824, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22

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

Calcium

(Ca)

5 atoms

The binding sites of Magnesium atom in the Tubulin-Eribulin Complex (pdb code 5jh7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Tubulin-Eribulin Complex, PDB code: 5jh7:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:48.8 occ:1.00 O2G A:GTP501 2.1 40.3 1.0 O A:HOH669 2.1 48.5 1.0 O A:HOH629 2.1 44.2 1.0 O1B A:GTP501 2.1 38.1 1.0 O A:HOH680 2.1 47.0 1.0 O A:HOH705 2.1 41.8 1.0 PG A:GTP501 3.2 51.7 1.0 PB A:GTP501 3.3 43.0 1.0 O3B A:GTP501 3.6 84.8 1.0 O3A A:GTP501 3.8 60.9 1.0 O1G A:GTP501 3.8 57.9 1.0 OE1 A:GLU71 3.9 68.8 1.0 NZ B:LYS254 4.0 55.8 1.0 OD1 A:ASP69 4.1 57.5 1.0 CB A:GLN11 4.1 47.8 1.0 OD2 A:ASP98 4.3 61.7 1.0 OD2 A:ASP69 4.3 54.6 1.0 N A:GLN11 4.4 50.8 1.0 CB A:ASP98 4.4 54.3 1.0 O3G A:GTP501 4.5 46.9 1.0 O2B A:GTP501 4.5 43.3 1.0 OE1 A:GLN11 4.5 63.6 1.0 CG A:ASP69 4.7 60.6 1.0 O1A A:GTP501 4.7 43.6 1.0 CG A:ASP98 4.7 55.5 1.0 PA A:GTP501 4.8 51.5 1.0 CD A:GLU71 4.8 73.4 1.0 CA A:GLN11 4.9 57.2 1.0 CB A:GLU71 5.0 74.4 1.0 CE B:LYS254 5.0 49.9 1.0

Magnesium binding site 2 out of 3 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:40.9 occ:1.00 O1G C:GTP501 2.0 42.6 1.0 O1B C:GTP501 2.0 52.8 1.0 O C:HOH631 2.1 41.2 1.0 O C:HOH665 2.1 39.6 1.0 O C:HOH723 2.1 41.1 1.0 O C:HOH749 2.2 41.1 1.0 PG C:GTP501 3.1 38.4 1.0 PB C:GTP501 3.1 51.7 1.0 O3B C:GTP501 3.5 47.2 1.0 O3A C:GTP501 3.6 53.2 1.0 O2G C:GTP501 3.6 45.5 1.0 NZ D:LYS254 4.0 50.2 1.0 OD1 C:ASP69 4.0 39.5 1.0 OE1 C:GLU71 4.2 59.8 1.0 CB C:GLN11 4.2 41.1 1.0 OD2 C:ASP69 4.2 38.0 1.0 OD2 C:ASP98 4.3 51.1 1.0 CG C:GLU71 4.3 52.0 1.0 N C:GLN11 4.4 40.8 1.0 O3G C:GTP501 4.4 35.1 1.0 O2B C:GTP501 4.4 45.5 1.0 O C:HOH654 4.5 61.1 1.0 CB C:ASP98 4.5 35.3 1.0 O1A C:GTP501 4.5 45.1 1.0 CG C:ASP69 4.6 47.7 1.0 OE1 C:GLN11 4.7 54.5 1.0 PA C:GTP501 4.7 36.2 1.0 CD C:GLU71 4.8 61.0 1.0 O C:HOH608 4.8 84.8 1.0 CG C:ASP98 4.8 45.4 1.0 CA C:GLN11 4.9 40.0 1.0

Magnesium binding site 3 out of 3 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:88.0 occ:1.00 O1B F:ACP400 2.3 0.9 1.0 O F:HOH501 2.4 73.8 1.0 OE2 F:GLU331 2.5 99.9 1.0 O1G F:ACP400 2.9 88.1 1.0 OE1 F:GLU331 2.9 0.2 1.0 ND2 F:ASN333 3.1 89.1 1.0 CD F:GLU331 3.1 93.0 1.0 NZ F:LYS74 3.4 88.6 1.0 PB F:ACP400 3.7 0.3 1.0 CG F:ASN333 4.1 86.0 1.0 O2B F:ACP400 4.2 0.9 1.0 PG F:ACP400 4.3 0.4 1.0 OD1 F:ASN333 4.6 93.5 1.0 C3B F:ACP400 4.6 79.7 1.0 CG F:GLU331 4.6 75.5 1.0 O F:HOH507 4.8 81.9 1.0 CE F:LYS74 4.8 79.6 1.0 O3A F:ACP400 4.8 0.1 1.0 O F:HOH502 5.0 85.6 1.0

H.Doodhi, A.E.Prota, R.Rodriguez-Garcia, H.Xiao, D.W.Custar, K.Bargsten, E.A.Katrukha, M.Hilbert, S.Hua, K.Jiang, I.Grigoriev, C.P.Yang, D.Cox, S.B.Horwitz, L.C.Kapitein, A.Akhmanova, M.O.Steinmetz. Termination of Protofilament Elongation By Eribulin Induces Lattice Defects That Promote Microtubule Catastrophes. Curr.Biol. V. 26 1713 2016.
ISSN: ISSN 0960-9822
PubMed: 27321995
DOI: 10.1016/J.CUB.2016.04.053