Magnesium in PDB 5fnv: A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone

The structure of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone, PDB code: 5fnv was solved by Y.Wang, J.Naismith, X.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.88 / 2.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.160, 157.200, 181.680, 90.00, 90.00, 90.00
R / Rfree (%)	18.575 / 22.555

The structure of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone (pdb code 5fnv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone, PDB code: 5fnv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1439 b:51.9 occ:1.00 O1G A:GTP1438 1.9 49.1 1.0 O2B A:GTP1438 1.9 54.5 1.0 O A:HOH2004 2.0 46.1 1.0 O A:HOH2002 2.1 40.8 1.0 O A:HOH2006 2.1 46.0 1.0 O A:HOH2005 2.1 38.8 1.0 PG A:GTP1438 3.0 55.1 1.0 PB A:GTP1438 3.0 50.6 1.0 O3B A:GTP1438 3.3 53.6 1.0 O2G A:GTP1438 3.4 54.2 1.0 O3A A:GTP1438 3.7 52.0 1.0 NZ B:LYS252 3.9 51.5 1.0 OD1 A:ASP69 4.2 63.6 1.0 OE2 A:GLU71 4.2 75.1 1.0 OD2 A:ASP98 4.3 61.0 1.0 CB A:GLN11 4.3 59.4 1.0 OD2 A:ASP69 4.3 64.0 1.0 O3G A:GTP1438 4.3 48.3 1.0 O1B A:GTP1438 4.4 57.8 1.0 CG A:GLU71 4.5 73.7 1.0 N A:GLN11 4.5 65.5 1.0 CB A:ASP98 4.5 62.0 1.0 O1A A:GTP1438 4.5 49.8 1.0 CG A:ASP69 4.7 65.8 1.0 PA A:GTP1438 4.7 48.8 1.0 CG A:ASP98 4.7 61.0 1.0 OE1 A:GLN11 4.9 65.2 1.0 CD A:GLU71 4.9 74.4 1.0 OG1 A:THR145 5.0 60.8 1.0

Magnesium binding site 2 out of 4 in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1430 b:75.3 occ:1.00 O1A B:GDP1429 1.9 66.9 1.0 OE1 B:GLN11 2.5 91.5 1.0 O B:HOH2002 2.7 52.5 1.0 OD2 B:ASP177 3.1 82.7 1.0 PA B:GDP1429 3.4 51.9 1.0 CD B:GLN11 3.5 88.8 1.0 O3A B:GDP1429 3.9 52.1 1.0 ND2 B:ASN99 4.0 64.8 1.0 NE2 B:GLN11 4.0 91.8 1.0 CG B:ASP177 4.1 86.4 1.0 O5' B:GDP1429 4.1 48.7 1.0 C5' B:GDP1429 4.1 51.0 1.0 CB B:GLN11 4.3 72.4 1.0 CG B:GLN11 4.5 81.0 1.0 O2A B:GDP1429 4.6 47.9 1.0 O2B B:GDP1429 4.7 50.9 1.0 CB B:ASP177 4.7 81.9 1.0 C8 B:GDP1429 4.8 55.8 1.0 PB B:GDP1429 4.9 53.7 1.0 OE2 C:GLU254 4.9 99.0 1.0 OD1 B:ASP177 5.0 91.1 1.0

Magnesium binding site 3 out of 4 in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1441 b:50.8 occ:1.00 O1G C:GTP1440 1.9 42.7 1.0 O1B C:GTP1440 1.9 48.6 1.0 O C:HOH2008 2.0 42.0 1.0 O C:HOH2006 2.0 43.9 1.0 O C:HOH2003 2.1 39.0 1.0 O C:HOH2005 2.1 38.5 1.0 PG C:GTP1440 2.9 48.9 1.0 PB C:GTP1440 3.0 46.4 1.0 O2G C:GTP1440 3.2 43.6 1.0 O3B C:GTP1440 3.3 45.2 1.0 O3A C:GTP1440 3.6 49.9 1.0 NZ D:LYS252 3.9 54.0 1.0 OD1 C:ASP69 4.0 55.1 1.0 OE2 C:GLU71 4.2 65.6 1.0 OD2 C:ASP69 4.2 55.9 1.0 OD2 C:ASP98 4.3 58.4 1.0 O3G C:GTP1440 4.3 41.4 1.0 O2B C:GTP1440 4.4 53.9 1.0 CB C:GLN11 4.4 56.0 1.0 CB C:ASP98 4.4 59.0 1.0 CG C:GLU71 4.5 61.1 1.0 N C:GLN11 4.5 52.2 1.0 O1A C:GTP1440 4.6 49.1 1.0 CG C:ASP69 4.6 56.1 1.0 PA C:GTP1440 4.6 47.5 1.0 CG C:ASP98 4.7 57.9 1.0 OG1 C:THR145 4.8 48.5 1.0 CD C:GLU71 4.9 64.8 1.0

Magnesium binding site 4 out of 4 in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1432 b:85.0 occ:1.00 O3G D:GTP1431 1.9 79.9 1.0 O1B D:GTP1431 2.9 78.7 1.0 PG D:GTP1431 3.0 0.3 1.0 O1G D:GTP1431 3.2 85.6 1.0 OE1 D:GLU69 3.6 0.4 1.0 O3B D:GTP1431 3.8 93.3 1.0 PB D:GTP1431 3.8 84.7 1.0 OD2 D:ASP67 3.9 0.6 1.0 CB D:GLN11 3.9 0.5 1.0 OD1 D:ASP67 4.1 0.2 1.0 O3A D:GTP1431 4.1 90.4 1.0 N D:GLN11 4.1 97.9 1.0 OE1 D:GLN11 4.2 0.2 1.0 CB D:GLU69 4.4 0.8 1.0 O2G D:GTP1431 4.4 79.2 1.0 CG D:ASP67 4.4 0.2 1.0 CA D:GLN11 4.5 0.1 1.0 CD D:GLU69 4.6 0.7 1.0 CG D:GLU69 4.7 0.0 1.0 CG2 D:THR72 4.8 0.0 1.0 O2A D:GTP1431 4.8 97.0 1.0 CG D:GLN11 4.9 0.4 1.0 PA D:GTP1431 5.0 83.4 1.0 CD D:GLN11 5.0 0.3 1.0

J.Yang, Y.Wang, T.Wang, J.Jiang, C.H.Botting, H.Liu, Q.Chen, J.Yang, J.H.Naismith, X.Zhu, L.Chen. Pironetin Reacts Covalently with Cysteine-316 of Alpha-Tubulin to Destabilize Microtubule. Nat.Commun. V. 7 12103 2016.
ISSN: ISSN 2041-1723
PubMed: 27357539
DOI: 10.1038/NCOMMS12103