Magnesium in PDB 4o4j: Tubulin-Peloruside A Complex

The structure of Tubulin-Peloruside A Complex, PDB code: 4o4j was solved by A.E.Prota, K.Bargsten, P.T.Northcote, M.Marsh, K.H.Altmann, J.H.Miller, J.F.Diaz, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.30 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.370, 157.840, 180.360, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 23.9

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

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Tubulin-Peloruside A Complex (pdb code 4o4j). 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-Peloruside A Complex, PDB code: 4o4j:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Tubulin-Peloruside A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Peloruside A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:14.7 occ:1.00 O A:HOH606 1.9 20.5 1.0 O2G A:GTP501 2.0 13.3 1.0 O A:HOH601 2.1 11.4 1.0 O1B A:GTP501 2.1 14.4 1.0 O A:HOH602 2.1 14.4 1.0 O A:HOH604 2.2 22.8 1.0 PG A:GTP501 3.2 17.0 1.0 PB A:GTP501 3.3 15.0 1.0 O3B A:GTP501 3.6 41.8 1.0 O1G A:GTP501 3.7 21.4 1.0 O3A A:GTP501 3.8 19.3 1.0 NZ B:LYS254 4.0 21.4 1.0 OD1 A:ASP69 4.0 20.7 1.0 CB A:GLN11 4.1 14.9 1.0 O A:HOH701 4.2 47.1 1.0 OE1 A:GLU71 4.2 39.0 1.0 OD2 A:ASP69 4.2 18.5 1.0 O1A A:GTP501 4.3 14.1 1.0 CG A:GLU71 4.3 28.4 1.0 N A:GLN11 4.3 15.3 1.0 OD2 A:ASP98 4.4 22.4 1.0 CB A:ASP98 4.4 18.2 1.0 O3G A:GTP501 4.5 19.5 1.0 O2B A:GTP501 4.5 16.7 1.0 CG A:ASP69 4.6 25.1 1.0 OE1 A:GLN11 4.6 35.6 1.0 PA A:GTP501 4.7 14.5 1.0 CG A:ASP98 4.8 25.9 1.0 CD A:GLU71 4.8 33.6 1.0 CA A:GLN11 4.8 21.8 1.0

Magnesium binding site 2 out of 4 in the Tubulin-Peloruside A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Peloruside A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:9.3 occ:1.00 O B:HOH606 2.0 22.4 1.0 O1A B:GDP501 2.1 11.6 1.0 OE1 B:GLN11 2.2 21.3 1.0 O C:HOH847 2.3 40.0 1.0 O B:HOH627 2.6 33.2 1.0 O B:HOH605 2.6 25.5 1.0 O B:HOH737 3.0 45.3 1.0 CD B:GLN11 3.4 21.0 1.0 PA B:GDP501 3.4 15.0 1.0 O3A B:GDP501 3.8 22.6 1.0 CB B:GLN11 3.9 15.0 1.0 OD2 B:ASP179 4.0 24.6 1.0 CG B:GLN11 4.1 16.1 1.0 O5' B:GDP501 4.4 14.4 1.0 C5' B:GDP501 4.4 19.3 1.0 NE2 B:GLN11 4.4 29.4 1.0 O2A B:GDP501 4.5 13.5 1.0 OD1 B:ASN101 4.5 18.7 1.0 O1B B:GDP501 4.6 15.0 1.0 PB B:GDP501 4.8 12.3 1.0 C8 B:GDP501 4.8 20.1 1.0 OE1 C:GLU254 4.8 21.5 1.0 O B:HOH771 4.8 46.3 1.0 O C:HOH746 5.0 40.6 1.0

Magnesium binding site 3 out of 4 in the Tubulin-Peloruside A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Peloruside A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:18.3 occ:1.00 O1G C:GTP501 2.0 13.2 1.0 O C:HOH602 2.0 11.0 1.0 O C:HOH611 2.0 18.2 1.0 O1B C:GTP501 2.1 11.3 1.0 O C:HOH606 2.2 8.4 1.0 PG C:GTP501 3.1 12.5 1.0 PB C:GTP501 3.2 11.9 1.0 O3G C:GTP501 3.5 13.3 1.0 O3B C:GTP501 3.6 30.7 1.0 O3A C:GTP501 3.7 22.8 1.0 OE1 C:GLU71 3.9 31.5 1.0 NZ D:LYS254 3.9 18.1 1.0 OD2 C:ASP98 4.1 21.1 1.0 OD1 C:ASP69 4.1 19.6 1.0 CG C:GLU71 4.2 20.8 1.0 OD2 C:ASP69 4.3 12.9 1.0 CB C:ASP98 4.3 18.5 1.0 CB C:GLN11 4.4 12.8 1.0 O2G C:GTP501 4.4 16.3 1.0 O C:HOH745 4.5 45.2 1.0 N C:GLN11 4.5 14.4 1.0 O C:HOH752 4.5 38.8 1.0 O2B C:GTP501 4.5 13.1 1.0 CD C:GLU71 4.6 27.1 1.0 CG C:ASP98 4.6 20.5 1.0 CG C:ASP69 4.6 21.3 1.0 O1A C:GTP501 4.6 19.8 1.0 PA C:GTP501 4.8 14.7 1.0 OG1 C:THR145 5.0 12.9 1.0

Magnesium binding site 4 out of 4 in the Tubulin-Peloruside A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Peloruside A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:67.4 occ:1.00 O D:HOH665 3.0 36.0 1.0 OE1 D:GLN11 3.0 46.5 1.0 O1A D:GDP501 3.1 45.5 1.0 O1B D:GDP501 3.2 36.9 1.0 CB D:GLN11 3.5 39.1 1.0 CD D:GLN11 3.6 45.7 1.0 O3A D:GDP501 3.8 36.8 1.0 PB D:GDP501 3.9 38.5 1.0 PA D:GDP501 4.0 44.0 1.0 CG D:GLN11 4.1 44.5 1.0 O D:HOH658 4.3 49.6 1.0 O3B D:GDP501 4.3 33.4 1.0 NE2 D:GLN11 4.3 41.2 1.0 O D:HOH694 4.4 39.5 1.0 OE1 D:GLU71 4.4 86.2 1.0 O2A D:GDP501 4.7 43.2 1.0 CA D:GLN11 4.8 40.5 1.0 OD1 D:ASN101 4.8 49.0 1.0 O D:HOH715 4.8 42.1 1.0 N D:GLN11 4.9 37.2 1.0

A.E.Prota, K.Bargsten, P.T.Northcote, M.Marsh, K.H.Altmann, J.H.Miller, J.F.Diaz, M.O.Steinmetz. Structural Basis of Microtubule Stabilization By Laulimalide and Peloruside A. Angew.Chem.Int.Ed.Engl. V. 53 1621 2014.
ISSN: ISSN 1433-7851
PubMed: 24470331
DOI: 10.1002/ANIE.201307749