Magnesium in PDB 4o4h: Tubulin-Laulimalide Complex

The structure of Tubulin-Laulimalide Complex, PDB code: 4o4h 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)	71.90 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.693, 156.868, 180.451, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.4

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

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Tubulin-Laulimalide Complex (pdb code 4o4h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Laulimalide Complex, PDB code: 4o4h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Laulimalide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Laulimalide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.3 occ:1.00 O A:HOH704 2.3 32.1 1.0 O1G A:GTP501 2.3 31.1 1.0 O A:HOH602 2.3 30.4 1.0 O1B A:GTP501 2.4 29.5 1.0 O A:HOH601 2.4 32.6 1.0 O A:HOH603 2.4 31.6 1.0 PG A:GTP501 3.4 30.9 1.0 PB A:GTP501 3.4 25.1 1.0 O2G A:GTP501 3.7 29.6 1.0 O3B A:GTP501 3.8 43.6 1.0 O3A A:GTP501 3.9 34.6 1.0 NZ B:LYS254 3.9 32.5 1.0 OE1 A:GLU71 3.9 54.8 1.0 OD1 A:ASP69 3.9 39.0 1.0 CB A:GLN11 4.0 25.6 1.0 OD2 A:ASP69 4.1 34.4 1.0 CG A:GLU71 4.2 44.1 1.0 N A:GLN11 4.3 29.1 1.0 CB A:ASP98 4.4 32.7 1.0 OD2 A:ASP98 4.4 44.0 1.0 CG A:ASP69 4.5 38.4 1.0 CD A:GLU71 4.6 53.1 1.0 O3G A:GTP501 4.7 29.3 1.0 OE1 A:GLN11 4.7 43.5 1.0 O1A A:GTP501 4.7 33.3 1.0 CA A:GLN11 4.7 31.8 1.0 CG A:ASP98 4.7 34.0 1.0 O2B A:GTP501 4.8 33.5 1.0 O A:HOH707 4.8 57.8 1.0 PA A:GTP501 4.9 30.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Laulimalide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Laulimalide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:22.8 occ:1.00 O B:HOH604 2.3 31.1 1.0 O1A B:GDP501 2.3 24.3 1.0 O B:HOH609 2.6 37.9 1.0 OE1 B:GLN11 2.6 38.3 1.0 O C:HOH749 2.6 45.1 1.0 O B:HOH605 2.6 35.1 1.0 O B:HOH725 3.3 71.2 1.0 PA B:GDP501 3.6 27.0 1.0 CD B:GLN11 3.7 48.0 1.0 O3A B:GDP501 3.7 37.6 1.0 OD2 B:ASP179 3.8 34.2 1.0 CB B:GLN11 4.2 26.0 1.0 C5' B:GDP501 4.3 30.7 1.0 CG B:GLN11 4.3 27.0 1.0 O5' B:GDP501 4.4 34.1 1.0 OD1 B:ASN101 4.4 32.5 1.0 OE1 C:GLU254 4.6 39.3 1.0 O C:HOH831 4.6 53.2 1.0 O2A B:GDP501 4.6 29.3 1.0 C8 B:GDP501 4.7 26.5 1.0 O2B B:GDP501 4.7 22.4 1.0 CG B:ASP179 4.8 43.2 1.0 NE2 B:GLN11 4.8 50.7 1.0 PB B:GDP501 4.9 27.6 1.0 ND2 B:ASN101 5.0 32.6 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Laulimalide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Laulimalide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:34.3 occ:1.00 O1G C:GTP501 2.2 24.9 1.0 O1B C:GTP501 2.3 22.4 1.0 O C:HOH827 2.3 27.9 1.0 O C:HOH826 2.3 30.1 1.0 O C:HOH828 2.4 30.4 1.0 O C:HOH829 2.6 35.9 1.0 PG C:GTP501 3.3 27.4 1.0 PB C:GTP501 3.4 25.3 1.0 O3B C:GTP501 3.7 36.6 1.0 O2G C:GTP501 3.8 27.7 1.0 O3A C:GTP501 3.9 34.0 1.0 OE1 C:GLU71 4.0 41.4 1.0 NZ D:LYS254 4.0 34.8 1.0 OD1 C:ASP69 4.0 28.3 1.0 CB C:GLN11 4.1 19.8 1.0 OD2 C:ASP69 4.2 23.4 1.0 CG C:GLU71 4.2 34.3 1.0 OD2 C:ASP98 4.3 33.8 1.0 N C:GLN11 4.4 23.2 1.0 CB C:ASP98 4.4 25.0 1.0 CG C:ASP69 4.5 28.4 1.0 CD C:GLU71 4.6 39.3 1.0 NE2 C:GLN11 4.6 35.0 1.0 O C:HOH602 4.6 74.3 1.0 O3G C:GTP501 4.7 25.2 1.0 O2B C:GTP501 4.7 27.4 1.0 O1A C:GTP501 4.7 27.7 1.0 CG C:ASP98 4.8 29.3 1.0 CA C:GLN11 4.8 23.6 1.0 PA C:GTP501 4.9 27.0 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Laulimalide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Laulimalide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:44.6 occ:1.00 O D:HOH607 1.8 42.3 1.0 OE1 D:GLN11 1.9 53.2 1.0 O D:HOH657 2.1 55.6 1.0 O1A D:GDP501 2.4 51.0 1.0 O D:HOH613 2.7 45.8 1.0 CD D:GLN11 3.1 55.7 1.0 OD2 D:ASP179 3.1 77.5 1.0 PA D:GDP501 3.7 51.5 1.0 O3A D:GDP501 4.0 51.5 1.0 CG D:GLN11 4.0 49.9 1.0 CB D:GLN11 4.1 47.5 1.0 NE2 D:GLN11 4.1 53.1 1.0 CG D:ASP179 4.4 89.8 1.0 C5' D:GDP501 4.6 46.5 1.0 O5' D:GDP501 4.6 49.1 1.0 O2A D:GDP501 4.6 53.4 1.0 C8 D:GDP501 4.7 40.2 1.0 ND2 D:ASN101 4.8 53.9 1.0 O2B D:GDP501 4.9 43.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Laulimalide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Laulimalide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:30.0 occ:1.00 C3B F:ACP401 2.3 0.8 1.0 OE2 F:GLU331 2.3 88.4 1.0 ND2 F:ASN333 2.8 82.6 1.0 CD F:GLU331 3.1 75.6 1.0 OE1 F:GLU331 3.3 75.8 1.0 NZ F:LYS74 3.5 75.9 1.0 PG F:ACP401 3.5 0.2 1.0 PB F:ACP401 3.7 89.0 1.0 O1G F:ACP401 3.7 65.3 1.0 O1B F:ACP401 3.8 0.9 1.0 O3G F:ACP401 3.8 0.9 1.0 CG F:ASN333 4.0 75.8 1.0 OD1 F:ASN333 4.3 88.1 1.0 O3A F:ACP401 4.3 84.9 1.0 CG F:GLU331 4.5 63.6 1.0 CE F:LYS74 4.7 71.2 1.0 O2G F:ACP401 4.9 0.4 1.0 O2B F:ACP401 4.9 92.9 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