Magnesium in PDB 4tv9: Tubulin-PM060184 Complex

The structure of Tubulin-PM060184 Complex, PDB code: 4tv9 was solved by A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, K.H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.04 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.200, 157.290, 180.220, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.8

The structure of Tubulin-PM060184 Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Tubulin-PM060184 Complex (pdb code 4tv9). 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-PM060184 Complex, PDB code: 4tv9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-PM060184 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-PM060184 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.9 occ:1.00 O2G A:GTP501 2.0 31.7 1.0 O A:HOH721 2.1 42.2 1.0 O1B A:GTP501 2.1 36.6 1.0 O A:HOH720 2.1 38.4 1.0 O A:HOH702 2.1 39.0 1.0 O A:HOH719 2.1 40.1 1.0 PG A:GTP501 3.2 38.6 1.0 PB A:GTP501 3.2 38.2 1.0 O3B A:GTP501 3.6 57.0 1.0 O1G A:GTP501 3.7 42.8 1.0 O3A A:GTP501 3.8 41.6 1.0 NZ B:LYS254 3.8 42.3 1.0 OE1 A:GLU71 3.9 69.7 1.0 OD1 A:ASP69 4.0 45.5 1.0 CB A:GLN11 4.1 35.8 1.0 CG A:GLU71 4.2 62.2 1.0 OD2 A:ASP69 4.2 46.6 1.0 N A:GLN11 4.3 42.0 1.0 OD2 A:ASP98 4.4 51.1 1.0 CB A:ASP98 4.4 45.8 1.0 O1A A:GTP501 4.4 38.8 1.0 O3G A:GTP501 4.5 37.9 1.0 CD A:GLU71 4.6 65.1 1.0 OE1 A:GLN11 4.6 54.1 1.0 CG A:ASP69 4.6 50.5 1.0 O2B A:GTP501 4.6 39.2 1.0 PA A:GTP501 4.7 39.1 1.0 CG A:ASP98 4.8 47.6 1.0 CA A:GLN11 4.8 41.8 1.0 CE B:LYS254 4.9 41.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-PM060184 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-PM060184 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:30.6 occ:1.00 O B:HOH671 2.0 42.3 1.0 OE1 B:GLN11 2.2 47.1 1.0 O1A B:GDP501 2.2 36.4 1.0 O C:HOH776 2.3 57.9 1.0 O B:HOH616 2.5 40.0 1.0 O B:HOH729 2.5 40.6 1.0 O B:HOH612 2.5 64.0 1.0 CD B:GLN11 3.4 47.5 1.0 PA B:GDP501 3.6 34.9 1.0 OD2 B:ASP179 3.9 43.0 1.0 O3A B:GDP501 4.0 38.0 1.0 CB B:GLN11 4.1 32.8 1.0 O B:HOH613 4.1 66.8 1.0 CG B:GLN11 4.2 40.1 1.0 C5' B:GDP501 4.4 37.0 1.0 NE2 B:GLN11 4.4 50.1 1.0 O5' B:GDP501 4.4 34.6 1.0 OD1 B:ASN101 4.4 43.8 1.0 OE1 C:GLU254 4.6 48.1 1.0 O1B B:GDP501 4.6 34.7 1.0 O C:HOH752 4.6 51.3 1.0 O2A B:GDP501 4.8 35.2 1.0 C8 B:GDP501 4.9 38.0 1.0 CG B:ASP179 4.9 47.1 1.0 PB B:GDP501 5.0 35.5 1.0 ND2 B:ASN101 5.0 40.5 1.0

Magnesium binding site 3 out of 5 in the Tubulin-PM060184 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-PM060184 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:34.1 occ:1.00 O C:HOH842 2.0 34.8 1.0 O1G C:GTP501 2.0 31.2 1.0 O1B C:GTP501 2.0 34.8 1.0 O C:HOH840 2.0 34.4 1.0 O C:HOH624 2.1 39.1 1.0 O C:HOH841 2.2 34.0 1.0 PG C:GTP501 3.2 36.0 1.0 PB C:GTP501 3.2 35.6 1.0 O3B C:GTP501 3.5 36.1 1.0 O2G C:GTP501 3.6 34.9 1.0 O3A C:GTP501 3.8 38.6 1.0 NZ D:LYS254 3.9 40.6 1.0 OE1 C:GLU71 4.0 52.1 1.0 OD1 C:ASP69 4.1 40.2 1.0 CB C:GLN11 4.2 27.6 1.0 OD2 C:ASP69 4.2 36.0 1.0 CG C:GLU71 4.2 43.2 1.0 N C:GLN11 4.4 29.4 1.0 OD2 C:ASP98 4.4 44.1 1.0 CB C:ASP98 4.4 39.5 1.0 O3G C:GTP501 4.5 33.2 1.0 O2B C:GTP501 4.5 34.3 1.0 O1A C:GTP501 4.5 34.0 1.0 CG C:ASP69 4.6 38.7 1.0 O C:HOH736 4.6 53.7 1.0 CD C:GLU71 4.6 47.2 1.0 PA C:GTP501 4.7 35.3 1.0 CG C:ASP98 4.8 44.2 1.0 OE1 C:GLN11 4.8 49.2 1.0 CA C:GLN11 4.9 33.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-PM060184 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-PM060184 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:52.8 occ:1.00 O D:HOH705 1.9 51.2 1.0 OE1 D:GLN11 2.0 68.3 1.0 O1A D:GDP501 2.1 71.7 1.0 O D:HOH707 2.1 66.3 1.0 O D:HOH685 2.3 54.8 1.0 O D:HOH684 2.6 74.1 1.0 CD D:GLN11 3.2 75.2 1.0 PA D:GDP501 3.6 64.2 1.0 O D:HOH706 4.0 74.8 1.0 C5' D:GDP501 4.0 60.8 1.0 NE2 D:GLN11 4.1 75.8 1.0 CG D:GLN11 4.1 70.3 1.0 CB D:GLN11 4.1 62.9 1.0 O5' D:GDP501 4.3 60.3 1.0 O3A D:GDP501 4.5 59.5 1.0 O2A D:GDP501 4.6 65.2 1.0 O1B D:GDP501 4.6 52.5 1.0 C8 D:GDP501 4.7 49.0 1.0 OD1 D:ASN101 4.8 73.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-PM060184 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-PM060184 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:74.8 occ:1.00 O1B F:ACP401 2.4 0.7 1.0 OE2 F:GLU331 2.6 92.0 1.0 O1G F:ACP401 2.7 0.9 1.0 OE1 F:GLU331 3.0 89.2 1.0 CD F:GLU331 3.2 85.9 1.0 OD1 F:ASN333 3.3 0.5 1.0 NZ F:LYS74 3.3 95.6 1.0 PB F:ACP401 3.7 96.8 1.0 PG F:ACP401 3.9 0.5 1.0 O2B F:ACP401 4.0 0.7 1.0 O3G F:ACP401 4.2 0.2 1.0 CG F:ASN333 4.4 93.5 1.0 C3B F:ACP401 4.4 96.8 1.0 CE F:LYS74 4.6 91.2 1.0 CG F:GLU331 4.7 78.2 1.0 O3A F:ACP401 5.0 0.3 1.0

A.E.Prota, K.Bargsten, J.F.Diaz, M.Marsh, C.Cuevas, M.Liniger, C.Neuhaus, J.M.Andreu, K.H.Altmann, M.O.Steinmetz. A New Tubulin-Binding Site and Pharmacophore For Microtubule-Destabilizing Anticancer Drugs. Proc.Natl.Acad.Sci.Usa V. 111 13817 2014.
ISSN: ESSN 1091-6490
PubMed: 25114240
DOI: 10.1073/PNAS.1408124111