Magnesium in PDB 6gze: Tubulin-Gdp.Bef Complex

The structure of Tubulin-Gdp.Bef Complex, PDB code: 6gze was solved by M.A.Oliva, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.46 / 2.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.176, 156.744, 180.587, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.7

The structure of Tubulin-Gdp.Bef Complex also contains other interesting chemical elements:

Fluorine	(F)	3 atoms
Calcium	(Ca)	3 atoms

The binding sites of Magnesium atom in the Tubulin-Gdp.Bef Complex (pdb code 6gze). 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-Gdp.Bef Complex, PDB code: 6gze:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Gdp.Bef Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Gdp.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:52.9 occ:1.00 O A:HOH602 2.1 44.9 1.0 O A:HOH601 2.1 59.3 1.0 O A:HOH606 2.1 39.8 0.7 O A:HOH604 2.1 44.6 0.8 O1B A:GTP501 2.1 53.9 1.0 O1G A:GTP501 2.1 43.6 1.0 HB2 A:GLN11 3.2 64.5 1.0 HZ1 B:LYS254 3.3 65.0 1.0 PB A:GTP501 3.3 83.6 1.0 PG A:GTP501 3.3 57.1 1.0 HG2 A:GLU71 3.4 89.5 1.0 OE2 A:GLU71 3.7 92.2 1.0 H A:GLN11 3.7 61.9 1.0 O3B A:GTP501 3.7 77.1 1.0 O3A A:GTP501 3.7 65.8 1.0 O3G A:GTP501 3.8 55.3 1.0 HG3 A:GLU71 3.9 89.5 1.0 HB2 A:ASP98 4.0 69.2 1.0 CG A:GLU71 4.0 88.0 1.0 HZ2 B:LYS254 4.0 65.0 1.0 NZ B:LYS254 4.0 66.0 1.0 CB A:GLN11 4.1 65.0 1.0 OD1 A:ASP69 4.2 65.3 1.0 OD2 A:ASP69 4.2 70.1 1.0 HB3 A:GLN11 4.2 64.5 1.0 OD2 A:ASP98 4.2 70.5 1.0 CD A:GLU71 4.3 90.6 1.0 N A:GLN11 4.4 62.0 1.0 HZ3 B:LYS254 4.4 65.0 1.0 HB3 A:ASP98 4.4 69.2 1.0 O2B A:GTP501 4.6 78.7 1.0 O2G A:GTP501 4.6 48.2 1.0 CB A:ASP98 4.6 67.4 1.0 CG A:ASP69 4.6 67.0 1.0 O1A A:GTP501 4.7 54.5 1.0 HG21 A:VAL74 4.7 75.0 1.0 PA A:GTP501 4.8 55.0 1.0 HA2 A:GLY10 4.8 67.5 1.0 CA A:GLN11 4.8 63.3 1.0 CG A:ASP98 4.9 68.6 1.0 OE1 A:GLN11 4.9 69.7 1.0 HG1 A:THR145 4.9 63.7 1.0 HE3 B:LYS254 4.9 64.7 1.0 HB A:THR145 5.0 63.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Gdp.Bef Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Gdp.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:64.7 occ:1.00 O B:HOH602 2.1 60.5 1.0 OE1 B:GLN11 2.1 55.8 1.0 O B:HOH609 2.1 30.3 1.0 O C:HOH619 2.1 67.5 1.0 O B:HOH610 2.1 74.1 1.0 O1A B:GDP501 2.3 54.5 1.0 CD B:GLN11 3.2 56.8 1.0 HB3 B:GLN11 3.5 56.4 1.0 PA B:GDP501 3.5 49.7 1.0 O3A B:GDP501 3.7 53.2 1.0 HB2 B:GLN11 3.8 56.4 1.0 OD2 B:ASP179 3.9 68.1 1.0 CB B:GLN11 4.0 55.7 1.0 HE22 B:GLN11 4.0 66.1 1.0 NE2 B:GLN11 4.0 58.4 1.0 CG B:GLN11 4.1 57.2 1.0 H8 B:GDP501 4.1 56.1 1.0 OD1 B:ASN101 4.2 50.0 1.0 HD21 B:ASN101 4.2 50.6 1.0 O1B B:GDP501 4.4 45.1 1.0 HG2 B:GLN11 4.4 60.1 1.0 O5' B:GDP501 4.5 48.1 1.0 C5' B:GDP501 4.5 48.4 1.0 O2A B:GDP501 4.6 52.5 1.0 OE1 C:GLU254 4.7 67.1 1.0 PB B:GDP501 4.7 71.8 1.0 HE21 B:GLN11 4.8 66.1 1.0 ND2 B:ASN101 4.9 52.3 1.0 CG B:ASN101 4.9 51.3 1.0 HG3 B:GLN11 4.9 60.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Gdp.Bef Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Gdp.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:89.0 occ:1.00 O B:HOH603 1.9 88.5 1.0 O B:HOH608 2.1 89.8 1.0 HB3 B:ASP116 3.5 70.2 1.0 OD2 B:ASP120 3.8 78.8 1.0 OD2 B:ASP116 4.0 67.0 1.0 OD1 B:ASP120 4.3 76.9 1.0 CB B:ASP116 4.4 67.6 1.0 CG B:ASP120 4.5 78.3 1.0 CG B:ASP116 4.5 66.1 1.0 HB2 B:ASP116 4.8 70.2 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Gdp.Bef Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Gdp.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:51.4 occ:1.00 O C:HOH603 2.1 46.9 1.0 O C:HOH613 2.1 55.7 1.0 O C:HOH602 2.1 50.7 1.0 O C:HOH615 2.1 49.4 1.0 O1G C:GTP501 2.2 46.4 1.0 O1B C:GTP501 2.2 54.5 1.0 PG C:GTP501 3.2 62.0 1.0 PB C:GTP501 3.3 88.3 1.0 O3G C:GTP501 3.5 47.4 1.0 HB2 C:GLN11 3.5 58.6 1.0 O3A C:GTP501 3.6 76.7 1.0 HZ1 D:LYS254 3.6 61.2 1.0 O3B C:GTP501 3.7 70.0 1.0 H C:GLN11 3.7 51.9 1.0 HB2 C:ASP98 3.8 62.8 1.0 HE21 C:GLN11 3.8 60.9 1.0 OE1 C:GLU71 3.9 77.4 1.0 HZ3 D:LYS254 4.1 61.2 1.0 OD1 C:ASP69 4.1 56.7 1.0 OD2 C:ASP69 4.1 58.6 1.0 HB3 C:GLN11 4.1 58.6 1.0 HB3 C:GLU71 4.2 74.5 1.0 OD2 C:ASP98 4.2 63.4 1.0 HB3 C:ASP98 4.2 62.8 1.0 CB C:GLN11 4.3 55.5 1.0 NZ D:LYS254 4.3 62.6 1.0 CB C:ASP98 4.4 62.6 1.0 N C:GLN11 4.4 51.3 1.0 NE2 C:GLN11 4.5 57.5 1.0 CG C:ASP69 4.5 56.6 1.0 O2G C:GTP501 4.5 44.4 1.0 HG1 C:THR145 4.6 50.3 1.0 O2B C:GTP501 4.6 82.6 1.0 CD C:GLU71 4.7 77.9 1.0 HA2 C:GLY10 4.7 50.2 1.0 CG C:ASP98 4.7 63.7 1.0 PA C:GTP501 4.8 81.0 1.0 HZ2 D:LYS254 4.8 61.2 1.0 HE22 C:GLN11 4.8 60.9 1.0 HB C:THR145 4.9 50.1 1.0 O1A C:GTP501 4.9 66.1 1.0 HG21 C:VAL74 4.9 61.6 1.0 CA C:GLN11 4.9 54.2 1.0 OG1 C:THR145 5.0 53.0 1.0 HB2 C:GLU71 5.0 74.5 1.0 CB C:GLU71 5.0 73.2 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Gdp.Bef Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Gdp.Bef Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:0.1 occ:1.00 O D:HOH603 2.1 0.8 1.0 O D:HOH602 2.1 1.0 1.0 O D:HOH601 2.1 0.2 1.0 F1 D:BEF503 2.4 82.4 1.0 O1B D:GDP501 2.7 93.6 1.0 HB2 D:GLN11 2.9 0.1 1.0 HG3 D:GLU71 3.0 0.1 1.0 BE D:BEF503 3.1 84.7 1.0 O3B D:GDP501 3.2 91.9 1.0 F2 D:BEF503 3.3 80.2 1.0 H D:GLN11 3.6 0.2 1.0 PB D:GDP501 3.6 89.0 1.0 CB D:GLN11 3.8 0.7 1.0 CG D:GLU71 3.9 0.2 1.0 HB3 D:GLN11 4.0 0.1 1.0 O1A D:GDP501 4.0 98.7 1.0 HB2 D:GLU71 4.0 0.3 1.0 OD2 D:ASP69 4.2 0.0 1.0 HG2 D:GLU71 4.2 0.1 1.0 N D:GLN11 4.2 0.8 1.0 OD1 D:ASP69 4.2 0.3 1.0 CB D:GLU71 4.6 0.9 1.0 CA D:GLN11 4.6 0.4 1.0 F3 D:BEF503 4.6 81.1 1.0 O2B D:GDP501 4.6 0.4 1.0 O3A D:GDP501 4.6 83.1 1.0 CG D:ASP69 4.7 100.0 1.0 HA2 D:GLY10 4.7 98.8 1.0 CD D:GLN11 4.7 0.1 1.0 HA D:GLN11 4.8 0.6 1.0 PA D:GDP501 4.8 79.3 1.0 CG D:GLN11 4.8 0.6 1.0 OE1 D:GLN11 4.9 0.8 1.0 CD D:GLU71 4.9 0.2 1.0 HG1 D:THR145 4.9 92.0 1.0

F.Josa-Prado, J.Estevez-Gallego, R.M.Buey, F.A.Balaguer, A.E.Prota, M.O.Steinmetz, I.Barasoain, S.Kamimura, J.F.Diaz, M.A.Oliva. Structural Basis For Tubulin Activation Revealed By A Gtp Mimicking State To Be Published.