Magnesium in PDB 6s9e: Tubulin-Gdp.Alf Complex

The structure of Tubulin-Gdp.Alf Complex, PDB code: 6s9e was solved by M.A.Oliva, J.Estevez-Gallego, J.F.Diaz, A.E.Prota, M.O.Steinmetz, F.A.Balaguer, D.Lucena-Agell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.999, 157.357, 180.261, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 22.8

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

Fluorine	(F)	3 atoms
Aluminium	(Al)	1 atom
Calcium	(Ca)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Tubulin-Gdp.Alf Complex (pdb code 6s9e). 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.Alf Complex, PDB code: 6s9e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Gdp.Alf 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.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.5 occ:1.00 O A:HOH617 2.1 41.0 1.0 O A:HOH610 2.1 40.4 1.0 O A:HOH628 2.1 38.7 1.0 O2G A:GTP501 2.1 32.1 1.0 O A:HOH630 2.1 37.5 1.0 O2B A:GTP501 2.1 31.6 1.0 HZ2 B:LYS254 3.2 54.7 1.0 PG A:GTP501 3.2 44.3 1.0 PB A:GTP501 3.3 39.2 1.0 HB2 A:GLN11 3.4 52.1 1.0 HG2 A:GLU71 3.5 72.1 1.0 H A:GLN11 3.6 49.1 1.0 O3G A:GTP501 3.7 37.6 1.0 O3B A:GTP501 3.7 47.1 1.0 O3A A:GTP501 3.8 42.2 1.0 HB2 A:ASP98 3.8 52.3 1.0 OE1 A:GLU71 3.9 70.7 1.0 NZ B:LYS254 3.9 50.7 1.0 HZ3 B:LYS254 4.0 54.7 1.0 OD1 A:ASP69 4.0 57.1 1.0 HG3 A:GLU71 4.0 72.1 1.0 HB3 A:GLN11 4.1 52.1 1.0 CG A:GLU71 4.1 68.1 1.0 CB A:GLN11 4.2 46.4 1.0 OD2 A:ASP69 4.2 58.0 1.0 HZ1 B:LYS254 4.3 54.7 1.0 HB3 A:ASP98 4.3 52.3 1.0 N A:GLN11 4.3 42.6 1.0 OD2 A:ASP98 4.4 50.5 1.0 CB A:ASP98 4.5 46.2 1.0 O1G A:GTP501 4.5 40.2 1.0 CG A:ASP69 4.5 56.8 1.0 CD A:GLU71 4.5 69.7 1.0 O1B A:GTP501 4.6 46.5 1.0 O2A A:GTP501 4.6 44.8 1.0 OE1 A:GLN11 4.6 51.0 1.0 HA2 A:GLY10 4.7 45.3 1.0 HG1 A:THR145 4.7 58.6 1.0 PA A:GTP501 4.7 42.1 1.0 HB A:THR145 4.8 43.9 1.0 CG A:ASP98 4.8 48.2 1.0 CA A:GLN11 4.8 44.1 1.0 HG21 A:VAL74 4.9 77.2 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Gdp.Alf 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.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.5 occ:1.00 F2 B:AF3507 1.7 63.9 0.9 O B:HOH626 2.1 39.9 1.0 O B:HOH608 2.1 51.6 1.0 O C:HOH651 2.1 45.7 1.0 OE1 B:GLN11 2.1 53.5 1.0 O1A B:GDP501 2.4 32.7 1.0 AL B:AF3507 2.8 96.0 0.9 CD B:GLN11 3.4 51.6 1.0 HB3 B:GLN11 3.6 50.4 1.0 PA B:GDP501 3.7 35.3 1.0 H8 B:GDP501 3.7 54.5 1.0 F1 B:AF3507 3.7 78.8 0.9 F3 B:AF3507 3.9 71.9 0.9 OD2 B:ASP179 3.9 49.0 1.0 O3A B:GDP501 4.0 34.9 1.0 HB2 B:GLN11 4.1 50.4 1.0 CB B:GLN11 4.2 45.9 1.0 CG B:GLN11 4.2 47.3 1.0 HE22 B:GLN11 4.3 59.8 1.0 HD21 B:ASN101 4.3 47.9 1.0 NE2 B:GLN11 4.3 54.3 1.0 OD1 B:ASN101 4.3 41.5 1.0 C5' B:GDP501 4.4 34.6 1.0 HG2 B:GLN11 4.4 60.5 1.0 OE1 C:GLU254 4.5 48.1 1.0 O5' B:GDP501 4.5 34.6 1.0 C8 B:GDP501 4.7 44.8 1.0 O2A B:GDP501 4.8 34.9 1.0 CG B:ASP179 4.8 49.4 1.0 O1B B:GDP501 4.9 28.3 1.0 HB3 B:ASP179 5.0 54.4 1.0 ND2 B:ASN101 5.0 45.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Gdp.Alf 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.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:33.0 occ:1.00 O2B C:GTP501 2.0 33.0 1.0 O3G C:GTP501 2.0 34.1 1.0 O C:HOH614 2.1 35.5 1.0 O C:HOH637 2.1 38.2 1.0 O C:HOH654 2.1 36.4 1.0 O C:HOH663 2.1 34.6 1.0 PB C:GTP501 3.1 36.8 1.0 PG C:GTP501 3.2 39.7 1.0 HZ1 D:LYS254 3.2 50.3 1.0 HB2 C:GLN11 3.4 36.8 1.0 O1G C:GTP501 3.6 34.1 1.0 O3A C:GTP501 3.6 34.2 1.0 O3B C:GTP501 3.6 40.2 1.0 H C:GLN11 3.6 37.6 1.0 HG2 C:GLU71 3.7 52.2 1.0 HB2 C:ASP98 3.9 49.6 1.0 NZ D:LYS254 4.0 45.6 1.0 OD1 C:ASP69 4.0 41.0 1.0 HZ2 D:LYS254 4.1 50.3 1.0 HG3 C:GLU71 4.1 52.2 1.0 HB3 C:GLN11 4.1 36.8 1.0 OD2 C:ASP69 4.2 42.6 1.0 CB C:GLN11 4.2 41.2 1.0 OE1 C:GLU71 4.2 51.2 1.0 HZ3 D:LYS254 4.2 50.3 1.0 CG C:GLU71 4.3 50.0 1.0 N C:GLN11 4.4 40.3 1.0 OD2 C:ASP98 4.4 48.3 1.0 HB3 C:ASP98 4.4 49.6 1.0 O1B C:GTP501 4.4 38.1 1.0 O2G C:GTP501 4.4 32.3 1.0 CB C:ASP98 4.5 46.4 1.0 CG C:ASP69 4.6 41.6 1.0 O2A C:GTP501 4.6 36.4 1.0 PA C:GTP501 4.6 38.2 1.0 HA2 C:GLY10 4.7 43.2 1.0 HB C:THR145 4.7 42.9 1.0 OE1 C:GLN11 4.8 43.3 1.0 CD C:GLU71 4.8 51.2 1.0 HG1 C:THR145 4.8 49.0 1.0 HG21 C:VAL74 4.9 52.6 1.0 CA C:GLN11 4.9 40.5 1.0 CG C:ASP98 4.9 47.5 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Gdp.Alf 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.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:62.6 occ:1.00 O D:HOH602 2.1 51.8 1.0 O D:HOH601 2.1 61.2 1.0 OE1 D:GLN11 2.1 77.9 1.0 OD1 D:ASP179 2.2 68.8 0.4 O1A D:GDP501 2.3 66.0 1.0 CD D:GLN11 3.4 76.1 1.0 CG D:ASP179 3.4 68.9 0.4 H8 D:GDP501 3.4 81.8 1.0 HD21 D:ASN101 3.7 98.7 1.0 PA D:GDP501 3.8 61.0 1.0 HB3 D:GLN11 4.0 88.3 1.0 OD2 D:ASP179 4.1 68.4 0.4 C5' D:GDP501 4.1 64.7 1.0 HE22 D:GLN11 4.1 77.8 1.0 NE2 D:GLN11 4.2 76.3 1.0 HB3 D:ASP179 4.3 80.2 0.4 O3A D:GDP501 4.3 57.6 1.0 CG D:GLN11 4.3 73.3 1.0 C8 D:GDP501 4.4 67.6 1.0 CB D:ASP179 4.4 69.5 0.4 O5' D:GDP501 4.4 59.6 1.0 HG2 D:GLN11 4.4 0.9 1.0 CB D:GLN11 4.5 70.9 1.0 HB2 D:GLN11 4.5 88.3 1.0 ND2 D:ASN101 4.5 77.2 1.0 HB2 D:ASP179 4.6 80.2 0.4 O2A D:GDP501 4.8 61.1 1.0 H2' D:GDP501 4.9 70.4 1.0 N7 D:GDP501 4.9 55.1 1.0 HD22 D:ASN101 4.9 98.7 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Gdp.Alf 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.Alf Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg502 b:91.4 occ:1.00 O1B F:ACP501 2.0 0.1 1.0 OE1 F:GLU331 2.1 82.6 1.0 OE2 F:GLU331 2.1 83.3 1.0 CD F:GLU331 2.4 82.5 1.0 O2G F:ACP501 2.8 0.8 1.0 OD1 F:ASN333 3.1 81.2 1.0 PB F:ACP501 3.4 0.9 1.0 HD21 F:ASN333 3.5 0.3 1.0 HE3 F:LYS74 3.8 0.1 1.0 HE2 F:LYS74 3.8 0.1 1.0 O3A F:ACP501 3.8 0.6 1.0 CG F:GLU331 3.9 81.7 1.0 CG F:ASN333 3.9 79.8 1.0 PG F:ACP501 3.9 0.2 1.0 ND2 F:ASN333 4.0 79.4 1.0 HG3 F:GLU331 4.2 97.7 1.0 O1G F:ACP501 4.2 92.4 1.0 CE F:LYS74 4.2 82.2 1.0 HG2 F:GLU331 4.3 97.7 1.0 C3B F:ACP501 4.3 0.8 1.0 O2B F:ACP501 4.4 0.1 1.0 HZ2 F:LYS74 4.4 0.9 1.0 HB2 F:GLU331 4.5 0.7 1.0 H3B1 F:ACP501 4.7 0.5 1.0 CB F:GLU331 4.8 83.8 1.0 HD22 F:ASN333 4.8 0.3 1.0 NZ F:LYS74 4.9 82.7 1.0 HA F:ASN333 4.9 83.9 1.0 HB3 F:SER152 4.9 28.5 1.0 HB3 F:GLU331 5.0 0.7 1.0

J.Estevez-Gallego, F.Josa-Prado, R.M.Buey, F.A.Balaguer, A.E.Prota, D.Lucenal-Agell, C.Kamma-Lorger, M.O.Steinmetz, I.Barasoain, S.Kamimura, J.F.Diaz, M.A.Oliva. Structural Model For Differential Cap Maturation at Growing Microtubule Ends Elife 2020.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.50155