Magnesium in PDB 3ryf: Gtp-Tubulin: RB3 Stathmin-Like Domain Complex

The structure of Gtp-Tubulin: RB3 Stathmin-Like Domain Complex, PDB code: 3ryf was solved by A.Nawrotek, M.Knossow, B.Gigant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.90 / 2.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.640, 127.440, 250.260, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.8

The binding sites of Magnesium atom in the Gtp-Tubulin: RB3 Stathmin-Like Domain Complex (pdb code 3ryf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Gtp-Tubulin: RB3 Stathmin-Like Domain Complex, PDB code: 3ryf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Gtp-Tubulin: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gtp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:48.5 occ:1.00 O A:HOH611 2.0 45.1 1.0 O A:HOH613 2.0 44.2 1.0 O1G A:GTP600 2.1 49.2 1.0 O1B A:GTP600 2.1 47.9 1.0 O A:HOH610 2.2 46.1 1.0 O A:HOH612 2.2 49.9 1.0 PG A:GTP600 3.1 47.5 1.0 PB A:GTP600 3.2 48.0 1.0 O3B A:GTP600 3.5 48.2 1.0 O2G A:GTP600 3.6 49.0 1.0 O3A A:GTP600 3.7 47.9 1.0 OE1 A:GLU71 3.7 77.8 1.0 OD2 A:ASP69 4.0 55.9 1.0 NZ B:LYS254 4.1 69.1 1.0 OD2 A:ASP98 4.2 52.6 1.0 OD1 A:ASP69 4.3 51.8 1.0 CB A:GLN11 4.3 49.8 1.0 N A:GLN11 4.4 48.8 1.0 CB A:ASP98 4.4 53.5 1.0 O3G A:GTP600 4.5 49.8 1.0 O2B A:GTP600 4.6 47.7 1.0 CG A:ASP69 4.6 54.2 1.0 CG A:ASP98 4.6 55.5 1.0 O1A A:GTP600 4.7 48.4 1.0 PA A:GTP600 4.8 48.0 1.0 OG1 A:THR145 4.9 45.1 1.0 CD A:GLU71 4.9 82.1 1.0 CA A:GLN11 5.0 49.3 1.0

Magnesium binding site 2 out of 4 in the Gtp-Tubulin: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gtp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:84.9 occ:0.60 O B:HOH610 2.0 71.9 0.6 O B:HOH611 2.1 78.6 0.6 O B:HOH610 2.1 38.8 0.4 O B:HOH611 2.1 49.7 0.4 O2G B:GTP600 2.1 81.4 0.6 O1B B:GTP600 2.2 77.2 0.6 O B:HOH612 2.2 80.7 0.6 O1B B:GTP600 2.9 32.9 0.4 PG B:GTP600 3.2 79.6 0.6 PB B:GTP600 3.4 76.8 0.6 O3G B:GTP600 3.4 82.2 0.6 O3B B:GTP600 3.8 76.5 0.6 PB B:GTP600 4.0 32.4 0.4 CB B:GLN11 4.1 58.8 1.0 O B:HOH652 4.1 81.3 1.0 O3A B:GTP600 4.2 76.8 0.6 O B:HOH612 4.2 31.3 0.4 O3A B:GTP600 4.3 32.7 0.4 O1G B:GTP600 4.4 81.1 0.6 OD2 B:ASP69 4.4 62.7 1.0 N B:GLN11 4.5 54.1 1.0 OD1 B:ASP69 4.5 58.3 1.0 O3B B:GTP600 4.5 31.7 0.4 O B:HOH670 4.5 69.9 1.0 CB B:GLU71 4.5 76.6 1.0 O2B B:GTP600 4.5 76.5 0.6 O1A B:GTP600 4.6 78.4 0.6 OE1 B:GLU71 4.8 0.6 1.0 PA B:GTP600 4.8 77.0 0.6 CA B:GLN11 4.8 56.6 1.0 CG B:ASP69 4.9 60.1 1.0 CG B:GLU71 4.9 90.0 1.0 CG B:GLN11 4.9 79.8 1.0 O2A B:GTP600 5.0 77.4 0.6 O B:HOH677 5.0 87.2 1.0

Magnesium binding site 3 out of 4 in the Gtp-Tubulin: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gtp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:47.4 occ:1.00 O C:HOH613 1.9 52.6 1.0 O D:HOH610 2.0 52.2 1.0 O C:HOH611 2.0 41.7 1.0 O1G C:GTP600 2.0 51.2 1.0 O C:HOH612 2.1 47.3 1.0 O1B C:GTP600 2.1 51.8 1.0 PG C:GTP600 3.1 48.5 1.0 PB C:GTP600 3.2 52.0 1.0 O3B C:GTP600 3.5 51.2 1.0 O2G C:GTP600 3.6 49.3 1.0 O3A C:GTP600 3.7 53.7 1.0 OD2 C:ASP69 4.0 56.8 1.0 NZ D:LYS254 4.1 49.7 1.0 OD1 C:ASP69 4.1 56.9 1.0 OD2 C:ASP98 4.2 55.0 1.0 CB C:GLN11 4.3 52.0 1.0 OE1 C:GLU71 4.4 87.7 1.0 N C:GLN11 4.4 48.9 1.0 CB C:ASP98 4.4 52.6 1.0 O3G C:GTP600 4.5 48.5 1.0 CG C:ASP69 4.5 57.5 1.0 O2B C:GTP600 4.5 51.1 1.0 CG C:ASP98 4.7 55.7 1.0 O1A C:GTP600 4.7 55.6 1.0 CD C:GLU71 4.7 91.8 1.0 OE2 C:GLU71 4.8 98.2 1.0 PA C:GTP600 4.9 54.6 1.0 OG1 C:THR145 4.9 61.6 1.0 CA C:GLN11 5.0 50.2 1.0

Magnesium binding site 4 out of 4 in the Gtp-Tubulin: RB3 Stathmin-Like Domain Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gtp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:64.0 occ:1.00 O D:HOH611 2.1 55.7 1.0 O D:HOH696 2.2 61.9 1.0 O1B D:GTP600 2.3 53.6 1.0 O D:HOH612 2.4 79.5 1.0 O1G D:GTP600 2.4 61.9 1.0 PG D:GTP600 3.3 59.7 1.0 PB D:GTP600 3.4 53.7 1.0 O2G D:GTP600 3.4 62.6 1.0 O3B D:GTP600 3.7 54.9 1.0 OE1 D:GLU71 3.8 0.2 1.0 CB D:GLN11 3.9 50.6 1.0 O3A D:GTP600 4.0 52.4 1.0 N D:GLN11 4.1 49.0 1.0 O1A D:GTP600 4.2 52.9 1.0 O D:HOH640 4.3 47.0 1.0 OD2 D:ASP69 4.3 72.0 1.0 OD1 D:ASP69 4.3 65.5 1.0 CA D:GLN11 4.6 49.7 1.0 PA D:GTP600 4.6 52.1 1.0 CB D:GLU71 4.7 70.1 1.0 O2B D:GTP600 4.7 52.9 1.0 OE1 D:GLN11 4.7 85.9 1.0 O3G D:GTP600 4.8 62.5 1.0 CG D:ASP69 4.8 66.6 1.0 CD D:GLU71 4.8 0.3 1.0 O2A D:GTP600 4.8 51.8 1.0 CG D:GLN11 4.9 64.9 1.0

A.Nawrotek, M.Knossow, B.Gigant. The Determinants That Govern Microtubule Assembly From the Atomic Structure of Gtp-Tubulin. J.Mol.Biol. V. 412 35 2011.
ISSN: ISSN 0022-2836
PubMed: 21787788
DOI: 10.1016/J.JMB.2011.07.029