Magnesium in PDB 3ryh: Gmpcpp-Tubulin: RB3 Stathmin-Like Domain Complex

The structure of Gmpcpp-Tubulin: RB3 Stathmin-Like Domain Complex, PDB code: 3ryh 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)	42.13 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.270, 128.210, 250.430, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 21.7

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

Magnesium binding site 1 out of 4 in the Gmpcpp-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 Gmpcpp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:75.1 occ:1.00 O A:HOH613 2.0 76.6 1.0 O A:HOH612 2.1 56.4 1.0 O1G A:GTP600 2.1 59.4 1.0 O A:HOH610 2.1 53.3 1.0 O A:HOH611 2.2 58.6 1.0 O1B A:GTP600 2.3 57.2 1.0 PG A:GTP600 3.3 57.5 1.0 PB A:GTP600 3.4 57.4 1.0 O3A A:GTP600 3.8 57.9 1.0 O3B A:GTP600 3.8 57.4 1.0 NZ B:LYS254 3.9 81.9 1.0 O2G A:GTP600 4.0 58.8 1.0 OD2 A:ASP98 4.0 77.3 1.0 OD2 A:ASP69 4.2 77.9 1.0 OD1 A:ASP69 4.3 78.8 1.0 CB A:GLN11 4.3 60.2 1.0 CB A:ASP98 4.4 70.7 1.0 O3G A:GTP600 4.5 56.3 1.0 OE1 A:GLU71 4.5 79.6 1.0 CG A:ASP98 4.6 73.8 1.0 N A:GLN11 4.6 60.0 1.0 CG A:ASP69 4.7 77.6 1.0 O2B A:GTP600 4.7 57.5 1.0 O1A A:GTP600 4.7 58.0 1.0 PA A:GTP600 4.8 57.9 1.0 CE B:LYS254 4.9 75.7 1.0 CB A:GLU71 5.0 78.7 1.0

Magnesium binding site 2 out of 4 in the Gmpcpp-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 Gmpcpp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:50.7 occ:1.00 O B:HOH611 2.1 51.8 1.0 O B:HOH610 2.1 64.0 1.0 O1B B:G2P600 2.4 71.8 1.0 O1G B:G2P600 2.5 74.3 1.0 PG B:G2P600 3.5 73.6 1.0 PB B:G2P600 3.7 68.4 1.0 O3B B:G2P600 3.8 70.4 1.0 O2G B:G2P600 3.9 76.0 1.0 CB B:GLN11 4.2 70.6 1.0 OD2 B:ASP69 4.2 84.2 1.0 C3A B:G2P600 4.2 66.4 1.0 N B:GLN11 4.5 67.2 1.0 OD1 B:ASP69 4.5 78.0 1.0 CB B:GLU71 4.6 77.7 1.0 O1A B:G2P600 4.6 64.9 1.0 OE1 B:GLU71 4.6 0.6 1.0 CG B:ASP69 4.8 79.9 1.0 O3G B:G2P600 4.9 71.8 1.0 PA B:G2P600 4.9 65.7 1.0 CA B:GLN11 4.9 68.6 1.0

Magnesium binding site 3 out of 4 in the Gmpcpp-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 Gmpcpp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:67.8 occ:1.00 O C:HOH611 2.0 79.2 1.0 O C:HOH610 2.0 76.9 1.0 O1B C:GTP600 2.0 69.8 1.0 O1G C:GTP600 2.1 72.9 1.0 O C:HOH612 2.1 66.9 1.0 O C:HOH613 2.2 52.7 1.0 PB C:GTP600 3.2 69.6 1.0 PG C:GTP600 3.3 70.0 1.0 O3B C:GTP600 3.7 69.4 1.0 O3A C:GTP600 3.7 70.3 1.0 OE1 C:GLU71 4.0 0.2 1.0 O2G C:GTP600 4.1 71.0 1.0 CB C:GLN11 4.1 62.9 1.0 OD2 C:ASP98 4.1 78.6 1.0 OD2 C:ASP69 4.2 75.5 1.0 NZ D:LYS254 4.2 89.0 1.0 O1A C:GTP600 4.2 72.1 1.0 O3G C:GTP600 4.4 70.7 1.0 N C:GLN11 4.5 61.9 1.0 O2B C:GTP600 4.5 69.7 1.0 PA C:GTP600 4.5 71.4 1.0 OD1 C:ASP69 4.5 73.5 1.0 CB C:ASP98 4.5 64.7 1.0 CD C:GLU71 4.6 0.8 1.0 CG C:ASP98 4.7 73.4 1.0 CG C:ASP69 4.8 73.4 1.0 CA C:GLN11 4.9 61.9 1.0 OE2 C:GLU71 4.9 94.7 1.0 OG1 C:THR145 5.0 61.8 1.0

Magnesium binding site 4 out of 4 in the Gmpcpp-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 Gmpcpp-Tubulin: RB3 Stathmin-Like Domain Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:75.2 occ:1.00 O D:HOH615 2.0 99.5 1.0 O D:HOH613 2.0 0.5 1.0 O D:HOH614 2.1 90.2 1.0 O1B D:G2P600 2.1 72.7 1.0 O D:HOH612 2.1 61.1 1.0 O1G D:G2P600 2.1 84.4 1.0 PG D:G2P600 3.1 81.1 1.0 PB D:G2P600 3.3 70.8 1.0 O3B D:G2P600 3.4 76.6 1.0 O2G D:G2P600 3.4 84.4 1.0 C3A D:G2P600 3.9 68.9 1.0 OD1 D:ASP69 4.2 80.3 1.0 CB D:GLN11 4.2 73.7 1.0 N D:GLN11 4.3 71.8 1.0 OD2 D:ASP69 4.4 85.8 1.0 O1A D:G2P600 4.4 70.5 1.0 CB D:GLU71 4.4 88.4 1.0 O3G D:G2P600 4.5 80.4 1.0 O2B D:G2P600 4.6 67.1 1.0 PA D:G2P600 4.6 70.2 1.0 CG D:ASP69 4.7 80.6 1.0 OE1 D:GLU71 4.8 0.7 1.0 CA D:GLN11 4.9 72.2 1.0 CG D:GLU71 4.9 99.4 1.0 OG1 D:THR145 4.9 84.5 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