Magnesium in PDB 4drx: Gtp-Tubulin in Complex with A Darpin

The structure of Gtp-Tubulin in Complex with A Darpin, PDB code: 4drx was solved by L.Pecqueur, B.Gigant, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.19 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	104.884, 90.596, 117.575, 90.00, 90.02, 90.00
R / Rfree (%)	15.9 / 19.4

The binding sites of Magnesium atom in the Gtp-Tubulin in Complex with A Darpin (pdb code 4drx). 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 in Complex with A Darpin, PDB code: 4drx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Gtp-Tubulin in Complex with A Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gtp-Tubulin in Complex with A Darpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:29.2 occ:1.00 O A:HOH779 1.8 33.0 1.0 O A:HOH780 1.9 19.5 1.0 O2B A:GTP600 1.9 29.2 1.0 O A:HOH777 1.9 36.8 1.0 O2G A:GTP600 2.1 35.5 1.0 O A:HOH778 2.1 32.5 1.0 PB A:GTP600 3.1 19.3 1.0 PG A:GTP600 3.1 25.4 1.0 O3G A:GTP600 3.5 33.0 1.0 O3B A:GTP600 3.5 29.0 1.0 OE1 A:GLU71 3.6 55.5 1.0 O3A A:GTP600 3.9 23.7 1.0 OD2 A:ASP69 4.0 26.8 1.0 O2A A:GTP600 4.1 38.7 1.0 CB A:GLN11 4.2 19.9 1.0 NZ B:LYS254 4.2 28.6 1.0 OD2 A:ASP98 4.3 30.1 1.0 O1B A:GTP600 4.3 20.7 1.0 OD1 A:ASP69 4.3 31.8 1.0 N A:GLN11 4.4 29.2 1.0 O1G A:GTP600 4.5 19.6 1.0 CB A:ASP98 4.6 32.7 1.0 CG A:ASP69 4.6 36.5 1.0 PA A:GTP600 4.6 26.8 1.0 OE1 A:GLN11 4.7 40.3 1.0 CG A:ASP98 4.7 34.6 1.0 CD A:GLU71 4.8 56.3 1.0 CA A:GLN11 4.9 27.4 1.0 O A:HOH714 5.0 40.3 1.0

Magnesium binding site 2 out of 4 in the Gtp-Tubulin in Complex with A Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gtp-Tubulin in Complex with A Darpin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:47.6 occ:1.00 O2B B:GTP600 2.1 32.4 1.0 O3G B:GTP600 2.5 69.9 1.0 O B:HOH724 3.0 44.1 1.0 O2G B:GTP600 3.1 58.8 1.0 PG B:GTP600 3.2 61.6 1.0 PB B:GTP600 3.2 36.5 1.0 O3B B:GTP600 3.6 93.4 1.0 OD1 B:ASP69 3.7 46.8 1.0 OD2 B:ASP69 3.8 56.6 1.0 CB B:GLU71 3.8 66.6 1.0 O3A B:GTP600 3.8 0.9 1.0 N B:GLN11 4.0 39.3 1.0 CB B:GLN11 4.1 41.9 1.0 CG B:ASP69 4.2 55.1 1.0 CG B:GLU71 4.3 71.8 1.0 O1B B:GTP600 4.5 51.5 1.0 O1G B:GTP600 4.6 54.1 1.0 CA B:GLN11 4.6 46.9 1.0 OG1 B:THR145 4.7 42.1 1.0 O2A B:GTP600 4.8 51.8 1.0 OE1 B:GLN11 4.8 70.6 1.0 CA B:GLY10 4.9 29.7 1.0 C B:GLY10 4.9 35.9 1.0 OE1 B:GLU71 4.9 82.5 1.0

Magnesium binding site 3 out of 4 in the Gtp-Tubulin in Complex with A Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gtp-Tubulin in Complex with A Darpin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:39.0 occ:1.00 O C:HOH800 1.9 75.0 1.0 O2B C:GTP600 2.1 21.9 1.0 O3G C:GTP600 2.1 20.2 1.0 O C:HOH798 2.2 25.7 1.0 O C:HOH799 2.4 29.7 1.0 O C:HOH755 2.7 20.8 1.0 PB C:GTP600 3.1 31.1 1.0 PG C:GTP600 3.2 27.1 1.0 O3A C:GTP600 3.5 56.9 1.0 O1G C:GTP600 3.5 34.2 1.0 O3B C:GTP600 3.6 33.8 1.0 OE1 C:GLU71 3.6 57.4 1.0 NZ D:LYS254 3.9 31.1 1.0 CB C:GLN11 4.1 21.2 1.0 OD2 C:ASP69 4.2 31.4 1.0 OD2 C:ASP98 4.2 31.9 1.0 O2A C:GTP600 4.4 33.2 1.0 O C:HOH736 4.4 52.2 1.0 PA C:GTP600 4.5 30.4 1.0 O1B C:GTP600 4.5 25.4 1.0 N C:GLN11 4.5 25.0 1.0 OD1 C:ASP69 4.5 34.1 1.0 O2G C:GTP600 4.5 20.9 1.0 OE1 C:GLN11 4.5 37.0 1.0 CB C:ASP98 4.6 32.8 1.0 CG C:ASP98 4.7 32.6 1.0 CG C:ASP69 4.8 35.2 1.0 CD C:GLU71 4.8 55.2 1.0 O1A C:GTP600 4.8 41.5 1.0 CA C:GLN11 4.9 29.0 1.0 CE D:LYS254 5.0 21.8 1.0

Magnesium binding site 4 out of 4 in the Gtp-Tubulin in Complex with A Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gtp-Tubulin in Complex with A Darpin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:67.9 occ:1.00 O1G D:GTP600 1.7 79.9 1.0 O2B D:GTP600 2.4 43.9 1.0 O D:HOH757 2.4 25.7 1.0 PG D:GTP600 2.7 58.6 1.0 O2G D:GTP600 2.9 61.8 1.0 PB D:GTP600 3.4 39.7 1.0 O3B D:GTP600 3.4 46.4 1.0 O3G D:GTP600 4.0 43.8 1.0 O3A D:GTP600 4.1 28.1 1.0 CB D:GLU71 4.2 66.7 1.0 O2A D:GTP600 4.4 45.3 1.0 OD1 D:ASP69 4.4 50.0 1.0 O1B D:GTP600 4.6 51.1 1.0 OG1 D:THR145 4.7 39.5 1.0 OD2 D:ASP69 4.7 58.0 1.0 CG D:GLU71 4.7 72.7 1.0 CB D:GLN11 4.7 42.2 1.0 N D:GLN11 4.8 39.8 1.0 OE1 D:GLU71 4.8 83.0 1.0 PA D:GTP600 4.9 35.6 1.0 CG D:ASP69 5.0 54.8 1.0

L.Pecqueur, C.Duellberg, B.Dreier, Q.Jiang, C.Wang, A.Pluckthun, T.Surrey, B.Gigant, M.Knossow. A Designed Ankyrin Repeat Protein Selected to Bind to Tubulin Caps the Microtubule Plus End. Proc.Natl.Acad.Sci.Usa V. 109 12011 2012.
ISSN: ISSN 0027-8424
PubMed: 22778434
DOI: 10.1073/PNAS.1204129109