Magnesium in PDB 7x4n: Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin

The structure of Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin, PDB code: 7x4n was solved by S.Taguchi, T.Imasaki, Y.Saijo-Hamano, N.Sakai, R.Nitta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.25 / 2.88
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.33, 80.98, 117.75, 90, 93.51, 90
R / Rfree (%)	21.1 / 29.6

The binding sites of Magnesium atom in the Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin (pdb code 7x4n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin, PDB code: 7x4n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:46.6 occ:1.00 O2B A:GTP501 2.0 43.3 1.0 OE1 A:GLU71 2.0 60.1 1.0 O2G A:GTP501 2.4 37.3 1.0 CD A:GLU71 3.2 56.7 1.0 PB A:GTP501 3.3 42.0 1.0 PG A:GTP501 3.6 41.8 1.0 O3B A:GTP501 3.7 46.6 1.0 CB A:GLN11 3.7 40.2 1.0 OD1 A:ASP69 3.8 57.7 1.0 OD2 A:ASP69 3.9 52.5 1.0 OE2 A:GLU71 4.0 51.8 1.0 CG A:GLU71 4.1 57.0 1.0 O3A A:GTP501 4.1 37.0 1.0 N A:GLN11 4.2 43.5 1.0 CG A:ASP69 4.3 55.3 1.0 O3G A:GTP501 4.3 32.4 1.0 CG A:GLN11 4.4 40.5 1.0 CA A:GLN11 4.4 41.5 1.0 O1B A:GTP501 4.5 48.9 1.0 O1A A:GTP501 4.6 41.1 1.0 NZ B:LYS252 4.6 44.6 1.0 O1G A:GTP501 4.7 29.1 1.0 PA A:GTP501 4.8 41.9 1.0 CD A:GLN11 4.9 43.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of C. Elegans Kinesin-4 Klp-12 Complexed with Tubulin and Darpin within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:40.7 occ:1.00 OG1 E:THR91 2.0 46.6 1.0 O1G E:ANP401 2.3 52.3 1.0 OG E:SER217 2.4 39.7 1.0 O1B E:ANP401 2.5 41.8 1.0 CB E:SER217 3.1 37.6 1.0 O E:LEU262 3.3 39.6 1.0 CB E:THR91 3.4 44.3 1.0 PG E:ANP401 3.4 39.2 1.0 OD2 E:ASP261 3.5 46.0 1.0 OD1 E:ASP261 3.5 44.4 1.0 O3G E:ANP401 3.6 30.8 1.0 N E:THR91 3.7 48.2 1.0 PB E:ANP401 3.7 47.9 1.0 CG E:ASP261 3.8 47.7 1.0 CB E:LYS90 3.9 40.2 1.0 CA E:THR91 4.0 39.1 1.0 CE E:LYS90 4.1 42.1 1.0 N3B E:ANP401 4.1 44.8 1.0 CG2 E:THR91 4.2 46.3 1.0 O2B E:ANP401 4.3 44.6 1.0 C E:LEU262 4.4 42.9 1.0 NH2 E:ARG205 4.4 42.2 1.0 CA E:SER217 4.4 45.0 1.0 N E:SER217 4.5 45.7 1.0 NH1 E:ARG205 4.5 44.2 1.0 C E:LYS90 4.6 46.0 1.0 O2G E:ANP401 4.7 38.8 1.0 NZ E:LYS90 4.7 44.1 1.0 CA E:ALA263 4.7 39.7 1.0 CZ E:ARG205 4.7 40.6 1.0 CD E:LYS90 4.8 42.0 1.0 CA E:LYS90 4.8 46.9 1.0 O E:ASP261 4.9 38.3 1.0 N E:ALA263 5.0 40.2 1.0 O3A E:ANP401 5.0 44.8 1.0 CG E:LYS90 5.0 44.0 1.0 O1A E:ANP401 5.0 35.8 1.0

S.Taguchi, J.Nakano, T.Imasaki, T.Kita, Y.Saijo-Hamano, N.Sakai, H.Shigematsu, H.Okuma, T.Shimizu, E.Nitta, S.Kikkawa, S.Mizobuchi, S.Niwa, R.Nitta. Structural Model of Microtubule Dynamics Inhibition By Kinesin-4 From the Crystal Structure of Klp-12 -Tubulin Complex. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 36065637
DOI: 10.7554/ELIFE.77877