Magnesium in PDB 5mio: KIF2C-Darpin Fusion Protein Bound to Tubulin

The structure of KIF2C-Darpin Fusion Protein Bound to Tubulin, PDB code: 5mio was solved by W.Wang, B.Gigant, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.91 / 3.19
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	51.810, 229.760, 293.950, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.7

The binding sites of Magnesium atom in the KIF2C-Darpin Fusion Protein Bound to Tubulin (pdb code 5mio). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the KIF2C-Darpin Fusion Protein Bound to Tubulin, PDB code: 5mio:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the KIF2C-Darpin Fusion Protein Bound to Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of KIF2C-Darpin Fusion Protein Bound to Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:54.5 occ:1.00 O1B A:GTP501 2.2 93.1 1.0 O1G A:GTP501 2.2 72.5 1.0 PB A:GTP501 3.4 89.3 1.0 PG A:GTP501 3.4 78.7 1.0 O3B A:GTP501 3.7 85.0 1.0 OE1 A:GLU71 3.8 0.4 1.0 OD1 A:ASP69 3.8 72.8 1.0 O3A A:GTP501 3.9 88.9 1.0 OD2 A:ASP69 3.9 72.2 1.0 CB A:GLN11 3.9 83.3 1.0 O2G A:GTP501 4.1 78.1 1.0 CG A:GLU71 4.2 99.0 1.0 N A:GLN11 4.2 82.0 1.0 NZ B:LYS254 4.2 0.6 1.0 CG A:ASP69 4.3 74.0 1.0 OE1 A:GLN11 4.4 0.4 1.0 OD2 A:ASP98 4.4 0.1 1.0 CD A:GLU71 4.4 0.1 1.0 CB A:ASP98 4.5 95.1 1.0 CA A:GLN11 4.6 82.0 1.0 O2B A:GTP501 4.6 88.5 1.0 O3G A:GTP501 4.7 73.5 1.0 O1A A:GTP501 4.8 87.6 1.0 ND2 B:ASN249 4.8 0.4 1.0 PA A:GTP501 4.9 87.2 1.0 OG1 A:THR145 4.9 92.8 1.0 CG A:ASP98 4.9 0.6 1.0

Magnesium binding site 2 out of 2 in the KIF2C-Darpin Fusion Protein Bound to Tubulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of KIF2C-Darpin Fusion Protein Bound to Tubulin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:70.6 occ:1.00 OG C:SER468 1.9 0.8 1.0 CB C:SER468 2.0 0.5 1.0 OG1 C:THR355 2.5 0.6 1.0 O1B C:ANP802 2.6 99.9 1.0 OD1 C:ASP492 2.9 0.4 1.0 O2G C:ANP802 3.2 0.3 1.0 OD2 C:ASP492 3.3 0.3 1.0 CG C:ASP492 3.4 0.6 1.0 NH2 C:ARG456 3.5 91.9 1.0 CA C:SER468 3.5 0.7 1.0 PB C:ANP802 3.9 0.1 1.0 CB C:THR355 4.0 0.3 1.0 O C:LEU493 4.0 77.3 1.0 CZ C:ARG456 4.1 0.3 1.0 N C:SER468 4.1 0.2 1.0 PG C:ANP802 4.1 0.8 1.0 O3G C:ANP802 4.2 0.1 1.0 CE C:LYS354 4.3 0.5 1.0 C C:SER468 4.4 0.7 1.0 N C:THR355 4.4 96.2 1.0 N3B C:ANP802 4.4 0.9 1.0 O C:SER468 4.5 0.8 1.0 NE C:ARG456 4.5 0.1 1.0 O2B C:ANP802 4.5 97.8 1.0 CA C:THR355 4.6 97.2 1.0 CB C:LYS354 4.6 91.0 1.0 NH1 C:ARG456 4.6 67.6 1.0 CB C:ASP492 4.8 77.5 1.0 CG2 C:THR355 4.9 0.7 1.0 CA C:ALA494 4.9 80.8 1.0 N C:GLY495 4.9 91.0 1.0 C C:LEU493 5.0 77.8 1.0

W.Wang, S.Cantos-Fernandes, Y.Lv, H.Kuerban, S.Ahmad, C.Wang, B.Gigant. Insight Into Microtubule Disassembly By Kinesin-13S From the Structure of KIF2C Bound to Tubulin. Nat Commun V. 8 70 2017.
ISSN: ESSN 2041-1723
PubMed: 28694425
DOI: 10.1038/S41467-017-00091-9