Magnesium in PDB 6bbn: Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A

The structure of Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A, PDB code: 6bbn was solved by J.S.Allingham, D.Trofimova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 3.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	145.052, 82.188, 147.658, 90.00, 109.33, 90.00
R / Rfree (%)	23.6 / 28.7

The binding sites of Magnesium atom in the Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A (pdb code 6bbn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A, PDB code: 6bbn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A


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 A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:0.7 occ:1.00 O2B A:GTP501 2.0 0.8 1.0 O1G A:GTP501 2.1 0.9 1.0 OE1 A:GLU71 2.1 1.0 1.0 O3G A:GTP501 2.2 0.1 1.0 PG A:GTP501 2.6 0.2 1.0 PB A:GTP501 3.1 0.8 1.0 CD A:GLU71 3.2 0.2 1.0 O3B A:GTP501 3.2 0.7 1.0 O3A A:GTP501 3.7 0.2 1.0 OE2 A:GLU71 3.8 0.2 1.0 O2G A:GTP501 4.0 0.0 1.0 CB A:GLN11 4.0 0.6 1.0 OE1 A:GLN11 4.1 0.1 1.0 N A:GLN11 4.3 0.2 1.0 CG A:GLU71 4.4 0.6 1.0 O1B A:GTP501 4.4 0.2 1.0 CB A:GLU71 4.4 0.8 1.0 OD2 A:ASP69 4.4 0.1 1.0 OD1 A:ASP69 4.5 0.6 1.0 CA A:GLN11 4.7 1.0 1.0 OG1 A:THR145 4.8 0.5 1.0 PA A:GTP501 4.8 0.5 1.0 CB A:ASP98 4.9 0.5 1.0 O2A A:GTP501 4.9 0.8 1.0 CG A:ASP69 4.9 0.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A


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 A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:0.7 occ:1.00 O2B B:GDP501 2.2 0.5 1.0 OE1 B:GLU71 2.9 0.4 1.0 PB B:GDP501 3.6 0.6 1.0 OG1 B:THR145 3.7 0.4 1.0 CB B:GLN11 3.8 0.4 1.0 CD B:GLU71 3.8 0.7 1.0 O3B B:GDP501 3.9 0.2 1.0 CG B:GLU71 3.9 0.3 1.0 CB B:GLU71 4.0 0.2 1.0 OD1 B:ASP69 4.1 0.3 1.0 OE1 B:GLN11 4.1 0.6 1.0 N B:GLN11 4.2 0.6 1.0 OD2 B:ASP69 4.4 0.8 1.0 O3A B:GDP501 4.4 1.0 1.0 CA B:GLN11 4.5 0.2 1.0 O1B B:GDP501 4.7 0.1 1.0 CG B:ASP69 4.7 0.7 1.0 CG B:GLN11 4.8 0.9 1.0 CB B:THR145 4.8 0.8 1.0 CD B:GLN11 4.9 0.5 1.0 N B:GLU71 4.9 0.2 1.0 OE2 B:GLU71 4.9 0.3 1.0 CA B:GLU71 5.0 0.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:0.3 occ:1.00 O2G C:GTP501 2.2 0.3 1.0 O2B C:GTP501 2.3 0.7 1.0 OD1 C:ASP69 2.5 0.6 1.0 OD2 C:ASP69 2.7 0.2 1.0 CG C:ASP69 3.0 0.9 1.0 PG C:GTP501 3.4 0.5 1.0 OE1 C:GLU71 3.4 0.3 1.0 PB C:GTP501 3.5 0.2 1.0 O3B C:GTP501 3.7 0.7 1.0 OG1 C:THR145 3.8 0.8 1.0 O3G C:GTP501 3.9 0.8 1.0 N C:GLN11 4.1 0.4 1.0 CB C:GLN11 4.4 0.6 1.0 O1B C:GTP501 4.4 0.8 1.0 CB C:ASP98 4.4 0.6 1.0 CB C:ASP69 4.5 0.8 1.0 CB C:GLU71 4.5 0.2 1.0 CG2 C:VAL74 4.6 0.2 1.0 CD C:GLU71 4.6 0.2 1.0 O1G C:GTP501 4.6 0.4 1.0 CB C:THR145 4.6 0.5 1.0 CA C:GLN11 4.6 1.0 1.0 O3A C:GTP501 4.7 0.7 1.0 OE1 C:GLN11 4.7 0.4 1.0 N C:GLU71 4.7 0.0 1.0 N C:LEU70 4.8 0.2 1.0 O C:GLU71 4.8 0.1 1.0 C C:GLY10 4.9 0.8 1.0 CA C:GLY10 4.9 0.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Curved Tubulin Complex Induced By the Kinesin- 13 KIF2A within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg602 b:0.3 occ:1.00 OG1 E:THR320 1.9 0.7 1.0 OG E:SER433 2.2 0.3 1.0 O2B E:ANP601 2.4 0.8 1.0 O2G E:ANP601 2.4 0.7 1.0 CB E:SER433 2.8 0.6 1.0 O1G E:ANP601 3.1 0.6 1.0 OD2 E:ASP457 3.1 0.4 1.0 PG E:ANP601 3.3 0.8 1.0 CB E:THR320 3.3 0.7 1.0 OD1 E:ASP457 3.5 0.2 1.0 O E:LEU458 3.6 0.3 1.0 CG E:ASP457 3.7 0.2 1.0 PB E:ANP601 3.8 0.1 1.0 N E:THR320 3.8 0.2 1.0 CA E:SER433 4.0 0.9 1.0 CA E:THR320 4.0 0.9 1.0 O1A E:ANP601 4.1 0.5 1.0 CG2 E:THR320 4.1 0.8 1.0 N E:SER433 4.2 0.5 1.0 O E:SER433 4.2 0.9 1.0 N3B E:ANP601 4.2 0.9 1.0 O2A E:ANP601 4.3 0.5 1.0 CE E:LYS319 4.3 0.9 1.0 NH1 E:ARG421 4.3 0.8 1.0 NH2 E:ARG421 4.5 0.3 1.0 O3G E:ANP601 4.6 0.5 1.0 O1B E:ANP601 4.6 0.1 1.0 PA E:ANP601 4.6 0.5 1.0 C E:SER433 4.6 0.6 1.0 C E:LEU458 4.6 0.8 1.0 CB E:LYS319 4.6 0.9 1.0 CZ E:ARG421 4.7 0.9 1.0 O3A E:ANP601 4.7 0.3 1.0 C E:LYS319 4.8 0.9 1.0 CA E:ALA459 4.9 0.5 1.0 NZ E:LYS319 4.9 0.8 1.0

D.Trofimova, M.Paydar, A.Zara, L.Talje, B.H.Kwok, J.S.Allingham. Ternary Complex of KIF2A-Bound Tandem Tubulin Heterodimers Represents A Kinesin-13-Mediated Microtubule Depolymerization Reaction Intermediate. Nat Commun V. 9 2628 2018.
ISSN: ESSN 2041-1723
PubMed: 29980677
DOI: 10.1038/S41467-018-05025-7