Magnesium in PDB 5xjb: The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx

The structure of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx, PDB code: 5xjb was solved by T.Ogawa, X.Jiang, N.Hirokawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.452, 166.593, 75.500, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26.1

The structure of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx (pdb code 5xjb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx, PDB code: 5xjb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:66.9 occ:1.00 OG1 A:THR351 2.4 60.6 1.0 OG A:SER463 2.5 0.7 1.0 O2B A:ADP601 2.5 82.9 1.0 F1 A:BEF602 2.9 0.5 1.0 O3A A:ADP601 3.3 73.0 1.0 BE A:BEF602 3.4 0.3 1.0 PB A:ADP601 3.5 75.8 1.0 CB A:THR351 3.6 62.2 1.0 CB A:SER463 3.8 1.0 1.0 O1B A:ADP601 4.0 76.2 1.0 F3 A:BEF602 4.0 0.5 1.0 OG A:SER464 4.3 0.2 1.0 CG2 A:THR351 4.3 63.5 1.0 OD2 A:ASP488 4.5 67.2 1.0 C A:SER463 4.5 0.4 1.0 N A:SER464 4.5 0.6 1.0 CB A:SER464 4.5 0.1 1.0 F2 A:BEF602 4.6 0.8 1.0 CA A:SER463 4.6 0.5 1.0 NH1 A:ARG452 4.6 0.6 1.0 OD1 A:ASP488 4.7 57.6 1.0 CA A:THR351 4.8 65.7 1.0 PA A:ADP601 4.8 75.7 1.0 N A:THR351 4.8 61.9 1.0 O3B A:ADP601 4.8 67.8 1.0 O A:SER463 4.9 94.3 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Befx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:62.7 occ:1.00 O1B B:ADP601 2.4 75.2 1.0 OG1 B:THR351 2.4 56.1 1.0 OG B:SER464 2.4 0.7 1.0 F1 B:BEF602 3.1 0.5 1.0 BE B:BEF602 3.1 1.0 1.0 F3 B:BEF602 3.4 0.5 1.0 PB B:ADP601 3.6 68.8 1.0 CB B:THR351 3.6 57.9 1.0 CB B:SER464 3.8 0.3 1.0 O3B B:ADP601 3.8 68.0 1.0 O2A B:ADP601 4.0 84.8 1.0 F2 B:BEF602 4.2 0.4 1.0 OD2 B:ASP488 4.3 65.6 1.0 OD1 B:ASP488 4.3 60.8 1.0 N B:SER464 4.4 0.2 1.0 CA B:SER464 4.4 0.0 1.0 CG2 B:THR351 4.4 59.6 1.0 NH1 B:ARG452 4.5 0.9 1.0 O2B B:ADP601 4.6 69.2 1.0 OG B:SER463 4.6 0.9 1.0 O3A B:ADP601 4.7 73.2 1.0 N B:THR351 4.7 55.3 1.0 C B:SER463 4.7 0.1 1.0 CA B:THR351 4.7 60.5 1.0 CG B:ASP488 4.8 59.9 1.0 CB B:SER463 4.8 0.1 1.0 PA B:ADP601 4.8 77.5 1.0

T.Ogawa, S.Saijo, N.Shimizu, X.Jiang, N.Hirokawa. Mechanism of Catalytic Microtubule Depolymerization Via KIF2-Tubulin Transitional Conformation Cell Rep V. 20 2626 2017.
ISSN: ESSN 2211-1247
PubMed: 28903043
DOI: 10.1016/J.CELREP.2017.08.067