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

The structure of The Crystal Structure of the Minimal Core Domain of the Microtubule Depolymerizer KIF2C Complexed with Adp-Mg-Alfx, PDB code: 5xja 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 / 3.43
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.098, 166.989, 74.991, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23

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

Fluorine	(F)	6 atoms
Aluminium	(Al)	2 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-Alfx (pdb code 5xja). 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-Alfx, PDB code: 5xja:
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-Alfx


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-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:1.0 occ:1.00 O1B A:ADP602 1.9 54.2 1.0 O2A A:ADP602 1.9 51.4 1.0 PA A:ADP602 2.4 50.7 1.0 OG1 A:THR351 2.6 39.2 1.0 F2 A:AF3603 2.6 32.1 1.0 O1A A:ADP602 2.7 49.5 1.0 O3A A:ADP602 2.8 50.6 1.0 PB A:ADP602 2.8 47.0 1.0 AL A:AF3603 2.9 34.8 1.0 CB A:THR351 2.9 51.6 1.0 O2B A:ADP602 3.4 46.5 1.0 N A:THR351 3.7 53.5 1.0 CA A:THR351 3.8 54.2 1.0 O5' A:ADP602 3.9 46.8 1.0 O3B A:ADP602 4.1 49.8 1.0 F3 A:AF3603 4.2 36.9 1.0 CG2 A:THR351 4.2 58.9 1.0 F1 A:AF3603 4.2 32.3 1.0 N A:HIS352 4.3 53.9 1.0 C A:THR351 4.5 53.3 1.0 C5' A:ADP602 4.7 50.4 1.0 N A:LYS350 4.8 50.3 1.0 OG A:SER463 4.8 54.2 1.0 C A:LYS350 4.9 48.9 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-Alfx


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-Alfx within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:58.4 occ:1.00 O3B B:ADP602 2.1 46.3 1.0 OG1 B:THR351 2.3 39.5 1.0 AL B:AF3603 2.3 35.0 1.0 O2A B:ADP602 2.7 57.0 1.0 F2 B:AF3603 2.8 33.9 1.0 CB B:THR351 2.9 56.4 1.0 F1 B:AF3603 2.9 34.3 1.0 PA B:ADP602 3.1 51.8 1.0 O1A B:ADP602 3.1 54.5 1.0 PB B:ADP602 3.2 57.4 1.0 O3A B:ADP602 3.6 56.4 1.0 O2B B:ADP602 3.7 61.6 1.0 F3 B:AF3603 3.9 34.7 1.0 CG2 B:THR351 3.9 60.6 1.0 N B:THR351 4.0 59.0 1.0 CA B:THR351 4.0 56.6 1.0 OG B:SER463 4.3 89.1 1.0 O1B B:ADP602 4.5 64.2 1.0 O5' B:ADP602 4.5 47.6 1.0 N B:HIS352 4.8 48.0 1.0 C5' B:ADP602 4.8 46.8 1.0 C B:THR351 4.8 50.4 1.0 OD2 B:ASP488 5.0 43.7 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