Magnesium in PDB 5w3d: The Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer

The structure of The Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer, PDB code: 5w3d was solved by H.W.Park, Z.Ma, J.Chacko, S.M.Jiang, R.C.Robinson, S.A.Endow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 2.79
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	163.271, 67.249, 94.421, 90.00, 97.92, 90.00
R / Rfree (%)	23.5 / 28

The binding sites of Magnesium atom in the The Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer (pdb code 5w3d). 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 Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer, PDB code: 5w3d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:63.8 occ:1.00 OG1 A:THR441 2.1 60.7 1.0 O2B A:ADP802 2.4 81.6 1.0 O3A A:ADP802 3.0 72.3 1.0 PB A:ADP802 3.3 73.2 1.0 CB A:THR441 3.4 58.5 1.0 N A:THR441 4.0 59.1 1.0 O3B A:ADP802 4.0 72.2 1.0 OD1 A:ASP580 4.0 83.1 1.0 OD2 A:ASP580 4.1 75.3 1.0 CA A:THR441 4.2 56.8 1.0 CG A:ASP580 4.5 76.9 1.0 CG2 A:THR441 4.5 56.0 1.0 O1B A:ADP802 4.5 86.3 1.0 PA A:ADP802 4.6 65.5 1.0 CB A:LYS440 4.8 50.9 1.0 NZ A:LYS440 5.0 55.6 1.0 O2A A:ADP802 5.0 80.2 1.0

Magnesium binding site 2 out of 2 in the The Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of Kinesin-14 Wild-Type Ncd-Adp Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:82.0 occ:1.00 O1B B:ADP802 2.0 99.9 1.0 OG1 B:THR441 2.1 79.5 1.0 PB B:ADP802 3.3 99.3 1.0 CB B:THR441 3.4 82.6 1.0 O3A B:ADP802 3.6 90.6 1.0 OD2 B:ASP580 3.8 97.3 1.0 CB B:SER551 3.8 94.7 1.0 CG2 B:THR441 3.9 82.6 1.0 OG B:SER551 4.1 93.3 1.0 O3B B:ADP802 4.2 0.9 1.0 O2B B:ADP802 4.4 96.4 1.0 CA B:THR441 4.5 82.3 1.0 N B:THR441 4.5 84.5 1.0 NZ B:LYS440 4.5 97.3 1.0 CG B:ASP580 4.7 0.7 1.0 NH2 B:ARG539 4.7 0.6 1.0 OD1 B:ASP580 4.7 0.6 1.0

H.W.Park, Z.Ma, H.Zhu, S.Jiang, R.C.Robinson, S.A.Endow. Structural Basis of Small Molecule Atpase Inhibition of A Human Mitotic Kinesin Motor Protein. Sci Rep V. 7 15121 2017.
ISSN: ESSN 2045-2322
PubMed: 29123223
DOI: 10.1038/S41598-017-14754-6