Magnesium in PDB 4hna: Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin

The structure of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin, PDB code: 4hna was solved by B.Gigant, M.Knossow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.14 / 3.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.050, 160.540, 174.950, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.1

The structure of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Aluminium	(Al)	2 atoms

The binding sites of Magnesium atom in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin (pdb code 4hna). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin, PDB code: 4hna:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:28.4 occ:1.00 O1G A:GTP600 2.2 65.6 1.0 O1B A:GTP600 2.3 70.1 1.0 PG A:GTP600 3.4 65.9 1.0 PB A:GTP600 3.4 69.6 1.0 O3B A:GTP600 3.7 68.7 1.0 O3A A:GTP600 3.8 68.5 1.0 O2G A:GTP600 3.9 70.4 1.0 NZ B:LYS254 3.9 70.4 1.0 CG A:GLU71 4.0 86.2 1.0 CB A:GLN11 4.1 62.9 1.0 OD2 A:ASP98 4.2 94.8 1.0 OD1 A:ASP69 4.2 73.6 1.0 OD2 A:ASP69 4.2 80.9 1.0 O1A A:GTP600 4.5 69.7 1.0 CD A:GLU71 4.5 0.4 1.0 N A:GLN11 4.5 61.4 1.0 OE1 A:GLN11 4.5 69.1 1.0 OE2 A:GLU71 4.5 0.7 1.0 CB A:ASP98 4.6 66.9 1.0 O3G A:GTP600 4.6 59.1 1.0 CG A:ASP69 4.7 73.8 1.0 PA A:GTP600 4.7 68.5 1.0 O2B A:GTP600 4.7 69.6 1.0 CG A:ASP98 4.8 84.0 1.0 CA A:GLN11 4.9 61.9 1.0

Magnesium binding site 2 out of 3 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:55.8 occ:1.00 F3 B:ALF503 2.1 98.0 1.0 O2B B:GDP501 2.9 76.2 1.0 OE1 B:GLU71 3.3 0.8 1.0 OE2 B:GLU71 3.4 0.9 1.0 CD B:GLU71 3.4 0.2 1.0 CB B:GLN11 3.6 75.8 1.0 F2 B:ALF503 3.7 96.0 1.0 AL B:ALF503 3.8 93.9 1.0 OD2 B:ASP69 3.8 97.5 1.0 CB B:GLU71 4.0 92.9 1.0 N B:GLN11 4.1 72.2 1.0 OD1 B:ASP69 4.2 86.7 1.0 OE1 B:GLN11 4.2 0.7 1.0 CG2 B:THR74 4.2 99.0 1.0 CG B:GLU71 4.2 0.1 1.0 PB B:GDP501 4.3 79.6 1.0 CA B:GLN11 4.3 73.3 1.0 F1 B:ALF503 4.4 99.1 1.0 CG B:ASP69 4.4 87.9 1.0 CG B:GLN11 4.4 89.6 1.0 O3B B:GDP501 4.6 85.3 1.0 CD B:GLN11 4.7 0.6 1.0 O1A B:GDP501 4.9 74.7 1.0 O3A B:GDP501 4.9 79.9 1.0

Magnesium binding site 3 out of 3 in the Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kinesin Motor Domain in the Adp-Mg-Alfx State in Complex with Tubulin and A Darpin within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg402 b:27.4 occ:1.00 OG1 K:THR92 1.9 63.3 1.0 O K:HOH501 2.1 0.8 1.0 O2B K:ADP401 2.1 59.2 1.0 F4 K:ALF403 2.2 55.5 1.0 O K:HOH502 2.3 17.7 1.0 OG K:SER202 2.6 64.2 1.0 CB K:THR92 2.9 61.4 1.0 PB K:ADP401 3.2 59.4 1.0 CB K:SER202 3.2 60.2 1.0 F1 K:ALF403 3.3 50.3 1.0 O1A K:ADP401 3.5 57.6 1.0 O3A K:ADP401 3.6 57.6 1.0 AL K:ALF403 3.6 52.8 1.0 O3B K:ADP401 3.6 55.7 1.0 N K:THR92 3.7 47.6 1.0 CA K:THR92 3.9 47.5 1.0 N K:SER202 3.9 62.5 1.0 CG2 K:THR92 3.9 62.7 1.0 PA K:ADP401 3.9 56.3 1.0 O2A K:ADP401 4.0 57.9 1.0 CA K:SER202 4.2 60.3 1.0 OD1 K:ASP231 4.4 67.9 1.0 OD2 K:ASP231 4.4 71.4 1.0 O1B K:ADP401 4.5 60.3 1.0 O K:HIS200 4.6 72.7 1.0 ND2 K:ASN198 4.7 61.1 1.0 F2 K:ALF403 4.7 54.5 1.0 C K:LYS91 4.9 51.0 1.0 CG K:ASP231 4.9 65.4 1.0 CB K:LYS91 4.9 46.3 1.0

B.Gigant, W.Wang, B.Dreier, Q.Jiang, L.Pecqueur, A.Pluckthun, C.Wang, M.Knossow. Structure of A Kinesin-Tubulin Complex and Implications For Kinesin Motility. Nat.Struct.Mol.Biol. V. 20 1001 2013.
ISSN: ISSN 1545-9993
PubMed: 23872990
DOI: 10.1038/NSMB.2624