Magnesium in PDB 6a1z: Crystal Structure of Dimeric Kinesin-3 KIF13B

The structure of Crystal Structure of Dimeric Kinesin-3 KIF13B, PDB code: 6a1z was solved by J.Q.Ren, S.Wang, W.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.87 / 2.58
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	87.380, 87.380, 97.490, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 28.6

The binding sites of Magnesium atom in the Crystal Structure of Dimeric Kinesin-3 KIF13B (pdb code 6a1z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Dimeric Kinesin-3 KIF13B, PDB code: 6a1z:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Dimeric Kinesin-3 KIF13B


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 Dimeric Kinesin-3 KIF13B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:54.4 occ:1.00 O A:HOH523 1.8 57.4 1.0 O1B A:ADP401 2.3 46.0 1.0 OG A:SER110 2.8 50.6 1.0 PB A:ADP401 3.6 47.6 1.0 CB A:SER110 3.6 42.8 1.0 OD2 A:ASP253 3.9 60.2 1.0 N A:SER110 3.9 48.5 1.0 O A:HOH514 4.0 57.4 1.0 OD1 A:ASP253 4.1 60.1 1.0 O3B A:ADP401 4.2 62.4 1.0 CA A:SER110 4.2 45.6 1.0 CG A:ASP253 4.4 61.0 1.0 O2B A:ADP401 4.4 55.8 1.0 O2A A:ADP401 4.5 62.8 1.0 CB A:LYS109 4.5 45.6 1.0 O3A A:ADP401 4.7 51.1 1.0 C A:LYS109 4.7 49.0 1.0 O A:LEU254 4.9 53.5 1.0 NH1 A:ARG208 4.9 66.5 1.0 NZ A:LYS109 5.0 45.3 1.0 CE A:LYS109 5.0 47.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Dimeric Kinesin-3 KIF13B


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 Dimeric Kinesin-3 KIF13B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:53.7 occ:1.00 O A:THR329 2.7 48.8 1.0 OG1 A:THR343 2.9 52.0 1.0 O A:HOH507 3.1 51.7 1.0 CB A:THR343 3.2 50.7 1.0 CG2 A:THR343 3.4 42.1 1.0 N A:GLN104 3.5 50.8 1.0 CA A:VAL330 3.5 49.4 1.0 C A:THR329 3.7 45.5 1.0 CG1 A:VAL330 3.7 51.2 1.0 CG A:GLN104 3.8 47.1 1.0 CA A:GLY103 3.8 45.9 1.0 CB A:VAL330 4.0 46.0 1.0 CB A:SER107 4.1 50.5 1.0 N A:VAL330 4.1 44.6 1.0 O A:GLU339 4.1 47.6 1.0 OG A:SER107 4.2 50.5 1.0 C A:GLY103 4.2 44.5 1.0 CB A:GLN104 4.2 50.5 1.0 OE1 A:GLN104 4.3 52.0 1.0 CA A:GLN104 4.5 51.0 1.0 CA A:THR340 4.5 50.1 1.0 CD A:GLN104 4.5 50.7 1.0 N A:SER331 4.6 54.2 1.0 C A:GLU339 4.6 47.9 1.0 C A:VAL330 4.6 52.4 1.0 CA A:THR343 4.7 51.9 1.0 N A:THR340 4.8 45.2 1.0 OG1 A:THR340 4.9 44.7 1.0 OG A:SER257 5.0 52.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Dimeric Kinesin-3 KIF13B


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 Dimeric Kinesin-3 KIF13B within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:54.3 occ:1.00 OG A:SER250 2.7 44.2 1.0 O A:ALA97 2.8 48.5 1.0 O A:LYS248 3.2 49.4 1.0 CB A:SER250 3.4 45.9 1.0 N A:SER250 3.5 51.0 1.0 C A:LYS248 3.8 50.3 1.0 OG A:SER317 3.8 52.9 1.0 C A:ALA97 3.9 48.9 1.0 C A:LEU249 4.0 50.7 1.0 CA A:SER250 4.1 47.5 1.0 CB A:LYS248 4.1 53.3 1.0 N A:ALA97 4.1 48.9 1.0 CA A:LEU249 4.2 54.0 1.0 OG A:SER322 4.2 46.0 1.0 N A:LEU249 4.3 50.5 1.0 CB A:ASN96 4.3 48.7 1.0 CB A:CYS98 4.3 48.4 1.0 CA A:LYS248 4.6 53.5 1.0 CA A:ALA97 4.6 45.2 1.0 C A:ASN96 4.7 50.2 1.0 CA A:ASN96 4.7 50.1 1.0 N A:CYS98 4.7 46.8 1.0 CA A:CYS98 4.8 47.3 1.0 O A:LEU249 4.8 47.0 1.0 CG A:ASN96 4.8 48.1 1.0 OD1 A:ASN96 4.9 49.1 1.0

J.Q.Ren, S.Wang, H.Chen, W.J.Wang, L.Huo, W.Feng. Coiled-Coil 1-Mediated Fastening of the Neck and Motor Domains For Kinesin-3 Autoinhibition. Proc. Natl. Acad. Sci. V. 115 11933 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30463954
DOI: 10.1073/PNAS.1811209115