Magnesium in PDB 9l7m: Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule

The binding sites of Magnesium atom in the Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule (pdb code 9l7m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule, PDB code: 9l7m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:57.3 occ:1.00 O3G A:GTP501 1.6 53.9 1.0 OE1 A:GLU71 1.9 55.0 1.0 O2G A:GTP501 1.9 53.9 1.0 O1B A:GTP501 1.9 53.9 1.0 CD A:GLU71 2.0 55.0 1.0 PG A:GTP501 2.1 53.9 1.0 OE2 A:GLU71 2.2 55.0 1.0 PB A:GTP501 2.9 53.9 1.0 O3B A:GTP501 3.0 53.9 1.0 CG A:GLU71 3.1 55.0 1.0 O1G A:GTP501 3.4 53.9 1.0 O1A A:GTP501 3.4 53.9 1.0 O3A A:GTP501 3.4 53.9 1.0 PA A:GTP501 4.1 53.9 1.0 O2B A:GTP501 4.2 53.9 1.0 CB A:GLU71 4.4 55.0 1.0 CG A:GLN11 4.4 51.9 1.0 N A:GLN11 4.5 51.9 1.0 OG1 A:THR145 4.5 52.6 1.0 CB A:GLN11 4.6 51.9 1.0 CB A:THR145 4.9 52.6 1.0 NE2 A:GLN11 5.0 51.9 1.0 O2A A:GTP501 5.0 53.9 1.0 CD A:GLN11 5.0 51.9 1.0

Magnesium binding site 2 out of 4 in the Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:44.9 occ:1.00 O1B B:GTP501 1.7 46.0 1.0 O2G B:GTP501 1.9 46.0 1.0 PG B:GTP501 2.0 46.0 1.0 O3B B:GTP501 2.0 46.0 1.0 O3G B:GTP501 2.0 46.0 1.0 PB B:GTP501 2.3 46.0 1.0 OE2 B:GLU71 2.4 40.1 1.0 O3A B:GTP501 3.3 46.0 1.0 CD B:GLU71 3.3 40.1 1.0 O1G B:GTP501 3.5 46.0 1.0 O2B B:GTP501 3.5 46.0 1.0 OE1 B:GLU71 3.9 40.1 1.0 OE1 A:GLU254 4.2 49.1 1.0 CG B:GLU71 4.4 40.1 1.0 OG1 B:THR145 4.6 43.5 1.0 PA B:GTP501 4.8 46.0 1.0 N B:GLY144 4.8 44.8 1.0 CB B:ALA99 4.9 42.4 1.0 N B:THR145 4.9 43.5 1.0 ND2 B:ASN101 4.9 43.0 1.0

Magnesium binding site 3 out of 4 in the Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.9 occ:1.00 O3G C:GTP501 1.6 38.6 1.0 OE1 C:GLU71 1.9 41.4 1.0 O2G C:GTP501 1.9 38.6 1.0 O1B C:GTP501 1.9 38.6 1.0 CD C:GLU71 2.0 41.4 1.0 PG C:GTP501 2.1 38.6 1.0 OE2 C:GLU71 2.2 41.4 1.0 PB C:GTP501 2.9 38.6 1.0 O3B C:GTP501 3.0 38.6 1.0 CG C:GLU71 3.1 41.4 1.0 O1G C:GTP501 3.4 38.6 1.0 O1A C:GTP501 3.4 38.6 1.0 O3A C:GTP501 3.4 38.6 1.0 PA C:GTP501 4.1 38.6 1.0 O2B C:GTP501 4.2 38.6 1.0 NZ B:LYS254 4.4 39.0 1.0 CB C:GLU71 4.4 41.4 1.0 CG C:GLN11 4.4 37.2 1.0 N C:GLN11 4.5 37.2 1.0 OG1 C:THR145 4.5 36.7 1.0 CB C:GLN11 4.6 37.2 1.0 CB C:THR145 4.9 36.7 1.0 NE2 C:GLN11 5.0 37.2 1.0 O2A C:GTP501 5.0 38.6 1.0 CD C:GLN11 5.0 37.2 1.0

Magnesium binding site 4 out of 4 in the Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nucleotide-Free Kinesin-1 Motor Domain Bound to the Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:44.1 occ:1.00 O1B D:GTP501 1.7 47.3 1.0 O2G D:GTP501 1.9 47.3 1.0 PG D:GTP501 2.0 47.3 1.0 O3B D:GTP501 2.0 47.3 1.0 O3G D:GTP501 2.0 47.3 1.0 PB D:GTP501 2.3 47.3 1.0 OE2 D:GLU71 2.4 41.5 1.0 O3A D:GTP501 3.3 47.3 1.0 CD D:GLU71 3.3 41.5 1.0 O1G D:GTP501 3.5 47.3 1.0 O2B D:GTP501 3.5 47.3 1.0 OE1 D:GLU71 3.9 41.5 1.0 OE1 C:GLU254 4.2 44.6 1.0 CG D:GLU71 4.4 41.5 1.0 OG1 D:THR145 4.6 44.8 1.0 PA D:GTP501 4.8 47.3 1.0 N D:GLY144 4.8 46.0 1.0 CB D:ALA99 4.9 42.8 1.0 N D:THR145 4.9 44.8 1.0 ND2 D:ASN101 4.9 43.1 1.0

T.Makino, R.Kanada, T.Mori, K.I.Miyazono, Y.Komori, H.Yanagisawa, S.Takada, M.Tanokura, M.Kikkawa, M.Tomishige. Tension-Induced Suppression of Allosteric Conformational Changes Coordinates Kinesin-1 Stepping Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.09.19.613825