Magnesium in PDB 8uty: KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule

The binding sites of Magnesium atom in the KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule (pdb code 8uty). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule, PDB code: 8uty:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:72.8 occ:1.00 O1G A:GTP501 1.9 82.0 1.0 O1B A:GTP501 2.0 84.3 1.0 OE2 A:GLU71 2.0 101.8 1.0 O3B A:GTP501 2.6 75.6 1.0 PG A:GTP501 2.7 75.3 1.0 PB A:GTP501 2.8 75.5 1.0 CD A:GLU71 3.0 102.8 1.0 CG A:GLU71 3.4 101.1 1.0 O2G A:GTP501 3.5 92.6 1.0 O2B A:GTP501 3.6 91.3 1.0 OD1 A:ASP69 3.9 97.2 1.0 O3G A:GTP501 4.0 92.8 1.0 O3A A:GTP501 4.1 75.2 1.0 OE1 A:GLU71 4.1 101.2 1.0 CB A:GLU71 4.3 99.3 1.0 NZ B:LYS252 4.4 75.7 1.0 OG1 A:THR145 4.4 93.5 1.0 CB A:ASP98 4.4 95.8 1.0 OE1 A:GLN11 4.6 89.8 1.0 CB A:GLN11 4.6 73.6 1.0 CG A:ASP69 4.7 96.6 1.0 OD2 A:ASP69 4.8 95.3 1.0 N A:GLN11 4.8 76.7 1.0 OD2 A:ASP98 4.9 104.8 1.0

Magnesium binding site 2 out of 4 in the KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:63.9 occ:1.00 O1B E:GTP501 2.0 80.9 1.0 O1G E:GTP501 2.0 73.5 1.0 OE1 E:GLU71 2.1 101.0 1.0 CD E:GLU71 2.4 101.5 1.0 OE2 E:GLU71 2.7 99.5 1.0 PB E:GTP501 2.9 76.3 1.0 O3B E:GTP501 2.9 59.7 1.0 PG E:GTP501 3.0 63.8 1.0 CG E:GLU71 3.6 98.6 1.0 O2B E:GTP501 3.7 84.2 1.0 OD2 E:ASP69 3.9 94.2 1.0 O2G E:GTP501 4.0 86.5 1.0 O3G E:GTP501 4.0 83.8 1.0 O3A E:GTP501 4.2 72.5 1.0 CG2 E:THR145 4.3 86.1 1.0 CB E:GLN11 4.4 81.4 1.0 CB E:GLU71 4.5 96.1 1.0 OE1 E:GLN11 4.5 94.4 1.0 N E:GLN11 4.6 78.2 1.0 CG E:ASP69 4.8 94.7 1.0 CB E:ASP98 4.8 90.7 1.0 OD1 E:ASP69 4.8 98.9 1.0

Magnesium binding site 3 out of 4 in the KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg501 b:101.6 occ:1.00 OG K:SER104 2.0 112.5 1.0 O2B K:ANP502 2.0 122.0 1.0 OG K:SER215 2.5 106.4 1.0 O1G K:ANP502 2.5 120.6 1.0 PB K:ANP502 3.2 118.3 1.0 CB K:SER104 3.3 113.6 1.0 OD2 K:ASP248 3.4 108.2 1.0 OD1 K:ASP248 3.4 106.0 1.0 CB K:SER215 3.4 104.6 1.0 O1B K:ANP502 3.5 117.8 1.0 PG K:ANP502 3.6 120.2 1.0 N K:SER104 3.6 110.8 1.0 CG K:ASP248 3.8 105.3 1.0 N3B K:ANP502 3.9 116.8 1.0 CA K:SER104 3.9 114.5 1.0 O3G K:ANP502 4.1 122.9 1.0 O K:LEU249 4.4 106.9 1.0 CB K:LYS103 4.4 116.4 1.0 O3A K:ANP502 4.5 116.4 1.0 C K:LYS103 4.6 114.6 1.0 CA K:SER215 4.6 103.2 1.0 O1A K:ANP502 4.6 123.4 1.0 N K:SER215 4.7 104.5 1.0 O2A K:ANP502 4.7 124.5 1.0 NH2 K:ARG203 4.8 100.6 1.0 NH1 K:ARG203 4.9 109.3 1.0 PA K:ANP502 4.9 126.0 1.0 O2G K:ANP502 4.9 119.2 1.0

Magnesium binding site 4 out of 4 in the KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of KIF1A[1-393] P364L Mutant Amp-Pnp Bound Two-Heads-Bound State in Complex with A Microtubule within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg502 b:122.8 occ:1.00 O1B S:GTP501 2.2 122.2 1.0 OE2 S:GLU71 2.2 133.1 1.0 O3B S:GTP501 2.2 110.8 1.0 CD S:GLU71 2.4 130.9 1.0 PB S:GTP501 2.5 123.7 1.0 OE1 S:GLU71 2.8 131.1 1.0 CG S:GLU71 3.2 127.4 1.0 O2B S:GTP501 3.2 115.6 1.0 CB S:GLU71 3.7 124.6 1.0 PG S:GTP501 3.8 118.5 1.0 OD1 S:ASP69 3.9 127.8 1.0 O3A S:GTP501 4.0 119.4 1.0 CB S:ASP98 4.1 132.4 1.0 O2G S:GTP501 4.2 117.8 1.0 O1G S:GTP501 4.4 116.7 1.0 OD2 S:ASP98 4.6 140.6 1.0 O3G S:GTP501 4.6 115.9 1.0 OE1 S:GLN11 4.7 106.8 1.0 OG1 S:THR145 4.7 114.4 1.0 CG2 S:THR145 4.7 119.7 1.0 CG S:ASP69 4.7 122.9 1.0 OD2 S:ASP69 4.8 119.7 1.0 CG S:ASP98 4.8 137.3 1.0 CB S:GLN11 4.9 108.3 1.0 N S:GLN11 4.9 109.8 1.0 N S:GLU71 5.0 134.2 1.0 CA S:GLU71 5.0 128.2 1.0

M.P.M.H.Benoit, L.Rao, A.B.Asenjo, A.Gennerich, H.Sosa. Cryo-Em of Human KIF1A Reveals Its Mechanism of Motility and the Effect of Its Pathogenic Variant P305L To Be Published.