Magnesium in PDB 8utp: KIF1A[1-393] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1

The binding sites of Magnesium atom in the KIF1A[1-393] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1 (pdb code 8utp). 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] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1, PDB code: 8utp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the KIF1A[1-393] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1


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] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1 within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg501 b:98.9 occ:1.00 O1G K:ANP502 2.0 108.5 1.0 O2B K:ANP502 2.0 102.4 1.0 OG K:SER215 2.0 93.5 1.0 OG K:SER104 2.1 100.0 1.0 PB K:ANP502 3.1 101.8 1.0 O1B K:ANP502 3.2 103.8 1.0 CB K:SER215 3.2 92.3 1.0 PG K:ANP502 3.3 106.3 1.0 CB K:SER104 3.4 99.8 1.0 N3B K:ANP502 3.9 102.4 1.0 O2G K:ANP502 4.0 103.2 1.0 N K:SER215 4.1 98.9 1.0 N K:SER104 4.1 97.6 1.0 O2A K:ANP502 4.2 102.5 1.0 OD1 K:ASP248 4.2 102.5 1.0 CA K:SER215 4.2 94.2 1.0 OD2 K:ASP248 4.3 104.0 1.0 CA K:SER104 4.3 96.9 1.0 NH1 K:ARG203 4.3 108.2 1.0 O3A K:ANP502 4.4 102.3 1.0 O3G K:ANP502 4.5 106.3 1.0 PA K:ANP502 4.6 109.9 1.0 O1A K:ANP502 4.7 112.2 1.0 CG K:ASP248 4.7 101.7 1.0 C K:SER214 5.0 110.9 1.0

Magnesium binding site 2 out of 4 in the KIF1A[1-393] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1


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] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:78.2 occ:1.00 O1B A:GTP501 1.9 89.8 1.0 O1G A:GTP501 1.9 75.2 1.0 OE2 A:GLU71 1.9 92.2 1.0 PB A:GTP501 3.2 73.1 1.0 CD A:GLU71 3.2 96.0 1.0 PG A:GTP501 3.2 80.0 1.0 O3B A:GTP501 3.6 71.2 1.0 O3A A:GTP501 3.8 63.6 1.0 O3G A:GTP501 3.9 89.6 1.0 OE1 A:GLN11 3.9 77.9 1.0 OE1 A:GLU71 4.0 92.4 1.0 CG A:GLU71 4.1 95.3 1.0 O2G A:GTP501 4.4 94.0 1.0 CB A:GLN11 4.4 69.3 1.0 O2B A:GTP501 4.4 90.8 1.0 OD2 A:ASP98 4.4 104.7 1.0 CD A:GLN11 4.9 79.3 1.0 O2A A:GTP501 5.0 89.4 1.0 CD B:LYS252 5.0 72.7 1.0 PA A:GTP501 5.0 82.8 1.0

Magnesium binding site 3 out of 4 in the KIF1A[1-393] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1


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] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:61.9 occ:1.00 O1B E:GTP501 1.9 84.8 1.0 OE2 E:GLU71 1.9 105.0 1.0 O1G E:GTP501 2.0 76.5 1.0 PB E:GTP501 3.1 64.0 1.0 PG E:GTP501 3.1 87.6 1.0 CD E:GLU71 3.2 103.5 1.0 O3B E:GTP501 3.2 66.5 1.0 O2G E:GTP501 4.0 91.6 1.0 CG E:GLU71 4.0 100.6 1.0 O2B E:GTP501 4.0 81.9 1.0 OE1 E:GLU71 4.1 95.6 1.0 O3A E:GTP501 4.2 64.1 1.0 O3G E:GTP501 4.2 89.3 1.0 OE1 E:GLN11 4.2 85.0 1.0 CB E:GLN11 4.5 76.5 1.0 OD2 E:ASP69 4.6 96.7 1.0 OD1 E:ASP69 4.6 98.7 1.0 O2A E:GTP501 4.6 77.2 1.0 NZ I:LYS252 4.9 77.3 1.0 N E:GLN11 4.9 75.2 1.0 CB E:GLU71 5.0 91.9 1.0

Magnesium binding site 4 out of 4 in the KIF1A[1-393] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1


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] - Amp-Pnp Two-Heads-Bound State in Complex with A Microtubule - Class T3L1 within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg502 b:117.4 occ:1.00 O1G S:GTP501 2.0 122.4 1.0 O3B S:GTP501 2.1 117.9 1.0 O1B S:GTP501 2.1 125.3 1.0 OE1 S:GLU71 2.3 125.7 1.0 PB S:GTP501 2.4 122.2 1.0 PG S:GTP501 2.5 125.6 1.0 O2B S:GTP501 2.9 121.5 1.0 CD S:GLU71 3.3 128.5 1.0 O2G S:GTP501 3.3 125.5 1.0 O3G S:GTP501 3.7 122.6 1.0 O3A S:GTP501 3.9 117.7 1.0 CG S:GLU71 3.9 129.0 1.0 OD1 S:ASP69 4.0 121.8 1.0 OE2 S:GLU71 4.2 127.5 1.0 OG1 S:THR145 4.4 124.3 1.0 CB S:THR145 4.5 121.3 1.0 N S:GLN11 4.7 113.9 1.0 O2A S:GTP501 4.8 123.2 1.0 CG S:ASP69 4.8 124.1 1.0 CB S:ASP98 4.9 126.8 1.0 OD2 S:ASP69 4.9 127.1 1.0 CB S:GLN11 4.9 116.2 1.0 CB S:GLU71 4.9 129.0 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.