Magnesium in PDB 9dkx: Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1.

The binding sites of Magnesium atom in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1. (pdb code 9dkx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1., PDB code: 9dkx:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4105 b:84.0 occ:1.00 O1B A:ADP4102 2.0 78.0 1.0 CG2 A:THR1803 2.5 72.9 1.0 PB A:ADP4102 3.1 89.0 1.0 O3B A:ADP4102 3.3 85.3 1.0 CB A:THR1803 3.7 71.1 1.0 OG1 A:THR1803 3.9 67.4 1.0 O2B A:ADP4102 4.1 85.7 1.0 O3A A:ADP4102 4.3 77.8 1.0 O1A A:ADP4102 4.5 87.5 1.0 CB A:ASP1848 4.5 84.6 1.0 OG1 A:THR1897 4.5 84.4 1.0 NZ A:LYS1802 4.6 80.5 1.0 ND2 A:ASN1899 4.6 90.9 1.0 CG A:ASP1848 4.7 89.0 1.0 N A:THR1803 4.7 71.0 1.0 N A:GLU1849 4.8 89.5 1.0 OD1 A:ASP1848 4.8 90.4 1.0 CA A:THR1803 4.8 69.1 1.0 OD1 A:ASN1899 4.8 92.8 1.0 PA A:ADP4102 4.9 87.3 1.0

Magnesium binding site 2 out of 3 in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4106 b:63.0 occ:1.00 O2B A:ATP4104 2.0 62.4 1.0 O2G A:ATP4104 2.0 59.7 1.0 OE2 A:GLU2195 2.2 78.5 1.0 OG1 A:THR2081 2.8 70.1 1.0 OD1 A:ASP2155 3.0 78.3 1.0 NH2 A:ARG2549 3.1 66.0 1.0 PB A:ATP4104 3.2 61.2 1.0 PG A:ATP4104 3.2 68.0 1.0 OD2 A:ASP2155 3.3 73.5 1.0 O3B A:ATP4104 3.4 60.1 1.0 CD A:GLU2195 3.5 75.5 1.0 CG A:ASP2155 3.5 78.2 1.0 O3G A:ATP4104 3.9 83.8 1.0 O1B A:ATP4104 4.0 70.9 1.0 CB A:THR2081 4.1 72.6 1.0 NH1 A:ARG2507 4.2 70.0 1.0 OE2 A:GLU2511 4.2 76.4 1.0 CG A:GLU2195 4.3 68.3 1.0 OE1 A:GLU2195 4.3 75.6 1.0 CZ A:ARG2549 4.4 67.6 1.0 O3A A:ATP4104 4.4 67.5 1.0 O1G A:ATP4104 4.4 67.9 1.0 NZ A:LYS2512 4.5 80.0 1.0 OE1 A:GLU2511 4.6 81.5 1.0 NH2 A:ARG2507 4.8 80.1 1.0 N A:THR2081 4.8 67.2 1.0 CD A:GLU2511 4.9 85.4 1.0 NE A:ARG2549 4.9 61.9 1.0 CG2 A:THR2081 4.9 78.3 1.0 CZ A:ARG2507 4.9 78.0 1.0

Magnesium binding site 3 out of 3 in the Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryoem Structures of Yeast Cytoplasmic Dynein in the Presence of Atp and LIS1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4107 b:58.0 occ:1.00 O3B A:ADP4103 2.0 73.0 1.0 PB A:ADP4103 2.4 69.4 1.0 O1B A:ADP4103 2.6 63.3 1.0 O2B A:ADP4103 2.8 66.5 1.0 OE2 A:GLU2488 3.9 94.6 1.0 O3A A:ADP4103 3.9 63.7 1.0 CE A:LYS2424 4.0 57.6 1.0 OG1 A:THR2425 4.0 69.0 1.0 O A:PRO2420 4.1 68.7 1.0 OD1 A:ASP2487 4.6 79.6 1.0 NZ A:LYS2424 4.6 61.6 1.0 O1A A:ADP4103 4.6 63.7 1.0 ND2 A:ASN2536 4.8 73.2 1.0 OD1 A:ASN2536 4.8 87.4 1.0 PA A:ADP4103 4.9 68.2 1.0 OD2 A:ASP2487 4.9 77.0 1.0 CD A:GLU2488 5.0 91.3 1.0 NH1 A:ARG2620 5.0 67.6 1.0 C A:PRO2420 5.0 68.9 1.0

A.A.Kendrick, K.H.V.Nguyen, W.Ma, E.P.Karasmanis, R.E.Amaro, S.L.Reck-Peterson, A.E.Leschziner. Multiple Steps of Dynein Activation By LIS1 Visualized By Cryo-Em. Nat.Struct.Mol.Biol. 2025.
ISSN: ESSN 1545-9985
PubMed: 40410592
DOI: 10.1038/S41594-025-01558-W