Magnesium in PDB 9e0z: Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition

The binding sites of Magnesium atom in the Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition (pdb code 9e0z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition, PDB code: 9e0z:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4705 b:28.0 occ:1.00 O2B A:ADP4701 2.0 32.7 1.0 OG1 A:THR1913 2.3 27.6 1.0 CB A:THR1913 3.2 27.6 1.0 PB A:ADP4701 3.3 32.7 1.0 OD1 A:ASP1958 3.7 32.2 1.0 NH2 A:ARG2358 3.7 31.7 1.0 O1B A:ADP4701 3.9 32.7 1.0 CG A:ASP1958 3.9 32.2 1.0 O3B A:ADP4701 4.0 32.7 1.0 CG2 A:THR2017 4.1 29.6 1.0 CG2 A:THR1913 4.1 27.6 1.0 CB A:ASP1958 4.2 32.2 1.0 N A:THR1913 4.3 27.6 1.0 OD2 A:ASP1958 4.3 32.2 1.0 CA A:THR1913 4.4 27.6 1.0 O2A A:ADP4701 4.4 32.7 1.0 O3A A:ADP4701 4.5 32.7 1.0 O1A A:ADP4701 4.7 32.7 1.0 PA A:ADP4701 4.7 32.7 1.0 NH2 A:ARG2091 4.7 33.0 1.0 OE2 A:GLU1959 4.9 31.4 1.0 CB A:THR2017 5.0 29.6 1.0

Magnesium binding site 2 out of 4 in the Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4706 b:31.3 occ:1.00 O2B A:ATP4702 2.0 39.1 1.0 O2G A:ATP4702 2.0 39.1 1.0 O3B A:ATP4702 2.2 39.1 1.0 PG A:ATP4702 2.4 39.1 1.0 OE2 A:GLU2344 2.5 30.7 1.0 PB A:ATP4702 2.6 39.1 1.0 OG A:SER2231 2.8 33.0 1.0 O1G A:ATP4702 3.0 39.1 1.0 O3A A:ATP4702 3.5 39.1 1.0 O1A A:ATP4702 3.5 39.1 1.0 CB A:SER2231 3.6 33.0 1.0 CD A:GLU2344 3.7 30.7 1.0 O1B A:ATP4702 3.8 39.1 1.0 O3G A:ATP4702 3.8 39.1 1.0 OE2 A:GLU2688 3.9 35.4 1.0 PA A:ATP4702 4.1 39.1 1.0 NH2 A:ARG2684 4.2 28.2 1.0 N A:SER2231 4.2 33.0 1.0 OE1 A:GLU2344 4.3 30.7 1.0 NH2 A:ARG2726 4.4 30.0 1.0 CA A:SER2231 4.5 33.0 1.0 OD2 A:ASP2304 4.6 29.5 1.0 CG A:GLU2344 4.8 30.7 1.0 CD A:GLU2688 4.8 35.4 1.0 CZ A:ARG2726 4.8 30.0 1.0 NZ A:LYS2230 4.9 32.1 1.0 OE1 A:GLU2688 4.9 35.4 1.0 CE A:LYS2230 4.9 32.1 1.0

Magnesium binding site 3 out of 4 in the Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4705 b:19.5 occ:1.00 O2B B:ADP4701 2.4 24.8 1.0 OG1 B:THR1913 2.4 20.0 1.0 O3B B:ADP4701 2.6 24.8 1.0 PB B:ADP4701 2.9 24.8 1.0 CB B:THR1913 3.5 20.0 1.0 O3A B:ADP4701 3.6 24.8 1.0 NH2 B:ARG2358 3.7 22.9 1.0 CG2 B:THR2017 3.9 24.7 1.0 CG B:ASP1958 4.0 24.9 1.0 OD2 B:ASP1958 4.1 24.9 1.0 CB B:ASP1958 4.2 24.9 1.0 OD1 B:ASP1958 4.3 24.9 1.0 O1B B:ADP4701 4.3 24.8 1.0 CG2 B:THR1913 4.4 20.0 1.0 O2A B:ADP4701 4.4 24.8 1.0 N B:THR1913 4.5 20.0 1.0 PA B:ADP4701 4.6 24.8 1.0 CA B:THR1913 4.6 20.0 1.0 CB B:THR2017 4.8 24.7 1.0 CZ B:ARG2358 4.9 22.9 1.0 NH2 B:ARG2091 4.9 25.2 1.0

Magnesium binding site 4 out of 4 in the Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under NDE1-LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4706 b:23.0 occ:1.00 O2G B:ATP4702 2.0 28.0 1.0 OG B:SER2231 2.1 23.9 1.0 O2B B:ATP4702 2.4 28.0 1.0 OE2 B:GLU2344 2.4 20.2 1.0 PG B:ATP4702 3.1 28.0 1.0 O3B B:ATP4702 3.2 28.0 1.0 CB B:SER2231 3.2 23.9 1.0 OE2 B:GLU2688 3.3 22.9 1.0 PB B:ATP4702 3.4 28.0 1.0 O1A B:ATP4702 3.5 28.0 1.0 CD B:GLU2344 3.6 20.2 1.0 O1G B:ATP4702 3.7 28.0 1.0 O3A B:ATP4702 4.1 28.0 1.0 OE1 B:GLU2344 4.1 20.2 1.0 OD2 B:ASP2304 4.1 22.8 1.0 CD B:GLU2688 4.2 22.9 1.0 N B:SER2231 4.3 23.9 1.0 CA B:SER2231 4.3 23.9 1.0 PA B:ATP4702 4.4 28.0 1.0 O3G B:ATP4702 4.4 28.0 1.0 OE1 B:GLU2688 4.5 22.9 1.0 NH2 B:ARG2726 4.6 21.7 1.0 O1B B:ATP4702 4.6 28.0 1.0 OD1 B:ASP2304 4.6 22.8 1.0 CG B:GLU2344 4.8 20.2 1.0 CG B:ASP2304 4.8 22.8 1.0

J.Yang, K.Zhang. NDE1 Promotes LIS1 Binding to Full-Length Autoinhibited Human Dynein-1 Nat.Chem.Biol. 2025.
ISSN: ESSN 1552-4469