Magnesium in PDB 9e11: Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under LIS1 Condition

The binding sites of Magnesium atom in the Dimeric Motor Domains From Phi-Like Dynein-1 Bound to A LIS1 Dimer Under LIS1 Condition (pdb code 9e11). 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 LIS1 Condition, PDB code: 9e11:
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 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 LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4705 b:4.3 occ:1.00 O2B A:ADP4701 2.2 16.6 1.0 OG1 A:THR1913 2.3 15.0 1.0 CB A:THR1913 3.4 7.9 1.0 PB A:ADP4701 3.4 11.2 1.0 O3B A:ADP4701 3.7 9.8 1.0 NH2 A:ARG2358 3.7 16.5 1.0 OD1 A:ASP1958 3.9 17.7 1.0 CG A:ASP1958 3.9 18.2 1.0 CB A:ASP1958 4.2 10.7 1.0 CG2 A:THR1913 4.2 9.0 1.0 CG2 A:THR2017 4.3 10.0 1.0 O1B A:ADP4701 4.3 10.8 1.0 N A:THR1913 4.4 4.8 1.0 OD2 A:ASP1958 4.4 18.5 1.0 O2A A:ADP4701 4.4 12.7 1.0 CA A:THR1913 4.5 4.9 1.0 O3A A:ADP4701 4.5 11.0 1.0 OE2 A:GLU1959 4.5 25.5 1.0 NH2 A:ARG2091 4.7 13.8 1.0 PA A:ADP4701 4.8 13.2 1.0 O1A A:ADP4701 4.9 10.4 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 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 LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4706 b:6.0 occ:1.00 O2B A:ATP4702 2.0 11.7 1.0 O2G A:ATP4702 2.1 19.1 1.0 OE2 A:GLU2344 2.4 10.8 1.0 OG A:SER2231 2.6 13.8 1.0 PG A:ATP4702 2.8 17.9 1.0 O3B A:ATP4702 2.8 9.4 1.0 PB A:ATP4702 3.0 8.3 1.0 O1G A:ATP4702 3.3 13.7 1.0 CB A:SER2231 3.5 8.8 1.0 OE2 A:GLU2688 3.5 35.0 1.0 CD A:GLU2344 3.6 8.5 1.0 O1A A:ATP4702 3.7 16.2 1.0 O3A A:ATP4702 3.8 11.4 1.0 NH2 A:ARG2684 4.0 13.8 1.0 O1B A:ATP4702 4.1 13.8 1.0 OE1 A:GLU2344 4.2 8.9 1.0 O3G A:ATP4702 4.2 16.8 1.0 N A:SER2231 4.3 6.5 1.0 OD2 A:ASP2304 4.3 18.3 1.0 NH2 A:ARG2726 4.3 9.1 1.0 PA A:ATP4702 4.4 14.6 1.0 CA A:SER2231 4.5 6.1 1.0 CD A:GLU2688 4.5 31.8 1.0 OE1 A:GLU2688 4.6 35.1 1.0 CG A:GLU2344 4.7 6.0 1.0 CZ A:ARG2726 4.8 8.1 1.0 OD1 A:ASP2304 4.9 15.4 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 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 LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4705 b:4.5 occ:1.00 O3B B:ADP4701 2.1 12.0 1.0 OG1 B:THR1913 2.2 7.0 1.0 PB B:ADP4701 3.0 10.8 1.0 O2B B:ADP4701 3.0 13.0 1.0 CB B:THR1913 3.4 4.7 1.0 O3A B:ADP4701 3.6 19.9 1.0 NH2 B:ARG2358 3.7 14.3 1.0 OD1 B:ASP1958 3.8 24.9 1.0 CG B:ASP1958 4.0 19.1 1.0 CG2 B:THR2017 4.1 8.5 1.0 CB B:ASP1958 4.2 12.2 1.0 CG2 B:THR1913 4.2 6.7 1.0 O1B B:ADP4701 4.4 5.6 1.0 N B:THR1913 4.4 3.7 1.0 O2A B:ADP4701 4.4 10.8 1.0 CA B:THR1913 4.5 2.8 1.0 PA B:ADP4701 4.6 12.4 1.0 OD2 B:ASP1958 4.6 15.5 1.0 NH2 B:ARG2091 4.9 11.6 1.0 CZ B:ARG2358 5.0 11.0 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 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 LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4706 b:2.1 occ:1.00 OG B:SER2231 2.0 7.2 1.0 O2B B:ATP4702 2.1 5.6 1.0 OE2 B:GLU2344 2.2 4.9 1.0 O2G B:ATP4702 2.6 10.5 1.0 O3B B:ATP4702 3.1 6.4 1.0 PB B:ATP4702 3.2 2.7 1.0 PG B:ATP4702 3.3 9.2 1.0 CB B:SER2231 3.3 3.6 1.0 CD B:GLU2344 3.3 4.2 1.0 OE2 B:GLU2688 3.5 41.5 1.0 O1G B:ATP4702 3.6 6.9 1.0 O1A B:ATP4702 3.7 13.0 1.0 OE1 B:GLU2344 3.9 5.2 1.0 OD2 B:ASP2304 4.0 22.7 1.0 O3A B:ATP4702 4.0 4.4 1.0 N B:SER2231 4.3 2.5 1.0 O1B B:ATP4702 4.3 6.1 1.0 CA B:SER2231 4.4 2.4 1.0 CD B:GLU2688 4.4 31.4 1.0 OD1 B:ASP2304 4.4 17.8 1.0 NH2 B:ARG2726 4.4 6.9 1.0 PA B:ATP4702 4.5 8.8 1.0 CG B:GLU2344 4.5 2.5 1.0 OE1 B:GLU2688 4.5 29.4 1.0 CG B:ASP2304 4.6 15.6 1.0 O3G B:ATP4702 4.7 9.1 1.0 CZ B:ARG2726 4.9 4.6 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