Magnesium in PDB 9e10: Dimeric Motor Domains From Phi Dynein-1 Under LIS1 Condition

The binding sites of Magnesium atom in the Dimeric Motor Domains From Phi Dynein-1 Under LIS1 Condition (pdb code 9e10). 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 Dynein-1 Under LIS1 Condition, PDB code: 9e10:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dimeric Motor Domains From Phi Dynein-1 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 Dynein-1 Under LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4705 b:0.3 occ:1.00 O3B A:ADP4701 2.1 2.8 1.0 OG1 A:THR1913 2.4 1.3 1.0 PB A:ADP4701 3.2 0.5 1.0 O1B A:ADP4701 3.3 1.0 1.0 CB A:THR1913 3.5 0.6 1.0 OD1 A:ASP1958 3.8 12.6 1.0 NH2 A:ARG2358 3.8 0.5 1.0 CG A:ASP1958 4.1 7.9 1.0 CG2 A:THR2017 4.2 0.8 1.0 O2B A:ADP4701 4.2 0.6 1.0 O3A A:ADP4701 4.3 0.6 1.0 N A:THR1913 4.3 0.3 1.0 O2A A:ADP4701 4.4 4.8 1.0 O1A A:ADP4701 4.4 0.7 1.0 CG2 A:THR1913 4.5 1.1 1.0 CA A:THR1913 4.5 0.3 1.0 PA A:ADP4701 4.5 0.5 1.0 OD2 A:ASP1958 4.6 5.7 1.0 CB A:ASP1958 4.6 1.4 1.0 NH2 A:ARG2091 4.8 1.7 1.0 OD2 A:ASP2320 5.0 20.2 1.0

Magnesium binding site 2 out of 4 in the Dimeric Motor Domains From Phi Dynein-1 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 Dynein-1 Under LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4706 b:0.1 occ:1.00 OE2 A:GLU2344 2.0 0.1 1.0 O2G A:ATP4702 2.0 7.5 1.0 OG A:SER2231 2.1 0.7 1.0 O2B A:ATP4702 2.4 0.1 1.0 CB A:SER2231 3.1 0.1 1.0 PG A:ATP4702 3.1 3.4 1.0 CD A:GLU2344 3.2 0.1 1.0 O3B A:ATP4702 3.3 0.2 1.0 PB A:ATP4702 3.5 0.0 1.0 OE2 A:GLU2688 3.5 15.4 1.0 O1A A:ATP4702 3.6 1.5 1.0 O1G A:ATP4702 3.7 0.5 1.0 OE1 A:GLU2344 3.8 0.2 1.0 OD2 A:ASP2304 4.0 5.3 1.0 NH2 A:ARG2726 4.0 0.2 1.0 N A:SER2231 4.1 0.1 1.0 CA A:SER2231 4.1 0.1 1.0 O3A A:ATP4702 4.2 0.2 1.0 CG A:GLU2344 4.3 0.1 1.0 O3G A:ATP4702 4.4 0.3 1.0 CD A:GLU2688 4.5 15.1 1.0 PA A:ATP4702 4.5 0.6 1.0 OD1 A:ASP2304 4.6 2.3 1.0 O1B A:ATP4702 4.6 0.2 1.0 CG A:ASP2304 4.7 1.9 1.0 OE1 A:GLU2688 4.7 17.8 1.0

Magnesium binding site 3 out of 4 in the Dimeric Motor Domains From Phi Dynein-1 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 Dynein-1 Under LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4705 b:0.3 occ:1.00 O3B B:ADP4701 2.2 16.2 1.0 OG1 B:THR1913 2.5 3.5 1.0 O1B B:ADP4701 2.8 2.1 1.0 PB B:ADP4701 3.0 0.9 1.0 CB B:THR1913 3.5 0.9 1.0 NH2 B:ARG2358 3.8 1.0 1.0 O3A B:ADP4701 3.9 0.8 1.0 CG2 B:THR2017 4.0 1.8 1.0 OD1 B:ASP1958 4.1 10.9 1.0 CG B:ASP1958 4.1 8.5 1.0 N B:THR1913 4.2 0.3 1.0 O2B B:ADP4701 4.3 0.8 1.0 O1A B:ADP4701 4.3 2.5 1.0 OD2 B:ASP1958 4.3 7.6 1.0 PA B:ADP4701 4.5 10.6 1.0 CG2 B:THR1913 4.5 1.3 1.0 CA B:THR1913 4.5 0.4 1.0 CB B:ASP1958 4.7 1.5 1.0 O2A B:ADP4701 4.7 33.6 1.0 NH2 B:ARG2091 4.7 11.3 1.0 CB B:THR2017 5.0 0.9 1.0

Magnesium binding site 4 out of 4 in the Dimeric Motor Domains From Phi Dynein-1 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 Dynein-1 Under LIS1 Condition within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4706 b:0.0 occ:1.00 OE2 B:GLU2344 2.0 0.1 1.0 O2G B:ATP4702 2.0 5.2 1.0 O2B B:ATP4702 2.5 0.2 1.0 OG B:SER2231 2.8 0.3 1.0 CB B:SER2231 3.0 0.1 1.0 CD B:GLU2344 3.1 0.1 1.0 PG B:ATP4702 3.2 3.3 1.0 O3B B:ATP4702 3.4 0.2 1.0 OE2 B:GLU2688 3.5 9.7 1.0 PB B:ATP4702 3.6 0.1 1.0 OE1 B:GLU2344 3.7 0.2 1.0 O1A B:ATP4702 3.7 1.7 1.0 O1G B:ATP4702 3.9 0.3 1.0 OD2 B:ASP2304 3.9 3.5 1.0 NH2 B:ARG2726 4.0 0.1 1.0 N B:SER2231 4.1 0.0 1.0 CA B:SER2231 4.1 0.0 1.0 CG B:GLU2344 4.2 0.0 1.0 O3A B:ATP4702 4.3 0.2 1.0 O3G B:ATP4702 4.4 0.4 1.0 NH2 B:ARG2684 4.5 0.2 1.0 CD B:GLU2688 4.6 11.4 1.0 PA B:ATP4702 4.6 0.2 1.0 OD1 B:ASP2304 4.6 1.3 1.0 CG B:ASP2304 4.7 0.9 1.0 O1B B:ATP4702 4.7 0.2 1.0 OE1 B:GLU2688 4.9 15.1 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