Magnesium in PDB 9bmd: Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition

The binding sites of Magnesium atom in the Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition (pdb code 9bmd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition, PDB code: 9bmd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4705 b:41.4 occ:1.00 O3A A:ADP4701 3.1 49.9 1.0 O3B A:ADP4701 3.3 47.3 1.0 PB A:ADP4701 3.8 41.2 1.0 O1A A:ADP4701 4.2 53.0 1.0 OD1 A:ASP1958 4.2 69.3 1.0 PA A:ADP4701 4.3 51.2 1.0 OD2 A:ASP1958 4.4 79.3 1.0 OE2 A:GLU1959 4.4 76.1 1.0 O2B A:ADP4701 4.5 43.6 1.0 N A:GLY1909 4.7 38.2 1.0 CG A:ASP1958 4.7 66.5 1.0 O5' A:ADP4701 4.9 49.8 1.0 CB A:ALA1908 4.9 48.7 1.0

Magnesium binding site 2 out of 4 in the Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4706 b:41.6 occ:1.00 OG A:SER2231 1.9 38.5 1.0 OE2 A:GLU2344 2.0 36.6 1.0 O1B A:ATP4702 2.1 45.4 1.0 O2G A:ATP4702 2.1 55.0 1.0 CD A:GLU2344 3.2 37.2 1.0 CB A:SER2231 3.2 33.0 1.0 OE2 A:GLU2688 3.3 47.8 1.0 PB A:ATP4702 3.3 36.2 1.0 PG A:ATP4702 3.4 48.4 1.0 O3B A:ATP4702 3.5 34.7 1.0 OD2 A:ASP2304 3.7 54.1 1.0 OE1 A:GLU2344 3.8 39.7 1.0 O3A A:ATP4702 4.2 27.3 1.0 N A:SER2231 4.2 29.0 1.0 OD1 A:ASP2304 4.3 52.2 1.0 CA A:SER2231 4.3 28.8 1.0 O3G A:ATP4702 4.3 40.6 1.0 CG A:GLU2344 4.3 35.4 1.0 CD A:GLU2688 4.4 56.3 1.0 O2A A:ATP4702 4.4 42.8 1.0 CG A:ASP2304 4.4 51.9 1.0 O2B A:ATP4702 4.5 37.5 1.0 O1G A:ATP4702 4.5 47.5 1.0 NH2 A:ARG2726 4.5 35.0 1.0 OE1 A:GLU2688 4.7 61.6 1.0 PA A:ATP4702 4.7 38.5 1.0 NH1 A:ARG2726 4.8 41.0 1.0 NH1 A:ARG2684 5.0 40.8 1.0 O1A A:ATP4702 5.0 42.5 1.0

Magnesium binding site 3 out of 4 in the Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4707 b:43.8 occ:1.00 OG1 A:THR2602 2.0 39.5 1.0 O3G A:ANP4703 2.0 51.3 1.0 O1B A:ANP4703 2.3 34.3 1.0 OD1 A:ASP2664 3.1 53.5 1.0 CB A:THR2602 3.2 33.0 1.0 PG A:ANP4703 3.4 44.7 1.0 PB A:ANP4703 3.5 32.2 1.0 N3B A:ANP4703 3.9 34.0 1.0 CG A:ASP2664 4.0 58.7 1.0 CG2 A:THR2602 4.1 36.6 1.0 OD2 A:ASP2664 4.1 61.0 1.0 O1A A:ANP4703 4.2 45.8 1.0 N A:THR2602 4.2 31.9 1.0 O2G A:ANP4703 4.2 47.8 1.0 CA A:THR2602 4.2 31.7 1.0 NH2 A:ARG3088 4.3 44.9 1.0 O1G A:ANP4703 4.5 44.3 1.0 O2B A:ANP4703 4.6 42.2 1.0 O3A A:ANP4703 4.6 27.6 1.0 OE2 A:GLU2665 4.7 63.5 1.0 PA A:ANP4703 4.8 40.6 1.0

Magnesium binding site 4 out of 4 in the Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Motor Domain From Full-Length Human Dynein-1 Bound to Microtubules in 5MM Amppnp Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4708 b:40.2 occ:1.00 OG1 A:THR2944 2.1 40.4 1.0 O1G A:ANP4704 2.2 51.1 1.0 O2B A:ANP4704 2.3 49.7 1.0 CB A:THR2944 3.3 31.4 1.0 PG A:ANP4704 3.5 53.1 1.0 PB A:ANP4704 3.6 34.7 1.0 N3B A:ANP4704 3.8 34.7 1.0 NH2 A:ARG3695 3.9 53.4 1.0 OD1 A:ASP2995 4.0 77.9 1.0 O1A A:ANP4704 4.1 42.9 1.0 CG2 A:THR2944 4.1 38.9 1.0 CG2 A:THR3067 4.2 49.1 1.0 O2G A:ANP4704 4.3 47.1 1.0 OE2 A:GLU3652 4.3 65.2 1.0 N A:THR2944 4.3 30.8 1.0 CA A:THR2944 4.4 32.0 1.0 CG A:ASP2995 4.5 84.4 1.0 O1B A:ANP4704 4.6 42.1 1.0 O3G A:ANP4704 4.7 52.2 1.0 O3A A:ANP4704 4.7 34.8 1.0 PA A:ANP4704 4.9 39.4 1.0 CB A:ASP2995 4.9 80.9 1.0

P.Chai, K.Zhang. Cryo-Em Reveals the Mechanochemical Cycle of Reactive Full-Length Human Dynein-1. To Be Published.