Magnesium in PDB 9dzy: Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1

The binding sites of Magnesium atom in the Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1 (pdb code 9dzy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1, PDB code: 9dzy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4703 b:78.3 occ:1.00 O2B B:ATP4702 2.0 82.6 1.0 OE2 B:GLU2344 2.0 84.6 1.0 OG B:SER2231 2.1 80.8 1.0 O1G B:ATP4702 2.1 87.0 1.0 CD B:GLU2344 3.2 83.8 1.0 CB B:SER2231 3.2 77.0 1.0 PB B:ATP4702 3.2 84.7 1.0 PG B:ATP4702 3.2 89.7 1.0 O3B B:ATP4702 3.4 80.4 1.0 OE2 B:GLU2688 3.7 83.7 1.0 OE1 B:GLU2344 3.7 84.3 1.0 O3A B:ATP4702 3.9 81.6 1.0 O1A B:ATP4702 3.9 89.0 1.0 O3G B:ATP4702 4.1 84.8 1.0 OD2 B:ASP2304 4.2 83.3 1.0 NH2 B:ARG2684 4.2 84.5 1.0 N B:SER2231 4.3 71.4 1.0 CA B:SER2231 4.3 72.5 1.0 CG B:GLU2344 4.3 74.3 1.0 NH2 B:ARG2726 4.4 80.0 1.0 O2G B:ATP4702 4.4 87.1 1.0 O1B B:ATP4702 4.5 86.5 1.0 CD B:GLU2688 4.5 81.6 1.0 OE1 B:GLU2688 4.5 83.7 1.0 PA B:ATP4702 4.5 86.9 1.0 OD1 B:ASP2304 4.6 88.5 1.0 CG B:ASP2304 4.8 84.5 1.0 NH2 B:ARG2729 4.9 77.0 1.0

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4704 b:68.4 occ:1.00 O2B B:ADP4706 2.0 81.7 1.0 OG1 B:THR1913 2.0 76.1 1.0 CB B:THR1913 3.1 73.8 1.0 PB B:ADP4706 3.3 86.5 1.0 O3B B:ADP4706 3.6 79.3 1.0 OD2 B:ASP1958 3.7 86.8 1.0 CG B:ASP1958 3.8 83.0 1.0 OD1 B:ASP1958 3.8 82.8 1.0 CG2 B:THR1913 4.0 73.6 1.0 CG2 B:THR2017 4.1 75.8 1.0 O3A B:ADP4706 4.1 82.1 1.0 N B:THR1913 4.3 75.4 1.0 CA B:THR1913 4.3 71.5 1.0 NH2 B:ARG2358 4.3 80.2 1.0 O2A B:ADP4706 4.4 83.6 1.0 O1B B:ADP4706 4.4 81.2 1.0 CB B:ASP1958 4.6 75.3 1.0 OD2 B:ASP2320 4.6 86.8 1.0 PA B:ADP4706 4.8 85.0 1.0 NH2 B:ARG2091 4.9 83.1 1.0 CB B:THR2017 5.0 71.2 1.0

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4704 b:104.4 occ:1.00 OG A:SER2231 2.1 103.5 1.0 OE2 A:GLU2344 2.1 108.5 1.0 OE1 A:GLU2344 2.3 114.5 1.0 OE2 A:GLU2688 2.3 106.6 1.0 CD A:GLU2344 2.5 109.5 1.0 OD2 A:ASP2304 2.6 103.5 1.0 O1G A:ATP4701 3.2 104.2 1.0 CB A:SER2231 3.4 103.1 1.0 CD A:GLU2688 3.5 102.4 1.0 CG A:ASP2304 3.6 103.8 1.0 OD1 A:ASP2304 3.8 106.3 1.0 NH2 A:ARG2684 4.0 102.6 1.0 OE1 A:GLU2688 4.0 104.0 1.0 CG A:GLU2344 4.0 98.8 1.0 O2B A:ATP4701 4.2 104.0 1.0 CE1 A:HIS2689 4.3 98.3 1.0 CA A:SER2231 4.5 100.1 1.0 NE2 A:HIS2689 4.5 104.9 1.0 PG A:ATP4701 4.5 106.6 1.0 NH2 A:ARG2726 4.6 101.4 1.0 CG A:GLU2688 4.7 93.2 1.0 CB A:GLU2344 4.8 95.4 1.0 O3G A:ATP4701 4.9 104.6 1.0 CB A:ASP2304 4.9 100.6 1.0 N A:SER2231 5.0 96.3 1.0

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg4705 b:85.6 occ:1.00 O2B A:ADP4706 2.0 98.3 1.0 OG1 A:THR1913 2.1 91.3 1.0 CB A:THR1913 3.2 88.8 1.0 OD2 A:ASP1958 3.4 103.5 1.0 PB A:ADP4706 3.4 103.5 1.0 CG A:ASP1958 3.7 96.1 1.0 O3B A:ADP4706 3.9 102.1 1.0 CG2 A:THR1913 4.0 88.0 1.0 NH2 A:ARG2358 4.1 103.2 1.0 CG2 A:THR2017 4.1 86.9 1.0 O3A A:ADP4706 4.1 102.2 1.0 OD1 A:ASP1958 4.2 94.6 1.0 O2A A:ADP4706 4.2 103.6 1.0 N A:THR1913 4.3 93.2 1.0 CA A:THR1913 4.3 91.0 1.0 CB A:ASP1958 4.3 89.5 1.0 OD2 A:ASP2320 4.4 109.4 1.0 O1B A:ADP4706 4.5 94.0 1.0 PA A:ADP4706 4.7 105.8 1.0 OE2 A:GLU1959 4.9 102.3 1.0

K.H.V.Nguyen, A.A.Kendrick, A.E.Leschziner. Cryo-Em Structure of Pre-Chi Dynein Bound to LIS1 To Be Published.