Magnesium in PDB 4w8f: Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State

All present enzymatic activity of Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State:
3.2.1.17;

The structure of Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State, PDB code: 4w8f was solved by H.-C.Cheng, G.Bhabha, N.Zhang, R.D.Vale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.40 / 3.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	137.730, 154.380, 177.550, 90.00, 96.59, 90.00
R / Rfree (%)	22.8 / 26.2

The binding sites of Magnesium atom in the Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State (pdb code 4w8f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State, PDB code: 4w8f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5005 b:50.4 occ:1.00 O3G A:ANP5002 1.9 96.2 1.0 HG1 A:THR2081 2.0 43.6 1.0 OG1 A:THR2081 2.6 36.3 1.0 OE1 A:GLU2195 2.6 28.9 1.0 O2B A:ANP5002 2.7 86.3 1.0 OE2 A:GLU2511 3.0 33.6 1.0 PG A:ANP5002 3.2 98.8 1.0 O1A A:ANP5002 3.4 62.0 1.0 HH21 A:ARG2549 3.5 32.5 1.0 N3B A:ANP5002 3.5 93.2 1.0 OE1 A:GLU2511 3.6 32.2 1.0 HH22 A:ARG2552 3.6 82.5 1.0 HH22 A:ARG2507 3.7 33.0 1.0 CD A:GLU2511 3.7 33.1 1.0 PB A:ANP5002 3.7 77.6 1.0 CD A:GLU2195 3.7 29.2 1.0 CB A:THR2081 3.8 35.1 1.0 HH12 A:ARG2507 3.8 34.5 1.0 HB A:THR2081 3.9 42.1 1.0 HH21 A:ARG2552 4.0 82.5 1.0 OD1 A:ASP2155 4.0 61.7 1.0 O2G A:ANP5002 4.1 0.0 1.0 HG21 A:THR2081 4.1 43.1 1.0 NH2 A:ARG2552 4.1 68.8 1.0 OD2 A:ASP2155 4.2 59.3 1.0 NH2 A:ARG2549 4.2 27.1 1.0 O1G A:ANP5002 4.3 0.2 1.0 OE2 A:GLU2195 4.3 29.9 1.0 H A:THR2081 4.4 45.4 1.0 HH22 A:ARG2549 4.4 32.5 1.0 HNB1 A:ANP5002 4.4 0.8 1.0 CG2 A:THR2081 4.4 35.9 1.0 NH2 A:ARG2507 4.4 27.5 1.0 CG A:ASP2155 4.5 58.9 1.0 HZ3 A:LYS2512 4.6 32.9 1.0 NH1 A:ARG2507 4.6 28.7 1.0 PA A:ANP5002 4.6 55.1 1.0 O3A A:ANP5002 4.6 72.0 1.0 HG3 A:GLU2195 4.6 34.5 1.0 HG23 A:THR2081 4.7 43.1 1.0 CG A:GLU2195 4.8 28.8 1.0 O1B A:ANP5002 4.8 74.2 1.0 HZ1 A:LYS2512 5.0 32.9 1.0 CA A:THR2081 5.0 35.2 1.0 HE A:ARG2549 5.0 32.8 1.0 N A:THR2081 5.0 37.8 1.0 CZ A:ARG2507 5.0 27.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Dynein Motor Domain in the Amppnp-Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg5005 b:54.4 occ:1.00 HG1 B:THR2081 1.7 44.4 1.0 O1G B:ANP5002 2.0 0.0 1.0 O2B B:ANP5002 2.1 76.8 1.0 OE2 B:GLU2195 2.1 37.0 1.0 OG1 B:THR2081 2.4 37.0 1.0 OE2 B:GLU2511 3.0 35.6 1.0 CD B:GLU2195 3.2 37.5 1.0 PG B:ANP5002 3.5 0.7 1.0 HH22 B:ARG2507 3.5 37.7 1.0 PB B:ANP5002 3.5 54.0 1.0 CB B:THR2081 3.6 37.9 1.0 OE1 B:GLU2195 3.7 37.6 1.0 HB B:THR2081 3.8 45.5 1.0 HH21 B:ARG2549 3.8 53.9 1.0 HG21 B:THR2081 3.8 45.9 1.0 CD B:GLU2511 3.8 35.2 1.0 OE1 B:GLU2511 3.9 35.5 1.0 OD1 B:ASP2155 3.9 59.9 1.0 N3B B:ANP5002 4.0 28.8 1.0 HH12 B:ARG2507 4.1 37.4 1.0 O2A B:ANP5002 4.1 61.9 1.0 CG2 B:THR2081 4.1 38.2 1.0 OD2 B:ASP2155 4.2 59.5 1.0 HH22 B:ARG2552 4.2 55.1 1.0 NH2 B:ARG2507 4.3 31.4 1.0 HG2 B:GLU2195 4.3 44.9 1.0 O3G B:ANP5002 4.3 1.0 1.0 HH21 B:ARG2552 4.3 55.1 1.0 O3A B:ANP5002 4.3 0.7 1.0 HG23 B:THR2081 4.3 45.9 1.0 CG B:GLU2195 4.3 37.4 1.0 H B:THR2081 4.4 45.8 1.0 O1B B:ANP5002 4.5 32.4 1.0 CG B:ASP2155 4.5 57.4 1.0 O2G B:ANP5002 4.5 0.4 1.0 NH2 B:ARG2552 4.5 46.0 1.0 NH2 B:ARG2549 4.6 44.9 1.0 PA B:ANP5002 4.7 42.3 1.0 HH21 B:ARG2507 4.7 37.7 1.0 HG3 B:GLU2195 4.7 44.9 1.0 NH1 B:ARG2507 4.8 31.1 1.0 CA B:THR2081 4.8 38.4 1.0 HH22 B:ARG2549 4.8 53.9 1.0 HNB1 B:ANP5002 4.9 34.6 1.0 N B:THR2081 4.9 38.2 1.0 CZ B:ARG2507 5.0 31.1 1.0 HA B:THR2081 5.0 46.0 1.0

G.Bhabha, N.Zhang, A.Moeller, M.Liao, J.A.Speir, Y.Cheng, R.D.Vale, H.-C.Cheng. Allosteric Communication in the Dynein Motor Domain To Be Published.