Magnesium in PDB 3vkg: X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain

The structure of X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain, PDB code: 3vkg was solved by T.Kon, T.Oyama, R.Shimo-Kon, K.Suto, G.Kurisu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	96.45 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	204.256, 221.806, 192.898, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 31.9

The binding sites of Magnesium atom in the X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain (pdb code 3vkg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain, PDB code: 3vkg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1 b:44.2 occ:1.00 OE2 A:GLU2396 2.1 51.4 1.0 OG1 A:THR2283 2.5 47.7 1.0 O1B A:ADP9002 2.7 51.7 1.0 O3B A:ADP9002 2.8 49.6 1.0 PB A:ADP9002 3.1 51.1 1.0 CD A:GLU2396 3.1 54.1 1.0 O3A A:ADP9002 3.2 52.2 1.0 NH1 A:ARG2806 3.5 52.8 1.0 OE1 A:GLU2396 3.6 54.0 1.0 CB A:THR2283 3.8 48.6 1.0 NH1 A:ARG2809 3.9 40.7 1.0 OE1 A:GLU2768 4.0 55.3 1.0 OD2 A:ASP2356 4.0 56.4 1.0 OE2 A:GLU2768 4.0 56.4 1.0 CZ A:ARG2806 4.1 53.4 1.0 NH1 A:ARG2764 4.2 45.0 1.0 NZ A:LYS2769 4.2 39.3 1.0 NH2 A:ARG2806 4.2 53.9 1.0 CD A:GLU2768 4.2 54.9 1.0 CG A:GLU2396 4.4 54.0 1.0 OD1 A:ASP2356 4.4 55.1 1.0 CG2 A:THR2283 4.5 45.6 1.0 O2B A:ADP9002 4.6 47.1 1.0 PA A:ADP9002 4.6 51.0 1.0 CG A:ASP2356 4.7 55.7 1.0 O1A A:ADP9002 4.8 54.9 1.0 N A:THR2283 4.8 47.7 1.0 CA A:THR2283 4.9 49.0 1.0

Magnesium binding site 2 out of 3 in the X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2 b:50.0 occ:1.00 O3B B:ADP9007 2.7 42.1 1.0 O2B B:ADP9007 2.7 42.3 1.0 PB B:ADP9007 3.0 41.6 1.0 OD2 B:ASP2026 3.1 48.1 1.0 O3A B:ADP9007 3.2 43.2 1.0 OG1 B:THR1981 3.7 41.9 1.0 CG B:ASP2026 3.9 45.9 1.0 OD1 B:ASP2026 4.0 47.0 1.0 CG B:GLU2027 4.4 48.3 1.0 O1B B:ADP9007 4.5 39.0 1.0 PA B:ADP9007 4.6 42.0 1.0 CB B:THR1981 4.6 38.0 1.0 CD B:GLU2027 4.7 54.4 1.0 O1A B:ADP9007 4.9 43.4 1.0 OE2 B:GLU2027 4.9 57.8 1.0 NZ B:LYS1980 4.9 39.4 1.0

Magnesium binding site 3 out of 3 in the X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of An Mtbd Truncation Mutant of Dynein Motor Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3 b:28.8 occ:1.00 OG1 B:THR2283 2.2 42.5 1.0 OE2 B:GLU2396 2.6 40.5 1.0 O3B B:ADP9008 2.8 45.8 1.0 O1B B:ADP9008 3.1 46.8 1.0 O3A B:ADP9008 3.2 50.1 1.0 PB B:ADP9008 3.2 47.3 1.0 OE2 B:GLU2768 3.3 51.4 1.0 CB B:THR2283 3.4 42.2 1.0 CD B:GLU2396 3.6 38.5 1.0 OE1 B:GLU2768 3.9 51.0 1.0 CD B:GLU2768 3.9 50.2 1.0 OE1 B:GLU2396 3.9 38.6 1.0 CG2 B:THR2283 4.1 40.9 1.0 O1A B:ADP9008 4.2 53.4 1.0 NH1 B:ARG2809 4.3 45.2 1.0 PA B:ADP9008 4.3 50.9 1.0 OD2 B:ASP2356 4.3 44.9 1.0 N B:THR2283 4.4 42.9 1.0 NH1 B:ARG2764 4.4 43.1 1.0 CA B:THR2283 4.5 42.7 1.0 NH2 B:ARG2806 4.7 39.0 1.0 O2B B:ADP9008 4.7 41.1 1.0 CG B:GLU2396 4.9 36.8 1.0 NZ B:LYS2769 5.0 43.3 1.0

T.Kon, T.Oyama, R.Shimo-Kon, K.Imamula, T.Shima, K.Sutoh, G.Kurisu. The 2.8 A Crystal Structure of the Dynein Motor Domain Nature V. 484 345 2012.
ISSN: ISSN 0028-0836
PubMed: 22398446
DOI: 10.1038/NATURE10955