Magnesium in PDB 1yxq: Crystal Structure of Actin in Complex with Swinholide A

The structure of Crystal Structure of Actin in Complex with Swinholide A, PDB code: 1yxq was solved by V.A.Klenchin, R.King, J.Tanaka, G.Marriott, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.000, 76.800, 98.400, 90.00, 101.20, 90.00
R / Rfree (%)	18.4 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of Actin in Complex with Swinholide A (pdb code 1yxq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Actin in Complex with Swinholide A, PDB code: 1yxq:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Actin in Complex with Swinholide A


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 Actin in Complex with Swinholide A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1390 b:26.9 occ:1.00 O3G A:ATP1380 2.0 18.1 1.0 O2B A:ATP1380 2.1 18.3 1.0 O A:HOH9004 2.1 20.0 1.0 O A:HOH9005 2.2 26.6 1.0 O A:HOH9002 2.2 20.4 1.0 O A:HOH9003 2.2 24.6 1.0 PG A:ATP1380 3.3 23.9 1.0 PB A:ATP1380 3.3 19.8 1.0 O3B A:ATP1380 3.6 23.3 1.0 O A:HOH9052 3.9 33.8 1.0 O3A A:ATP1380 4.0 21.8 1.0 O A:HOH9190 4.0 29.6 1.0 O A:HOH9140 4.1 47.5 1.0 O A:HOH9089 4.1 35.3 1.0 O1G A:ATP1380 4.1 22.7 1.0 O1A A:ATP1380 4.1 25.7 1.0 OE1 A:GLN137 4.2 17.2 1.0 OD2 A:ASP11 4.3 16.7 1.0 O2G A:ATP1380 4.4 24.7 1.0 NZ A:LYS18 4.4 22.4 1.0 OD2 A:ASP154 4.4 21.8 1.0 OD1 A:ASP11 4.4 18.0 1.0 O1B A:ATP1380 4.5 20.1 1.0 CD A:GLN137 4.6 19.4 1.0 O A:HOH9064 4.6 40.8 1.0 CA A:GLY13 4.6 19.4 1.0 PA A:ATP1380 4.6 24.3 1.0 CG A:ASP11 4.9 17.0 1.0 OD1 A:ASP154 4.9 36.8 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Actin in Complex with Swinholide A


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 Actin in Complex with Swinholide A within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg5001 b:56.1 occ:1.00 O A:HOH9006 2.0 61.2 1.0 O A:HOH9009 2.0 53.2 1.0 O A:HOH9010 2.2 43.5 1.0 O A:HOH9008 2.2 48.1 1.0 OE2 A:GLU205 2.2 32.8 1.0 O A:HOH9007 2.4 50.4 1.0 CD A:GLU205 3.3 35.4 1.0 OE1 A:GLU205 3.7 33.4 1.0 O A:HOH9121 4.3 43.0 1.0 O A:SER199 4.4 36.3 1.0 CG A:GLU205 4.6 30.5 1.0 O A:HOH9182 4.9 55.9 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Actin in Complex with Swinholide A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Actin in Complex with Swinholide A within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2390 b:47.7 occ:1.00 O B:HOH9003 1.9 40.7 1.0 O2B B:ATP2380 1.9 24.9 1.0 O B:HOH9006 2.0 44.2 1.0 O B:HOH9005 2.1 43.7 1.0 O3G B:ATP2380 2.2 27.1 1.0 O B:HOH9004 2.2 46.2 1.0 PB B:ATP2380 3.3 27.7 1.0 PG B:ATP2380 3.4 32.3 1.0 O3B B:ATP2380 3.7 25.3 1.0 OE1 B:GLN137 3.9 17.0 1.0 O1A B:ATP2380 3.9 25.6 1.0 O1G B:ATP2380 4.1 29.2 1.0 OD1 B:ASP11 4.1 17.8 1.0 O3A B:ATP2380 4.2 24.6 1.0 NZ B:LYS18 4.2 22.6 1.0 OD2 B:ASP11 4.3 13.0 1.0 OD1 B:ASP154 4.3 28.1 1.0 O1B B:ATP2380 4.4 29.0 1.0 OD2 B:ASP154 4.4 31.4 1.0 CD B:GLN137 4.4 17.0 1.0 PA B:ATP2380 4.5 26.5 1.0 CA B:GLY13 4.5 22.9 1.0 O2G B:ATP2380 4.6 31.6 1.0 CG B:ASP11 4.6 18.3 1.0 O2A B:ATP2380 4.8 24.8 1.0 CG B:ASP154 4.8 25.7 1.0 CG B:GLN137 4.9 16.3 1.0 CE B:LYS18 4.9 19.6 1.0 CG2 B:VAL339 4.9 17.7 1.0

V.A.Klenchin, R.King, J.Tanaka, G.Marriott, I.Rayment. Structural Basis of Swinholide A Binding to Actin Chem.Biol. V. 12 287 2005.
ISSN: ISSN 1074-5521
PubMed: 15797212
DOI: 10.1016/J.CHEMBIOL.2005.02.011