Magnesium in PDB 2x7d: Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron

The structure of Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron, PDB code: 2x7d was solved by H.Y.K.Kaan, V.Ulaganathan, O.Rath, C.Laggner, H.Prokopcova, D.Dallinger, C.O.Kappe, F.Kozielski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.58 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.515, 79.717, 159.277, 90.00, 90.00, 90.00
R / Rfree (%)	17.592 / 24.053

The binding sites of Magnesium atom in the Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron (pdb code 2x7d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron, PDB code: 2x7d:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron


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 Human Kinesin EG5 in Complex with (S)-Dimethylenastron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1367 b:12.8 occ:1.00 O A:HOH2282 2.0 6.7 1.0 O A:HOH2281 2.0 3.0 1.0 OG1 A:THR112 2.1 9.0 1.0 O1B A:ADP601 2.1 10.7 1.0 O A:HOH2222 2.1 8.4 1.0 O A:HOH2197 2.1 6.5 1.0 CB A:THR112 3.2 9.8 1.0 PB A:ADP601 3.2 10.6 1.0 O3B A:ADP601 3.4 12.8 1.0 N A:THR112 4.0 10.5 1.0 O A:HOH2224 4.0 10.1 1.0 O1A A:ADP601 4.1 9.5 1.0 CA A:THR112 4.1 9.8 1.0 OD2 A:ASP265 4.1 13.2 1.0 O A:SER232 4.2 14.5 1.0 O A:HOH2074 4.2 12.6 1.0 CG2 A:THR112 4.2 6.9 1.0 OD1 A:ASP265 4.3 10.9 1.0 O A:HOH2198 4.3 12.7 1.0 O2B A:ADP601 4.3 6.6 1.0 O A:HOH2085 4.3 12.5 1.0 O3A A:ADP601 4.3 10.2 1.0 O A:HOH2188 4.3 26.9 1.0 PA A:ADP601 4.6 11.4 1.0 CG A:ASP265 4.7 6.1 1.0 O2A A:ADP601 4.8 15.7 1.0 CB A:LYS111 4.8 10.4 1.0 CE A:LYS111 4.9 5.3 1.0 NZ A:LYS111 5.0 5.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron


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 Human Kinesin EG5 in Complex with (S)-Dimethylenastron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1368 b:17.5 occ:1.00 O A:HOH2202 2.6 31.2 1.0 O A:SER235 2.7 13.8 1.0 O A:HOH2224 2.7 10.1 1.0 O A:ASP265 2.8 9.7 1.0 O A:LEU266 3.2 10.9 1.0 OD1 A:ASP265 3.3 10.9 1.0 O A:HOH2222 3.4 8.4 1.0 C A:LEU266 3.5 9.6 1.0 C A:ASP265 3.6 7.5 1.0 C A:SER235 3.7 12.7 1.0 CG A:ASP265 3.7 6.1 1.0 N A:ALA267 3.9 8.0 1.0 O A:SER232 3.9 14.5 1.0 CA A:HIS236 4.1 12.2 1.0 OG A:SER235 4.1 8.9 1.0 N A:LEU266 4.2 8.4 1.0 CB A:ASP265 4.2 8.6 1.0 CA A:LEU266 4.2 7.2 1.0 CA A:ALA267 4.3 7.0 1.0 OD2 A:ASP265 4.3 13.2 1.0 N A:SER237 4.3 12.5 1.0 N A:HIS236 4.3 11.8 1.0 O A:HOH2197 4.4 6.5 1.0 CA A:ASP265 4.5 8.4 1.0 O A:HOH2145 4.5 20.4 1.0 C A:HIS236 4.6 13.6 1.0 OG A:SER237 4.6 17.8 1.0 CA A:SER235 4.7 11.5 1.0 N A:SER235 4.8 12.4 1.0 O A:HOH2223 4.9 23.9 1.0 C A:SER232 4.9 12.8 1.0 CB A:SER235 5.0 10.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron


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 Human Kinesin EG5 in Complex with (S)-Dimethylenastron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1367 b:8.5 occ:1.00 O B:HOH2239 2.0 7.3 1.0 O B:HOH2240 2.1 5.9 1.0 O1B B:ADP602 2.1 9.1 1.0 O B:HOH2182 2.1 3.6 1.0 OG1 B:THR112 2.1 8.7 1.0 O B:HOH2154 2.2 11.0 1.0 CB B:THR112 3.2 8.3 1.0 PB B:ADP602 3.3 10.0 1.0 O3B B:ADP602 3.6 10.0 1.0 N B:THR112 4.0 9.7 1.0 O B:HOH2183 4.0 10.8 1.0 O B:SER232 4.1 11.9 1.0 OD2 B:ASP265 4.1 9.7 1.0 CA B:THR112 4.2 8.4 1.0 O1A B:ADP602 4.2 10.3 1.0 O B:HOH2027 4.2 8.1 1.0 CG2 B:THR112 4.3 5.8 1.0 O2B B:ADP602 4.3 10.6 1.0 O3A B:ADP602 4.3 9.1 1.0 O B:HOH2065 4.3 6.7 1.0 O B:HOH2155 4.4 15.7 1.0 OD1 B:ASP265 4.4 13.8 1.0 PA B:ADP602 4.6 9.5 1.0 O B:HOH2147 4.6 22.8 1.0 CG B:ASP265 4.7 7.8 1.0 O2A B:ADP602 4.8 10.7 1.0 CE B:LYS111 4.8 8.8 1.0 CB B:LYS111 4.9 7.2 1.0 NZ B:LYS111 5.0 4.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Kinesin EG5 in Complex with (S)-Dimethylenastron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1368 b:3.5 occ:1.00 O B:HOH2161 2.6 19.9 1.0 O B:ASP265 2.7 5.5 1.0 O B:HOH2183 2.7 10.8 1.0 O B:SER235 2.7 11.9 1.0 OD1 B:ASP265 2.9 13.8 1.0 O B:LEU266 3.0 10.2 1.0 C B:ASP265 3.4 7.2 1.0 C B:LEU266 3.4 8.2 1.0 CG B:ASP265 3.4 7.8 1.0 O B:HOH2182 3.5 3.6 1.0 N B:ALA267 3.8 7.9 1.0 C B:SER235 3.8 10.5 1.0 CB B:ASP265 3.9 7.4 1.0 N B:LEU266 4.0 8.0 1.0 CA B:LEU266 4.1 7.9 1.0 OD2 B:ASP265 4.1 9.7 1.0 O B:SER232 4.2 11.9 1.0 CA B:HIS236 4.2 8.6 1.0 CA B:ALA267 4.2 7.0 1.0 CA B:ASP265 4.3 7.5 1.0 N B:SER237 4.4 11.0 1.0 O B:HOH2154 4.4 11.0 1.0 OG B:SER235 4.4 10.9 1.0 N B:HIS236 4.5 10.1 1.0 O B:HOH2114 4.6 3.0 1.0 C B:HIS236 4.6 11.1 1.0 O B:HOH2181 4.7 7.9 1.0 OG B:SER237 4.7 8.6 1.0 CA B:SER235 4.9 9.7 1.0

H.Y.K.Kaan, V.Ulaganathan, O.Rath, H.Prokopcova, D.Dallinger, C.O.Kappe, F.Kozielski. Structural Basis For Inhibition of EG5 By Dihydropyrimidines: Stereoselectivity of Antimitotic Inhibitors Enastron, Dimethylenastron and Fluorastrol. J.Med.Chem. V. 53 5676 2010.
ISSN: ISSN 0022-2623
PubMed: 20597485
DOI: 10.1021/JM100421N