Magnesium in PDB 2x9f: EPHB4 Kinase Domain Inhibitor Complex

All present enzymatic activity of EPHB4 Kinase Domain Inhibitor Complex:
2.7.10.1;

The structure of EPHB4 Kinase Domain Inhibitor Complex, PDB code: 2x9f was solved by J.Read, C.A.Brassington, I.Green, E.J.Mccall, A.L.Valentine, D.Barratt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.89 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.120, 52.479, 61.369, 90.00, 112.05, 90.00
R / Rfree (%)	15.7 / 19.4

The binding sites of Magnesium atom in the EPHB4 Kinase Domain Inhibitor Complex (pdb code 2x9f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the EPHB4 Kinase Domain Inhibitor Complex, PDB code: 2x9f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the EPHB4 Kinase Domain Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of EPHB4 Kinase Domain Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1890 b:18.7 occ:1.00 O A:HOH2127 2.0 16.1 1.0 OD2 A:ASP740 2.1 15.0 1.0 OD1 A:ASP758 2.1 15.1 1.0 O A:HOH2030 2.2 20.2 1.0 O A:HOH2029 2.2 22.8 1.0 O A:HOH2032 2.2 19.1 1.0 CG A:ASP758 3.1 13.0 1.0 CG A:ASP740 3.1 15.3 1.0 MG A:MG1891 3.2 17.5 1.0 OD2 A:ASP758 3.4 14.7 1.0 CB A:ASP740 3.6 13.3 1.0 OE2 A:GLU625 3.9 46.8 1.0 ND2 A:ASN745 3.9 12.9 1.0 O A:HOH2137 4.0 42.1 1.0 OE1 A:GLU625 4.1 42.7 1.0 O A:HOH2126 4.1 27.6 1.0 OD1 A:ASP740 4.2 15.3 1.0 O A:HOH2031 4.4 42.1 1.0 CB A:ASP758 4.4 12.4 1.0 CD A:GLU625 4.4 41.8 1.0 NH1 A:ARG744 4.4 19.0 1.0 O A:HOH2114 4.5 22.2 1.0 O A:HOH2033 4.6 34.3 1.0 O A:HOH2109 4.7 22.2 1.0 CG A:ASN745 4.8 13.8 1.0 OD1 A:ASN745 4.8 15.5 1.0

Magnesium binding site 2 out of 2 in the EPHB4 Kinase Domain Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of EPHB4 Kinase Domain Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1891 b:17.5 occ:1.00 O A:HOH2127 1.6 16.1 1.0 O A:HOH2126 1.7 27.6 1.0 O A:HOH2109 1.8 22.2 1.0 OD1 A:ASP758 3.2 15.1 1.0 MG A:MG1890 3.2 18.7 1.0 CB A:ASP740 3.4 13.3 1.0 O A:HOH2106 3.6 10.3 1.0 O A:ASP758 3.7 12.9 1.0 CG A:ASP758 3.7 13.0 1.0 OD2 A:ASP758 3.9 14.7 1.0 O A:HOH2032 3.9 19.1 1.0 O A:HIS738 4.0 12.8 1.0 OD2 A:ASP740 4.1 15.0 1.0 CG A:ASP740 4.3 15.3 1.0 O A:HOH2029 4.4 22.8 1.0 CE1 A:HIS738 4.5 15.4 1.0 C A:ASP758 4.5 13.8 1.0 N A:ASP740 4.5 12.5 1.0 CA A:ASP740 4.6 13.6 1.0 CB A:ASP758 4.7 12.4 1.0 O A:HOH2136 4.7 26.7 1.0 ND1 A:HIS738 4.7 13.5 1.0 NH2 A:ARG739 5.0 26.9 1.0

C.Bardelle, B.Barlaam, N.Brooks, T.Coleman, D.Cross, R.Ducray, I.Green, C.L.Brempt, A.Olivier, J.Read. Inhibitors of the Tyrosine Kinase EPHB4. Part 3: Identification of Non-Benzodioxole-Based Kinase Inhibitors. Bioorg.Med.Chem.Lett. V. 20 6242 2010.
ISSN: ISSN 0960-894X
PubMed: 20850301
DOI: 10.1016/J.BMCL.2010.08.100