Magnesium in PDB 2xvd: 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: 2xvd was solved by J.Read, C.A.Brassington, I.Green, E.J.Mccall, A.L.Valentine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.05 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.708, 53.315, 61.330, 90.00, 111.75, 90.00
R / Rfree (%)	17.5 / 20.9

The binding sites of Magnesium atom in the EPHB4 Kinase Domain Inhibitor Complex (pdb code 2xvd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the EPHB4 Kinase Domain Inhibitor Complex, PDB code: 2xvd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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:38.2 occ:1.00 O A:HOH2110 2.1 34.3 1.0 OD2 A:ASP758 2.1 34.1 1.0 OD2 A:ASP740 2.1 33.7 1.0 O A:HOH2113 2.2 39.4 1.0 O A:HOH2095 2.2 41.6 1.0 O A:HOH2112 2.2 39.9 1.0 CG A:ASP758 3.1 31.9 1.0 CG A:ASP740 3.1 32.5 1.0 MG A:MG1892 3.3 39.6 1.0 OD1 A:ASP758 3.5 35.9 1.0 CB A:ASP740 3.6 29.4 1.0 O A:HOH2121 4.0 59.1 1.0 ND2 A:ASN745 4.0 26.4 1.0 OD1 A:ASP740 4.2 31.4 1.0 O A:HOH2098 4.4 42.4 1.0 O A:HOH2119 4.4 61.0 1.0 CB A:ASP758 4.5 29.8 1.0 NH1 A:ARG744 4.7 35.4 1.0 O A:HOH2092 4.7 46.5 1.0 CG A:ASN745 4.8 27.0 1.0 OD1 A:ASN745 4.8 27.9 1.0

Magnesium binding site 2 out of 3 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:59.0 occ:1.00 O A:HOH2040 1.6 46.5 1.0 O A:HOH2039 2.5 39.3 1.0 O A:GLU672 3.1 32.1 1.0 O A:HOH2084 3.8 40.3 1.0 OE2 A:GLU672 3.9 51.7 1.0 CG A:GLU672 4.0 39.5 1.0 C A:GLU672 4.1 32.1 1.0 CB A:GLU672 4.3 34.9 1.0 O A:HOH2038 4.4 57.0 1.0 CD A:GLU672 4.4 45.7 1.0 CA A:GLU672 4.8 33.4 1.0

Magnesium binding site 3 out of 3 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 3 of EPHB4 Kinase Domain Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1892 b:39.6 occ:1.00 O A:HOH2110 1.5 34.3 1.0 O A:HOH2092 1.9 46.5 1.0 MG A:MG1890 3.3 38.2 1.0 OD2 A:ASP758 3.3 34.1 1.0 CB A:ASP740 3.5 29.4 1.0 O A:HOH2088 3.6 30.9 1.0 CG A:ASP758 3.7 31.9 1.0 OD1 A:ASP758 3.8 35.9 1.0 O A:ASP758 3.8 30.7 1.0 O A:HOH2112 3.8 39.9 1.0 O A:HIS738 4.0 27.9 1.0 OD2 A:ASP740 4.2 33.7 1.0 CG A:ASP740 4.4 32.5 1.0 O A:HOH2095 4.4 41.6 1.0 C A:ASP758 4.5 31.0 1.0 N A:ASP740 4.5 29.1 1.0 CE1 A:HIS738 4.5 25.8 1.0 O A:HOH2120 4.6 46.5 1.0 CA A:ASP740 4.6 29.6 1.0 CB A:ASP758 4.6 29.8 1.0 NH2 A:ARG739 4.8 45.5 1.0 ND1 A:HIS738 4.8 26.1 1.0

B.Barlaam, R.Ducray, C.Lambert-Van Der Brempt, P.Ple, C.Bardelle, N.Brooks, T.Coleman, D.Cross, J.G.Kettle, J.Read. Inhibitors of the Tyrosine Kinase EPHB4. Part 4: Discovery and Optimization of A Benzylic Alcohol Series. Bioorg.Med.Chem.Lett. V. 21 2207 2011.
ISSN: ISSN 0960-894X
PubMed: 21441027
DOI: 10.1016/J.BMCL.2011.03.009