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

Resolution Low / High (Å)	57.45 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.073, 53.479, 61.517, 90.00, 110.90, 90.00
R / Rfree (%)	18.7 / 23.8

The structure of EPHB4 Kinase Domain Inhibitor Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the EPHB4 Kinase Domain Inhibitor Complex (pdb code 2vwy). 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: 2vwy:
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:25.1 occ:1.00 O A:HOH2113 2.0 27.2 1.0 OD2 A:ASP740 2.0 24.1 1.0 OD1 A:ASP758 2.1 19.1 1.0 O A:HOH2111 2.1 25.4 1.0 O A:HOH2127 2.1 26.4 1.0 O A:HOH2126 2.2 21.2 1.0 CG A:ASP758 3.1 21.9 1.0 CG A:ASP740 3.2 23.4 1.0 MG A:MG1891 3.4 23.1 1.0 OD2 A:ASP758 3.5 21.9 1.0 O A:HOH2143 3.5 53.1 1.0 CB A:ASP740 3.8 20.7 1.0 O A:HOH2112 4.0 40.0 1.0 ND2 A:ASN745 4.1 16.3 1.0 O A:HOH2144 4.2 53.1 1.0 OD1 A:ASP740 4.2 24.5 1.0 O A:HOH2129 4.4 43.5 1.0 CB A:ASP758 4.4 19.9 1.0 O A:HOH2115 4.4 30.6 1.0 NH1 A:ARG744 4.8 29.8 1.0 O A:HOH2109 4.8 28.4 1.0 OD1 A:ASN745 4.9 16.8 1.0 CG A:ASN745 4.9 18.5 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:23.1 occ:1.00 O A:HOH2126 1.5 21.2 1.0 O A:HOH2109 1.8 28.4 1.0 O A:HOH2129 1.9 43.5 1.0 O A:HOH2110 3.3 18.5 1.0 OD1 A:ASP758 3.3 19.1 1.0 MG A:MG1890 3.4 25.1 1.0 CB A:ASP740 3.4 20.7 1.0 CG A:ASP758 3.6 21.9 1.0 O A:ASP758 3.7 20.4 1.0 O A:HOH2143 3.7 53.1 1.0 OD2 A:ASP758 3.8 21.9 1.0 O A:HIS738 3.9 18.4 1.0 O A:HOH2127 3.9 26.4 1.0 OD2 A:ASP740 4.0 24.1 1.0 CG A:ASP740 4.3 23.4 1.0 O A:HOH2113 4.4 27.2 1.0 CE1 A:HIS738 4.4 20.8 1.0 C A:ASP758 4.4 21.0 1.0 CB A:ASP758 4.5 19.9 1.0 N A:ASP740 4.6 19.0 1.0 O A:GLY760 4.6 31.1 1.0 CA A:ASP740 4.7 19.7 1.0 ND1 A:HIS738 4.7 18.3 1.0 N A:GLY760 4.8 26.6 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:53.2 occ:1.00 O A:HOH2087 1.9 43.0 1.0 O A:HOH2086 2.0 39.7 1.0 O A:HOH2167 2.1 35.2 1.0 O A:HOH2166 2.2 30.6 1.0 O A:HOH2225 2.7 48.0 1.0 OD1 A:ASP709 3.8 19.8 1.0 OD2 A:ASP709 4.0 27.4 1.0 O A:HOH2004 4.1 39.7 1.0 O A:SER815 4.2 18.5 1.0 CG A:ASP709 4.3 19.1 1.0 O A:HOH2165 4.6 24.0 1.0 O A:HOH2168 4.7 23.8 1.0 CG A:PRO843 4.9 24.5 1.0

C.Bardelle, T.Coleman, D.Cross, S.Davenport, J.G.Kettle, E.J.Ko, A.G.Leach, A.Mortlock, J.Read, N.J.Roberts, P.Robins, E.J.Williams. Inhibitors of the Tyrosine Kinase EPHB4. Part 2: Structure-Based Discovery and Optimisation of 3,5-Bis Substituted Anilinopyrimidines. Bioorg.Med.Chem.Lett. V. 18 5717 2008.
ISSN: ISSN 0960-894X
PubMed: 18851911
DOI: 10.1016/J.BMCL.2008.09.087