Atomistry » Magnesium » PDB 2vu9-2wb1 » 2vwz
Atomistry »
  Magnesium »
    PDB 2vu9-2wb1 »
      2vwz »

Magnesium in PDB 2vwz: EPHB4 Kinase Domain Inhibitor Complex

Enzymatic activity of EPHB4 Kinase Domain Inhibitor Complex

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

Protein crystallography data

The structure of EPHB4 Kinase Domain Inhibitor Complex, PDB code: 2vwz 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 (°) 45.810, 53.567, 61.373, 90.00, 110.64, 90.00
R / Rfree (%) 16.8 / 20.5

Other elements in 2vwz:

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

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the EPHB4 Kinase Domain Inhibitor Complex (pdb code 2vwz). 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: 2vwz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 2vwz

Go back to Magnesium Binding Sites List in 2vwz
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:22.7
occ:1.00
OD1 A:ASP758 2.0 18.1 1.0
O A:HOH2125 2.1 19.7 1.0
O A:HOH2124 2.1 23.1 1.0
O A:HOH2113 2.1 26.4 1.0
OD2 A:ASP740 2.1 21.3 1.0
O A:HOH2126 2.2 25.4 1.0
CG A:ASP758 3.1 19.2 1.0
CG A:ASP740 3.3 21.0 1.0
MG A:MG1891 3.3 22.1 1.0
OD2 A:ASP758 3.4 19.0 1.0
O A:HOH2139 3.5 53.0 1.0
CB A:ASP740 3.8 17.1 1.0
O A:HOH2114 4.0 33.6 1.0
ND2 A:ASN745 4.1 17.0 1.0
O A:HOH2140 4.2 40.7 1.0
O A:HOH2031 4.2 46.2 1.0
O A:HOH2128 4.2 43.1 1.0
OD1 A:ASP740 4.3 22.4 1.0
CB A:ASP758 4.4 15.9 1.0
O A:HOH2116 4.5 27.6 1.0
O A:HOH2112 4.7 24.9 1.0
NH1 A:ARG744 4.7 25.7 1.0
OD1 A:ASN745 5.0 15.3 1.0

Magnesium binding site 2 out of 3 in 2vwz

Go back to Magnesium Binding Sites List in 2vwz
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:22.1
occ:1.00
O A:HOH2125 1.5 19.7 1.0
O A:HOH2112 1.8 24.9 1.0
O A:HOH2128 1.9 43.1 1.0
OD1 A:ASP758 3.2 18.1 1.0
MG A:MG1890 3.3 22.7 1.0
O A:HOH2108 3.5 17.0 1.0
CB A:ASP740 3.5 17.1 1.0
CG A:ASP758 3.6 19.2 1.0
O A:HOH2139 3.6 53.0 1.0
OD2 A:ASP758 3.7 19.0 1.0
O A:ASP758 3.8 17.6 1.0
O A:HIS738 3.9 15.6 1.0
OD2 A:ASP740 4.0 21.3 1.0
O A:HOH2124 4.0 23.1 1.0
CG A:ASP740 4.3 21.0 1.0
C A:ASP758 4.4 17.3 1.0
CE1 A:HIS738 4.4 18.3 1.0
CB A:ASP758 4.4 15.9 1.0
O A:HOH2113 4.5 26.4 1.0
N A:ASP740 4.6 16.2 1.0
CA A:ASP740 4.7 15.6 1.0
ND1 A:HIS738 4.7 18.2 1.0
O A:GLY760 4.7 25.3 1.0
N A:GLY760 4.9 21.1 1.0

Magnesium binding site 3 out of 3 in 2vwz

Go back to Magnesium Binding Sites List in 2vwz
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:43.5
occ:1.00
O A:HOH2088 2.1 41.1 1.0
O A:HOH2165 2.1 34.3 1.0
O A:HOH2087 2.2 29.0 1.0
O A:HOH2164 2.2 31.1 1.0
OD1 A:ASP709 4.0 22.1 1.0
OD2 A:ASP709 4.1 27.5 1.0
O A:HOH2003 4.2 34.2 1.0
O A:SER815 4.2 15.9 1.0
CG A:ASP709 4.4 19.1 1.0
O A:HOH2162 4.5 22.0 1.0
O A:HOH2166 4.7 21.1 1.0
CG A:PRO843 4.9 22.4 1.0

Reference:

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
Page generated: Mon Dec 14 07:43:18 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy