Iron in PDB 4d4z: Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol

All present enzymatic activity of Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol:
1.14.99.29;

The structure of Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol, PDB code: 4d4z was solved by Z.Han, N.Sakai, R.Hilgenfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.051, 70.175, 101.275, 90.00, 102.71, 90.00
R / Rfree (%)	17.024 / 19.283

The binding sites of Iron atom in the Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol (pdb code 4d4z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol, PDB code: 4d4z:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:15.3 occ:1.00 OE1 A:GLU90 2.0 14.6 1.0 O A:OH303 2.0 18.9 1.0 O3 A:GOL305 2.1 20.6 1.0 O2 A:GOL305 2.2 16.8 1.0 NE2 A:HIS207 2.2 12.4 1.0 NE2 A:HIS89 2.2 15.0 1.0 C3 A:GOL305 2.9 21.8 1.0 C2 A:GOL305 3.0 24.8 1.0 CD A:GLU90 3.1 15.4 1.0 CD2 A:HIS89 3.1 15.2 1.0 CE1 A:HIS207 3.1 14.5 1.0 CD2 A:HIS207 3.2 13.3 1.0 CE1 A:HIS89 3.2 15.7 1.0 FE A:FE302 3.4 17.7 1.0 OE2 A:GLU90 3.5 16.3 1.0 OE1 A:GLU241 4.1 21.5 1.0 CD2 A:HIS56 4.1 15.2 1.0 ND1 A:HIS207 4.3 12.7 1.0 CG A:HIS89 4.3 13.5 1.0 CG A:HIS207 4.3 12.2 1.0 ND1 A:HIS89 4.3 14.3 1.0 C1 A:GOL305 4.4 26.0 1.0 NE2 A:HIS56 4.4 16.2 1.0 CG A:GLU90 4.4 13.1 1.0 SD A:MET237 4.6 77.4 0.2 SD A:MET237 4.6 86.8 0.2 SD A:MET237 4.7 77.4 0.5 O A:HOH2072 4.7 34.6 1.0 OE1 A:GLU93 4.7 22.9 1.0 CB A:GLU90 4.8 12.2 1.0 CG A:MET237 4.9 19.4 0.2 O A:HOH2001 5.0 17.6 1.0 CG A:MET237 5.0 18.9 0.2 CG A:MET237 5.0 26.8 0.5

Iron binding site 2 out of 4 in the Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:17.7 occ:1.00 OE1 A:GLU241 2.0 21.5 1.0 O A:HOH2001 2.1 17.6 1.0 O A:OH303 2.2 18.9 1.0 NE2 A:HIS56 2.2 16.2 1.0 NE2 A:HIS240 2.3 19.3 1.0 O3 A:GOL305 2.3 20.6 1.0 CD A:GLU241 3.1 20.1 1.0 CD2 A:HIS56 3.1 15.2 1.0 CE1 A:HIS240 3.2 18.8 1.0 CE1 A:HIS56 3.3 16.5 1.0 CD2 A:HIS240 3.3 21.1 1.0 FE A:FE301 3.4 15.3 1.0 C3 A:GOL305 3.5 21.8 1.0 OE2 A:GLU241 3.5 20.4 1.0 O A:HOH2072 3.7 34.6 1.0 OE1 A:GLU90 4.0 14.6 1.0 CD2 A:HIS207 4.1 13.3 1.0 O A:HOH2074 4.1 32.3 1.0 NE2 A:HIS207 4.2 12.4 1.0 CG A:HIS56 4.3 12.8 1.0 ND1 A:HIS56 4.3 14.3 1.0 ND1 A:HIS240 4.3 19.6 1.0 CG A:GLU241 4.4 17.7 1.0 CG A:HIS240 4.4 17.4 1.0 CE A:MET86 4.5 12.7 0.5 C2 A:GOL305 4.8 24.8 1.0 SD A:MET86 4.8 49.4 0.5 CB A:GLU241 4.9 15.7 1.0 O2 A:GOL305 4.9 16.8 1.0 CD A:GLU90 5.0 15.4 1.0

Iron binding site 3 out of 4 in the Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:15.8 occ:1.00 O B:OH303 1.9 19.1 1.0 O1 B:GOL305 2.1 20.3 1.0 OE1 B:GLU90 2.1 14.5 1.0 NE2 B:HIS207 2.2 13.3 1.0 O2 B:GOL305 2.2 19.5 1.0 NE2 B:HIS89 2.2 14.9 1.0 C1 B:GOL305 3.0 21.8 1.0 C2 B:GOL305 3.0 23.6 1.0 CD B:GLU90 3.1 14.7 1.0 CE1 B:HIS207 3.1 14.8 1.0 CD2 B:HIS89 3.1 14.3 1.0 CD2 B:HIS207 3.2 14.9 1.0 CE1 B:HIS89 3.3 15.3 1.0 OE2 B:GLU90 3.5 18.3 1.0 FE B:FE302 3.5 18.6 1.0 OE1 B:GLU241 4.1 21.4 1.0 CD2 B:HIS56 4.2 14.6 1.0 ND1 B:HIS207 4.2 13.3 1.0 CG B:HIS89 4.3 13.6 1.0 CG B:HIS207 4.3 12.5 1.0 ND1 B:HIS89 4.3 14.6 1.0 C3 B:GOL305 4.4 25.3 1.0 NE2 B:HIS56 4.5 17.1 1.0 CG B:GLU90 4.5 13.2 1.0 SD B:MET237 4.6 36.7 0.5 OE1 B:GLU93 4.7 22.4 1.0 O A:HOH2007 4.8 44.0 1.0 CB B:GLU90 4.8 11.9 1.0 O B:HOH2001 4.9 18.3 1.0 CG B:MET237 5.0 20.4 0.5

Iron binding site 4 out of 4 in the Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Deoxyhypusine Hydroxylase in Complex with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:18.6 occ:1.00 OE1 B:GLU241 2.0 21.4 1.0 O B:HOH2001 2.0 18.3 1.0 O B:OH303 2.2 19.1 1.0 NE2 B:HIS56 2.3 17.1 1.0 NE2 B:HIS240 2.3 17.4 1.0 O1 B:GOL305 2.4 20.3 1.0 CD B:GLU241 3.1 19.4 1.0 CD2 B:HIS56 3.2 14.6 1.0 CE1 B:HIS240 3.2 17.8 1.0 CE1 B:HIS56 3.3 18.4 1.0 CD2 B:HIS240 3.3 18.6 1.0 C1 B:GOL305 3.5 21.8 1.0 FE B:FE301 3.5 15.8 1.0 OE2 B:GLU241 3.5 21.0 1.0 O A:HOH2007 3.6 44.0 1.0 O B:HOH2057 3.9 31.3 1.0 CD2 B:HIS207 4.1 14.9 1.0 OE1 B:GLU90 4.1 14.5 1.0 NE2 B:HIS207 4.2 13.3 1.0 CG B:HIS56 4.3 13.7 1.0 ND1 B:HIS56 4.3 15.1 1.0 ND1 B:HIS240 4.4 18.7 1.0 CG B:HIS240 4.4 17.5 1.0 CE B:MET86 4.4 13.3 0.5 CG B:GLU241 4.4 18.1 1.0 C2 B:GOL305 4.8 23.6 1.0 CB B:GLU241 4.9 17.5 1.0 O2 B:GOL305 4.9 19.5 1.0 SD B:MET86 4.9 50.1 0.5 CG B:MET86 5.0 19.8 0.5 CD B:GLU90 5.0 14.7 1.0

Z.Han, N.Sakai, L.H.Bottger, S.Klinke, J.Hauber, A.X.Trautwein, R.Hilgenfeld. Crystal Structure of the Peroxo-Diiron(III) Intermediate of Deoxyhypusine Hydroxylase, An Oxygenase Involved in Hypusination. Structure V. 23 882 2015.
ISSN: ISSN 0969-2126
PubMed: 25865244
DOI: 10.1016/J.STR.2015.03.002