Iron in PDB 4d50: Structure of Human Deoxyhypusine Hydroxylase

All present enzymatic activity of Structure of Human Deoxyhypusine Hydroxylase:
1.14.99.29;

The structure of Structure of Human Deoxyhypusine Hydroxylase, PDB code: 4d50 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)	19.85 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.933, 48.636, 124.087, 90.00, 99.27, 90.00
R / Rfree (%)	20.261 / 24.65

The binding sites of Iron atom in the Structure of Human Deoxyhypusine Hydroxylase (pdb code 4d50). 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, PDB code: 4d50:
Jump to Iron binding site number: 1; 2; 3; 4;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:14.4 occ:1.00 OE1 A:GLU90 2.1 11.6 1.0 O A:HOH2003 2.1 26.4 1.0 O A:HOH2001 2.2 12.2 1.0 O1 A:PER303 2.2 21.4 1.0 NE2 A:HIS89 2.2 12.8 1.0 NE2 A:HIS207 2.3 9.6 1.0 CD2 A:HIS89 3.2 12.2 1.0 CD A:GLU90 3.2 10.7 1.0 CE1 A:HIS207 3.2 10.0 1.0 CD2 A:HIS207 3.2 9.3 1.0 CE1 A:HIS89 3.2 13.0 1.0 O2 A:PER303 3.5 18.9 1.0 OE2 A:GLU90 3.6 13.4 1.0 FE A:FE302 3.8 16.4 1.0 O A:HOH2193 4.0 33.3 1.0 CE A:MET237 4.1 12.8 0.5 CD2 A:HIS56 4.2 13.7 1.0 OE1 A:GLU241 4.3 15.7 1.0 ND1 A:HIS207 4.3 9.8 1.0 CG A:HIS89 4.3 10.8 1.0 ND1 A:HIS89 4.3 11.1 1.0 CG A:HIS207 4.4 9.4 1.0 CG A:GLU90 4.5 9.7 1.0 NE2 A:HIS56 4.5 13.5 1.0 OE1 A:GLU93 4.8 13.3 1.0 CB A:GLU90 4.8 8.8 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:16.4 occ:1.00 OE1 A:GLU241 2.1 15.7 1.0 O A:HOH2002 2.2 13.4 1.0 O2 A:PER303 2.2 18.9 1.0 NE2 A:HIS240 2.2 14.5 1.0 NE2 A:HIS56 2.3 13.5 1.0 O A:HOH2003 2.4 26.4 1.0 O1 A:PER303 2.8 21.4 1.0 CD A:GLU241 3.1 12.8 1.0 CD2 A:HIS240 3.1 14.9 1.0 CE1 A:HIS240 3.2 14.7 1.0 CD2 A:HIS56 3.3 13.7 1.0 CE1 A:HIS56 3.3 14.1 1.0 OE2 A:GLU241 3.5 17.4 1.0 FE A:FE301 3.8 14.4 1.0 O A:HOH2049 4.2 29.6 1.0 O A:HOH2053 4.2 29.5 1.0 CD2 A:HIS207 4.2 9.3 1.0 ND1 A:HIS240 4.3 14.1 1.0 CG A:HIS240 4.3 12.8 1.0 OE1 A:GLU90 4.3 11.6 1.0 CG A:HIS56 4.4 13.5 1.0 CE A:MET86 4.4 9.4 0.5 ND1 A:HIS56 4.4 14.5 1.0 CG A:GLU241 4.5 12.9 1.0 NE2 A:HIS207 4.5 9.6 1.0 CB A:GLU241 4.9 11.4 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:17.6 occ:1.00 OE1 B:GLU90 2.1 16.1 1.0 O B:HOH2001 2.1 30.3 1.0 O B:HOH2003 2.1 33.5 1.0 O1 B:PER303 2.2 28.0 1.0 NE2 B:HIS89 2.2 15.7 1.0 NE2 B:HIS207 2.2 13.8 1.0 CE1 B:HIS207 3.2 13.5 1.0 CD B:GLU90 3.2 16.0 1.0 CD2 B:HIS89 3.2 17.1 1.0 CD2 B:HIS207 3.2 13.3 1.0 CE1 B:HIS89 3.2 18.7 1.0 OE2 B:GLU90 3.5 19.5 1.0 O2 B:PER303 3.6 21.4 1.0 FE B:FE302 3.7 20.6 1.0 CD2 B:HIS56 4.2 16.8 1.0 ND1 B:HIS207 4.3 12.8 1.0 CG B:HIS89 4.3 15.2 1.0 ND1 B:HIS89 4.3 15.3 1.0 OE1 B:GLU241 4.4 16.4 1.0 CG B:HIS207 4.4 13.1 1.0 NE2 B:HIS56 4.4 15.0 1.0 CG B:GLU90 4.5 15.0 1.0 O B:HOH2002 4.8 27.1 1.0 OE1 B:GLU93 4.8 19.7 1.0 CB B:GLU90 4.8 13.5 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:20.6 occ:1.00 OE1 B:GLU241 2.0 16.4 1.0 O2 B:PER303 2.2 21.4 1.0 O B:HOH2002 2.2 27.1 1.0 O B:HOH2003 2.2 33.5 1.0 NE2 B:HIS240 2.3 18.4 1.0 NE2 B:HIS56 2.3 15.0 1.0 O1 B:PER303 2.6 28.0 1.0 CD B:GLU241 3.1 15.8 1.0 CD2 B:HIS240 3.2 18.6 1.0 CD2 B:HIS56 3.3 16.8 1.0 CE1 B:HIS56 3.3 16.1 1.0 CE1 B:HIS240 3.3 19.3 1.0 OE2 B:GLU241 3.6 18.9 1.0 FE B:FE301 3.7 17.6 1.0 CD2 B:HIS207 4.1 13.3 1.0 NE2 B:HIS207 4.3 13.8 1.0 OE1 B:GLU90 4.3 16.1 1.0 CG B:GLU241 4.4 15.1 1.0 ND1 B:HIS56 4.4 15.8 1.0 ND1 B:HIS240 4.4 16.7 1.0 CG B:HIS56 4.4 15.2 1.0 CE B:MET86 4.4 22.4 0.5 CG B:HIS240 4.4 15.7 1.0 O B:HOH2001 4.7 30.3 1.0 CB B:GLU241 4.8 14.4 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