Iron in PDB 2ibn: Crystal Structure of Human Myo-Inositol Oxygenase (Miox)

All present enzymatic activity of Crystal Structure of Human Myo-Inositol Oxygenase (Miox):
1.13.99.1;

The structure of Crystal Structure of Human Myo-Inositol Oxygenase (Miox), PDB code: 2ibn was solved by B.M.Hallberg, R.D.Busam, C.Arrowsmith, H.Berglund, R.Collins, A.Edwards, M.Ehn, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, M.Hogbom, L.Holmberg-Schiavone, I.Johansson, T.Karlberg, T.Kotenyova, P.Nilsson-Ehle, P.Nordlund, T.Nyman, D.Ogg, J.Sagemark, P.Stenmark, M.Sundstrom, J.Uppenberg, S.Van Den Berg, J.Weigelt, A.G.Thorsell, C.Persson, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.34 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.715, 55.861, 111.516, 90.00, 116.72, 90.00
R / Rfree (%)	20.6 / 24.8

The binding sites of Iron atom in the Crystal Structure of Human Myo-Inositol Oxygenase (Miox) (pdb code 2ibn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Human Myo-Inositol Oxygenase (Miox), PDB code: 2ibn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Human Myo-Inositol Oxygenase (Miox)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Human Myo-Inositol Oxygenase (Miox) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe703 b:16.6 occ:1.00 NE2 A:HIS98 2.0 13.9 1.0 OD1 A:ASP253 2.1 19.6 1.0 NE2 A:HIS123 2.1 12.4 1.0 O A:HOH812 2.2 13.0 1.0 OD2 A:ASP124 2.3 13.6 1.0 O A:HOH737 2.3 20.6 1.0 CE1 A:HIS98 3.0 17.9 1.0 CE1 A:HIS123 3.0 12.8 1.0 CD2 A:HIS98 3.0 16.3 1.0 CG A:ASP253 3.1 21.5 1.0 CG A:ASP124 3.1 14.9 1.0 CD2 A:HIS123 3.2 15.7 1.0 OD2 A:ASP253 3.3 18.6 1.0 OD1 A:ASP124 3.5 9.7 1.0 FE A:FE704 3.7 13.6 1.0 O1 A:I1N710 3.7 14.9 1.0 O A:HOH804 3.8 32.9 1.0 O A:HOH965 4.0 32.8 1.0 ND1 A:HIS98 4.1 16.1 1.0 CG A:HIS98 4.2 17.1 1.0 ND1 A:HIS123 4.2 14.7 1.0 CB A:ASP124 4.3 13.1 1.0 CG A:HIS123 4.3 14.1 1.0 CB A:ASP253 4.4 23.4 1.0 NZ A:LYS127 4.6 19.5 1.0 C1 A:I1N710 4.6 25.1 1.0 NE2 A:HIS220 4.8 11.7 1.0 CA A:ASP253 4.8 24.3 1.0 OG1 A:THR102 4.9 15.1 1.0 O A:ASP253 4.9 26.8 1.0 CD2 A:HIS220 5.0 9.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Human Myo-Inositol Oxygenase (Miox)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Human Myo-Inositol Oxygenase (Miox) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe704 b:13.6 occ:1.00 O1 A:I1N710 1.9 14.9 1.0 O A:HOH812 2.0 13.0 1.0 OD1 A:ASP124 2.0 9.7 1.0 NE2 A:HIS220 2.3 11.7 1.0 O6 A:I1N710 2.3 19.1 1.0 NE2 A:HIS194 2.3 12.2 1.0 C1 A:I1N710 2.7 25.1 1.0 C6 A:I1N710 3.0 24.2 1.0 CG A:ASP124 3.0 14.9 1.0 CD2 A:HIS220 3.1 9.3 1.0 CD2 A:HIS194 3.2 5.6 1.0 OD2 A:ASP124 3.3 13.6 1.0 CE1 A:HIS194 3.3 13.7 1.0 CE1 A:HIS220 3.3 12.2 1.0 FE A:FE703 3.7 16.6 1.0 OG A:SER221 3.7 10.9 1.0 CD2 A:HIS123 4.0 15.7 1.0 NZ A:LYS127 4.1 19.5 1.0 O A:HOH737 4.1 20.6 1.0 C2 A:I1N710 4.2 25.4 1.0 CE A:LYS127 4.2 17.9 1.0 NE2 A:HIS123 4.2 12.4 1.0 CG A:HIS220 4.3 14.5 1.0 CG A:HIS194 4.3 3.4 1.0 ND1 A:HIS194 4.4 8.4 1.0 C5 A:I1N710 4.4 26.8 1.0 ND1 A:HIS220 4.4 10.7 1.0 CB A:ASP124 4.4 13.1 1.0 OD2 A:ASP253 4.4 18.6 1.0 OD1 A:ASP195 4.6 16.8 1.0 O2 A:I1N710 4.6 22.5 1.0 CA A:ASP124 4.8 12.2 1.0 O A:HIS123 4.8 10.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Human Myo-Inositol Oxygenase (Miox)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Human Myo-Inositol Oxygenase (Miox) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe705 b:15.3 occ:1.00 NE2 B:HIS123 2.1 6.1 1.0 NE2 B:HIS98 2.1 11.2 1.0 OD1 B:ASP253 2.1 20.4 1.0 O B:HOH807 2.2 10.5 1.0 O B:HOH782 2.2 26.2 1.0 OD2 B:ASP124 2.3 12.3 1.0 CE1 B:HIS123 2.8 9.6 1.0 CD2 B:HIS98 2.9 13.1 1.0 CG B:ASP253 3.1 19.1 1.0 CE1 B:HIS98 3.1 16.6 1.0 CG B:ASP124 3.1 12.8 1.0 CD2 B:HIS123 3.2 9.3 1.0 OD2 B:ASP253 3.4 20.0 1.0 OD1 B:ASP124 3.5 8.8 1.0 O1 B:I1N709 3.8 19.6 1.0 FE B:FE706 3.8 15.0 1.0 O B:HOH949 4.0 40.1 1.0 ND1 B:HIS123 4.0 13.1 1.0 CG B:HIS98 4.1 16.7 1.0 ND1 B:HIS98 4.2 13.3 1.0 CG B:HIS123 4.2 9.1 1.0 CB B:ASP124 4.3 11.7 1.0 O B:HOH969 4.4 55.9 1.0 CB B:ASP253 4.4 21.4 1.0 C1 B:I1N709 4.7 24.9 1.0 NZ B:LYS127 4.7 18.2 1.0 CA B:ASP253 4.8 22.0 1.0 OG1 B:THR102 4.8 17.1 1.0 C B:ASP253 4.9 23.8 1.0 NE2 B:HIS220 5.0 2.0 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Human Myo-Inositol Oxygenase (Miox)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Human Myo-Inositol Oxygenase (Miox) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe706 b:15.0 occ:1.00 O1 B:I1N709 2.0 19.6 1.0 OD1 B:ASP124 2.1 8.8 1.0 NE2 B:HIS194 2.2 11.4 1.0 O B:HOH807 2.2 10.5 1.0 O6 B:I1N709 2.3 13.7 1.0 NE2 B:HIS220 2.3 2.0 1.0 C1 B:I1N709 2.7 24.9 1.0 C6 B:I1N709 3.0 24.7 1.0 CG B:ASP124 3.1 12.8 1.0 CD2 B:HIS194 3.1 10.2 1.0 CD2 B:HIS220 3.2 2.0 1.0 CE1 B:HIS194 3.2 11.2 1.0 OD2 B:ASP124 3.4 12.3 1.0 CE1 B:HIS220 3.4 14.4 1.0 OG B:SER221 3.7 4.3 1.0 FE B:FE705 3.8 15.3 1.0 CD2 B:HIS123 4.0 9.3 1.0 O B:HOH782 4.1 26.2 1.0 NZ B:LYS127 4.1 18.2 1.0 NE2 B:HIS123 4.2 6.1 1.0 C2 B:I1N709 4.2 28.0 1.0 CG B:HIS194 4.2 9.3 1.0 CE B:LYS127 4.2 20.4 1.0 ND1 B:HIS194 4.3 13.7 1.0 C5 B:I1N709 4.3 27.1 1.0 CG B:HIS220 4.4 10.1 1.0 ND1 B:HIS220 4.4 4.3 1.0 CB B:ASP124 4.4 11.7 1.0 OD1 B:ASP195 4.4 15.5 1.0 OD2 B:ASP253 4.5 20.0 1.0 O2 B:I1N709 4.6 24.4 1.0 O B:HIS123 4.7 9.0 1.0 CA B:ASP124 4.8 11.6 1.0 CB B:SER221 5.0 4.4 1.0

A.G.Thorsell, C.Persson, N.Voevodskaya, R.D.Busam, M.Hammarstrom, S.Graslund, A.Graslund, B.M.Hallberg. Structural and Biophysical Characterization of Human Myo-Inositol Oxygenase J.Biol.Chem. V. 283 15209 2008.
ISSN: ISSN 0021-9258
PubMed: 18364358
DOI: 10.1074/JBC.M800348200