Iron in PDB 3u9m: Structure of Reduced Human FBXL5 Hemerythrin Like Domain

The structure of Structure of Reduced Human FBXL5 Hemerythrin Like Domain, PDB code: 3u9m was solved by P.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.00 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.086, 77.538, 73.641, 90.00, 110.55, 90.00
R / Rfree (%)	20.4 / 24.8

The binding sites of Iron atom in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain (pdb code 3u9m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain, PDB code: 3u9m:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:35.6 occ:1.00 OE2 A:GLU130 2.0 33.1 1.0 O A:HOH191 2.2 30.5 1.0 NE2 A:HIS80 2.2 33.7 1.0 OE1 A:GLU58 2.2 42.3 1.0 OE1 A:GLU61 2.2 30.9 1.0 NE2 A:HIS126 2.3 40.1 1.0 CD A:GLU130 3.0 32.1 1.0 CD A:GLU58 3.1 34.4 1.0 CD2 A:HIS80 3.2 32.4 1.0 CE1 A:HIS80 3.2 30.3 1.0 CD2 A:HIS126 3.2 33.9 1.0 FE A:FE202 3.3 32.1 1.0 CD A:GLU61 3.3 33.7 1.0 OE2 A:GLU58 3.4 32.9 1.0 CE1 A:HIS126 3.4 39.5 1.0 OE1 A:GLU130 3.4 34.8 1.0 OE2 A:GLU61 3.7 32.3 1.0 O A:HOH199 4.0 45.2 1.0 ND1 A:HIS80 4.3 33.8 1.0 CG A:HIS80 4.3 35.4 1.0 CG A:GLU130 4.3 32.9 1.0 CG A:HIS126 4.4 37.3 1.0 ND1 A:HIS126 4.5 34.0 1.0 NE2 A:HIS57 4.5 26.5 1.0 CG A:GLU58 4.5 27.7 1.0 CG A:GLU61 4.6 30.2 1.0 CD2 A:HIS57 4.6 30.7 1.0 CB A:GLU61 4.7 31.5 1.0 CA A:GLU58 4.7 27.4 1.0 CB A:GLU58 4.8 27.4 1.0

Iron binding site 2 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:32.1 occ:1.00 O A:HOH191 2.1 30.5 1.0 OE2 A:GLU61 2.1 32.3 1.0 OE1 A:GLU130 2.2 34.8 1.0 NE2 A:HIS15 2.2 27.1 1.0 NE2 A:HIS57 2.3 26.5 1.0 CD A:GLU61 2.9 33.7 1.0 OE1 A:GLU61 3.0 30.9 1.0 CD2 A:HIS15 3.1 28.1 1.0 CD A:GLU130 3.1 32.1 1.0 CE1 A:HIS57 3.3 30.7 1.0 FE A:FE201 3.3 35.6 1.0 OE2 A:GLU130 3.3 33.1 1.0 CD2 A:HIS57 3.3 30.7 1.0 CE1 A:HIS15 3.3 24.1 1.0 CG A:HIS15 4.3 27.9 1.0 CD1 A:PHE11 4.3 26.2 1.0 CG A:GLU61 4.3 30.2 1.0 CG A:MET127 4.3 36.4 1.0 ND1 A:HIS15 4.4 28.6 1.0 ND1 A:HIS57 4.4 29.4 1.0 CG A:HIS57 4.4 30.0 1.0 CG A:GLU130 4.5 32.9 1.0 OE2 A:GLU58 4.6 32.9 1.0 O A:HOH161 4.6 29.8 1.0 OE1 A:GLU58 4.6 42.3 1.0 CE1 A:PHE11 4.6 29.0 1.0 CD2 A:HIS126 4.7 33.9 1.0 NE2 A:HIS126 4.8 40.1 1.0 CA A:MET127 4.8 36.5 1.0 CB A:GLU130 4.9 32.1 1.0 CD A:GLU58 5.0 34.4 1.0

Iron binding site 3 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe203 b:41.8 occ:1.00 OE2 C:GLU130 2.1 34.2 1.0 OE1 C:GLU58 2.2 44.4 1.0 OE1 C:GLU61 2.2 37.5 1.0 NE2 C:HIS126 2.3 43.9 1.0 NE2 C:HIS80 2.5 62.5 1.0 FE C:FE204 3.0 40.6 1.0 CD C:GLU58 3.0 41.8 1.0 CD2 C:HIS126 3.1 42.3 1.0 CD C:GLU130 3.1 37.2 1.0 OE2 C:GLU58 3.2 39.1 1.0 CD C:GLU61 3.2 38.1 1.0 CE1 C:HIS80 3.4 68.0 1.0 CE1 C:HIS126 3.4 41.2 1.0 CD2 C:HIS80 3.4 66.6 1.0 OE1 C:GLU130 3.4 32.6 1.0 OE2 C:GLU61 3.6 44.8 1.0 NE2 C:HIS57 4.2 33.3 1.0 CG C:HIS126 4.3 44.1 1.0 CD2 C:HIS57 4.4 31.2 1.0 CG C:GLU58 4.4 39.0 1.0 ND1 C:HIS126 4.4 44.0 1.0 CG C:GLU130 4.5 37.2 1.0 ND1 C:HIS80 4.6 71.5 1.0 CG C:GLU61 4.6 31.1 1.0 CG C:HIS80 4.6 71.9 1.0 CA C:GLU58 4.7 39.8 1.0 ND2 C:ASN83 4.8 0.0 1.0 CB C:GLU58 4.8 34.6 1.0 CB C:GLU61 4.9 29.6 1.0

Iron binding site 4 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe204 b:40.6 occ:1.00 NE2 C:HIS57 2.2 33.3 1.0 OE1 C:GLU130 2.3 32.6 1.0 NE2 C:HIS15 2.3 44.2 1.0 OE2 C:GLU61 2.4 44.8 1.0 CD C:GLU61 2.9 38.1 1.0 OE1 C:GLU61 3.0 37.5 1.0 FE C:FE203 3.0 41.8 1.0 CE1 C:HIS57 3.1 27.1 1.0 CD C:GLU130 3.1 37.2 1.0 CD2 C:HIS15 3.2 45.3 1.0 OE2 C:GLU130 3.2 34.2 1.0 CD2 C:HIS57 3.3 31.2 1.0 CE1 C:HIS15 3.3 38.2 1.0 CG C:MET127 4.1 40.5 1.0 ND1 C:HIS57 4.2 32.8 1.0 CG C:GLU61 4.3 31.1 1.0 CG C:HIS57 4.4 33.6 1.0 CG C:HIS15 4.4 43.0 1.0 CD1 C:PHE11 4.4 39.4 1.0 OE2 C:GLU58 4.4 39.1 1.0 ND1 C:HIS15 4.4 41.9 1.0 CD2 C:HIS126 4.5 42.3 1.0 CG C:GLU130 4.5 37.2 1.0 OE1 C:GLU58 4.6 44.4 1.0 NE2 C:HIS126 4.6 43.9 1.0 CA C:MET127 4.6 35.4 1.0 CB C:MET127 4.7 40.6 1.0 CE1 C:PHE11 4.7 36.0 1.0 O C:HOH177 4.8 34.4 1.0 CD C:GLU58 4.8 41.8 1.0 CB C:GLU130 4.9 35.5 1.0

Iron binding site 5 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe205 b:40.3 occ:1.00 O E:HOH185 2.1 35.4 1.0 OE2 E:GLU130 2.1 38.5 1.0 OE1 E:GLU58 2.2 38.0 1.0 NE2 E:HIS126 2.3 40.7 1.0 OE1 E:GLU61 2.3 30.0 1.0 NE2 E:HIS80 2.4 58.2 1.0 CD E:GLU58 3.2 33.4 1.0 CD E:GLU130 3.2 39.0 1.0 CD2 E:HIS126 3.2 38.0 1.0 CD2 E:HIS80 3.2 60.4 1.0 FE E:FE206 3.2 36.0 1.0 CE1 E:HIS126 3.3 40.3 1.0 OE2 E:GLU58 3.4 36.1 1.0 CD E:GLU61 3.4 30.9 1.0 CE1 E:HIS80 3.4 62.1 1.0 OE1 E:GLU130 3.6 35.1 1.0 OE2 E:GLU61 3.9 32.7 1.0 O E:HOH201 4.1 49.0 1.0 CG E:HIS126 4.4 39.9 1.0 ND1 E:HIS126 4.4 48.3 1.0 CG E:HIS80 4.4 67.9 1.0 CG E:GLU130 4.5 39.6 1.0 NE2 E:HIS57 4.5 33.2 1.0 ND1 E:HIS80 4.5 63.7 1.0 CG E:GLU58 4.5 28.5 1.0 CD2 E:HIS57 4.6 31.9 1.0 CG E:GLU61 4.7 32.9 1.0 CA E:GLU58 4.8 30.3 1.0 CB E:GLU61 4.8 35.0 1.0 CB E:GLU58 4.9 26.6 1.0 ND2 E:ASN83 5.0 65.9 1.0

Iron binding site 6 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe206 b:36.0 occ:1.00 O E:HOH185 2.1 35.4 1.0 OE2 E:GLU61 2.2 32.7 1.0 OE1 E:GLU130 2.3 35.1 1.0 NE2 E:HIS15 2.3 32.7 1.0 NE2 E:HIS57 2.3 33.2 1.0 CD E:GLU61 2.9 30.9 1.0 OE1 E:GLU61 3.0 30.0 1.0 CD E:GLU130 3.1 39.0 1.0 CE1 E:HIS57 3.2 30.1 1.0 CD2 E:HIS15 3.2 30.1 1.0 OE2 E:GLU130 3.2 38.5 1.0 FE E:FE205 3.2 40.3 1.0 CD2 E:HIS57 3.3 31.9 1.0 CE1 E:HIS15 3.3 33.6 1.0 CG E:MET127 4.1 35.2 1.0 ND1 E:HIS57 4.3 32.1 1.0 CG E:GLU61 4.3 32.9 1.0 CD1 E:PHE11 4.3 34.8 1.0 CG E:HIS15 4.4 33.4 1.0 ND1 E:HIS15 4.4 33.3 1.0 CG E:HIS57 4.4 31.3 1.0 OE2 E:GLU58 4.5 36.1 1.0 CG E:GLU130 4.5 39.6 1.0 OE1 E:GLU58 4.5 38.0 1.0 CE1 E:PHE11 4.6 29.6 1.0 CD2 E:HIS126 4.6 38.0 1.0 NE2 E:HIS126 4.7 40.7 1.0 CA E:MET127 4.7 37.8 1.0 O E:HOH167 4.7 40.7 1.0 CB E:MET127 4.8 40.4 1.0 CD E:GLU58 4.9 33.4 1.0 CB E:GLU130 4.9 39.8 1.0 SD E:MET127 5.0 34.7 1.0

Iron binding site 7 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe207 b:39.0 occ:1.00 OE2 G:GLU130 2.1 36.0 1.0 OE1 G:GLU58 2.1 35.1 1.0 OE1 G:GLU61 2.2 37.0 1.0 NE2 G:HIS126 2.4 37.3 1.0 NE2 G:HIS80 2.4 56.9 1.0 CD G:GLU130 3.0 41.7 1.0 CD G:GLU58 3.1 39.9 1.0 FE G:FE208 3.1 38.7 1.0 CE1 G:HIS126 3.2 39.9 1.0 CD G:GLU61 3.3 35.9 1.0 CD2 G:HIS80 3.3 67.5 1.0 OE2 G:GLU58 3.4 42.7 1.0 OE1 G:GLU130 3.4 38.3 1.0 CE1 G:HIS80 3.4 63.4 1.0 CD2 G:HIS126 3.5 40.5 1.0 OE2 G:GLU61 3.7 44.8 1.0 CG G:GLU130 4.3 38.4 1.0 ND1 G:HIS126 4.4 42.7 1.0 NE2 G:HIS57 4.4 41.1 1.0 CG G:GLU58 4.4 38.8 1.0 ND1 G:HIS80 4.5 59.4 1.0 CG G:HIS80 4.5 67.7 1.0 CG G:HIS126 4.5 45.7 1.0 CG G:GLU61 4.6 37.5 1.0 CA G:GLU58 4.6 43.1 1.0 CD2 G:HIS57 4.6 41.7 1.0 CB G:GLU58 4.7 40.3 1.0 CB G:GLU61 4.7 41.1 1.0 OD1 G:ASN83 4.9 66.9 1.0

Iron binding site 8 out of 8 in the Structure of Reduced Human FBXL5 Hemerythrin Like Domain


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Structure of Reduced Human FBXL5 Hemerythrin Like Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe208 b:38.7 occ:1.00 OE2 G:GLU61 2.1 44.8 1.0 NE2 G:HIS57 2.2 41.1 1.0 NE2 G:HIS15 2.3 42.9 1.0 OE1 G:GLU130 2.3 38.3 1.0 CD G:GLU61 2.8 35.9 1.0 OE1 G:GLU61 2.9 37.0 1.0 CE1 G:HIS57 3.1 34.6 1.0 FE G:FE207 3.1 39.0 1.0 CD2 G:HIS15 3.1 44.9 1.0 CD G:GLU130 3.2 41.7 1.0 CD2 G:HIS57 3.3 41.7 1.0 CE1 G:HIS15 3.3 42.8 1.0 OE2 G:GLU130 3.3 36.0 1.0 CG G:MET127 4.1 37.2 1.0 ND1 G:HIS57 4.2 38.6 1.0 CD1 G:PHE11 4.2 44.5 1.0 OE2 G:GLU58 4.2 42.7 1.0 CG G:GLU61 4.3 37.5 1.0 CG G:HIS57 4.3 40.3 1.0 CG G:HIS15 4.3 44.1 1.0 OE1 G:GLU58 4.4 35.1 1.0 ND1 G:HIS15 4.4 44.0 1.0 O G:HOH178 4.4 34.2 1.0 NE2 G:HIS126 4.4 37.3 1.0 CE1 G:PHE11 4.6 42.0 1.0 CG G:GLU130 4.6 38.4 1.0 CD G:GLU58 4.6 39.9 1.0 CD2 G:HIS126 4.7 40.5 1.0 CA G:MET127 4.8 45.8 1.0 CB G:MET127 4.9 43.1 1.0

C.Shu, M.W.Sung, M.D.Stewart, T.I.Igumenova, X.Tan, P.Li. The Structural Basis of Iron Sensing By the Human F-Box Protein FBXL5. Chembiochem V. 13 788 2012.
ISSN: ISSN 1439-4227
PubMed: 22492618
DOI: 10.1002/CBIC.201200043