Iron in PDB 6p5q: X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid

The structure of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid, PDB code: 6p5q was solved by L.J.Rajakovich, A.J.Mitchell, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.08 / 1.86
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.009, 74.148, 142.563, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 21.7

The binding sites of Iron atom in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid (pdb code 6p5q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid, PDB code: 6p5q:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:20.6 occ:0.55 OE1 A:GLU159 2.0 29.3 1.0 O A:HOH403 2.3 20.3 1.0 O A:HOH534 2.3 29.5 1.0 ND1 A:HIS201 2.5 44.7 1.0 CD A:GLU159 3.2 28.3 1.0 CE1 A:HIS201 3.3 39.4 1.0 HE1 A:HIS201 3.3 47.3 1.0 CG A:HIS201 3.6 40.2 1.0 HG2 A:GLU159 3.6 30.6 1.0 HB3 A:GLU159 3.7 22.3 1.0 HB3 A:HIS201 3.7 31.9 1.0 HB2 A:HIS201 3.8 31.9 1.0 OE2 A:GLU101 3.9 36.0 1.0 CG A:GLU159 3.9 25.5 1.0 CB A:HIS201 3.9 26.5 1.0 O A:HOH486 4.0 24.9 1.0 HD2 A:HIS194 4.1 21.8 1.0 OE2 A:GLU159 4.2 24.3 1.0 O2 A:DAO301 4.2 19.9 1.0 CB A:GLU159 4.3 18.5 1.0 NE2 A:HIS201 4.5 41.3 1.0 CD2 A:HIS201 4.6 36.1 1.0 OD2 A:ASP199 4.8 46.2 1.0 HE2 A:PHE68 4.8 20.8 1.0 HG3 A:GLU159 4.8 30.6 1.0 CD2 A:HIS194 4.8 18.2 1.0 FE A:FE303 4.9 21.3 1.0 HB2 A:GLU159 5.0 22.3 1.0 HE1 A:HIS104 5.0 20.8 1.0 HA A:GLU159 5.0 18.2 1.0

Iron binding site 2 out of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:21.3 occ:0.96 O A:HOH401 2.1 23.6 1.0 ND1 A:HIS104 2.2 15.1 1.0 O2 A:DAO301 2.2 19.9 1.0 NE2 A:HIS194 2.2 18.5 1.0 OE1 A:GLU101 2.3 22.8 1.0 CD A:GLU101 3.0 28.1 1.0 CE1 A:HIS104 3.0 17.3 1.0 OE2 A:GLU101 3.0 36.0 1.0 CE1 A:HIS194 3.1 20.8 1.0 HE1 A:HIS104 3.1 20.8 1.0 C1 A:DAO301 3.1 26.0 1.0 HE1 A:HIS194 3.1 25.0 1.0 CG A:HIS104 3.2 16.6 1.0 O1 A:DAO301 3.3 22.5 1.0 CD2 A:HIS194 3.3 18.2 1.0 HB3 A:HIS104 3.3 22.7 1.0 HD2 A:HIS194 3.6 21.8 1.0 CB A:HIS104 3.7 18.9 1.0 HB2 A:HIS104 3.7 22.7 1.0 O A:HOH416 3.9 31.2 1.0 O A:HOH403 3.9 20.3 1.0 HE1 A:TRP190 4.1 17.1 1.0 NE2 A:HIS104 4.2 15.6 1.0 HA A:GLU101 4.2 27.4 1.0 ND1 A:HIS194 4.2 16.2 1.0 CD2 A:HIS104 4.3 21.7 1.0 CG A:HIS194 4.4 19.2 1.0 CG A:GLU101 4.4 18.3 1.0 C2 A:DAO301 4.5 19.4 1.0 NE1 A:TRP190 4.6 14.2 1.0 HZ2 A:TRP190 4.6 17.1 1.0 HB3 A:GLU101 4.6 26.1 1.0 H22 A:DAO301 4.7 23.4 1.0 H21 A:DAO301 4.8 23.4 1.0 FE A:FE302 4.9 20.6 0.6 HG3 A:GLU101 4.9 22.0 1.0 HG13 A:VAL65 4.9 19.3 1.0 HE2 A:HIS104 4.9 18.7 1.0 CB A:GLU101 4.9 21.8 1.0 HG2 A:GLU101 4.9 22.0 1.0 CA A:GLU101 5.0 22.8 1.0 HD1 A:HIS194 5.0 19.5 1.0 HG12 A:VAL100 5.0 22.1 1.0

Iron binding site 3 out of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:53.8 occ:0.90 O B:HOH402 2.0 38.9 1.0 OE1 B:GLU159 2.2 46.7 1.0 ND1 B:HIS201 2.5 61.9 1.0 CD B:GLU159 3.2 38.8 1.0 HE1 B:HIS201 3.2 64.5 1.0 HG2 B:GLU159 3.3 38.6 1.0 CE1 B:HIS201 3.3 53.7 1.0 CG B:HIS201 3.7 59.7 1.0 CG B:GLU159 3.7 32.2 1.0 HD2 B:HIS194 3.8 32.5 1.0 HB2 B:HIS201 3.9 51.1 1.0 OE2 B:GLU101 3.9 47.9 1.0 HB3 B:HIS201 3.9 51.1 1.0 O1 B:DAO301 4.0 30.2 1.0 HB3 B:GLU159 4.0 35.1 1.0 CB B:HIS201 4.1 42.5 1.0 OE2 B:GLU159 4.3 29.6 1.0 CD2 B:HIS194 4.4 27.1 1.0 NE2 B:HIS201 4.5 61.3 1.0 CB B:GLU159 4.5 29.2 1.0 HG3 B:GLU159 4.5 38.6 1.0 HD22 B:ASN97 4.6 66.4 1.0 FE B:FE303 4.6 32.7 1.0 CD2 B:HIS201 4.7 61.5 1.0 HE1 B:HIS104 4.7 34.7 1.0 NE2 B:HIS194 4.8 31.9 1.0 HE2 B:PHE68 4.8 33.0 1.0 CD B:GLU101 5.0 38.5 1.0

Iron binding site 4 out of 4 in the X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of Fe(II)-Soaked Unda Bound to Lauric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:32.7 occ:0.97 O B:HOH401 2.1 27.3 1.0 OE1 B:GLU101 2.2 35.8 1.0 ND1 B:HIS104 2.2 30.7 1.0 O1 B:DAO301 2.2 30.2 1.0 NE2 B:HIS194 2.3 31.9 1.0 CE1 B:HIS194 3.0 33.0 1.0 HE1 B:HIS194 3.0 39.6 1.0 CD B:GLU101 3.1 38.5 1.0 C1 B:DAO301 3.1 34.6 1.0 HB3 B:HIS104 3.2 36.2 1.0 CE1 B:HIS104 3.2 28.9 1.0 CG B:HIS104 3.2 29.0 1.0 O2 B:DAO301 3.2 30.7 1.0 HE1 B:HIS104 3.3 34.7 1.0 OE2 B:GLU101 3.4 47.9 1.0 CD2 B:HIS194 3.4 27.1 1.0 CB B:HIS104 3.5 30.1 1.0 O B:HOH402 3.6 38.9 1.0 HB2 B:HIS104 3.6 36.2 1.0 HD2 B:HIS194 3.7 32.5 1.0 HE1 B:TRP190 4.1 29.9 1.0 HA B:GLU101 4.2 46.3 1.0 ND1 B:HIS194 4.2 32.1 1.0 NE2 B:HIS104 4.3 27.5 1.0 CD2 B:HIS104 4.4 33.5 1.0 CG B:HIS194 4.4 31.9 1.0 HB3 B:GLU101 4.5 40.8 1.0 CG B:GLU101 4.5 26.8 1.0 C2 B:DAO301 4.6 29.2 1.0 NE1 B:TRP190 4.6 24.9 1.0 FE B:FE302 4.6 53.8 0.9 HZ2 B:TRP190 4.7 29.9 1.0 H21 B:DAO301 4.8 35.1 1.0 HG13 B:VAL65 4.8 30.9 1.0 H22 B:DAO301 4.9 35.1 1.0 CB B:GLU101 4.9 34.0 1.0 HG3 B:GLU101 4.9 32.1 1.0 HD1 B:HIS194 5.0 38.6 1.0 HG12 B:VAL100 5.0 48.9 1.0 CA B:GLU101 5.0 38.5 1.0

B.Zhang, L.J.Rajakovich, D.Van Cura, E.J.Blaesi, A.J.Mitchell, C.R.Tysoe, X.Zhu, B.R.Streit, Z.Rui, W.Zhang, A.K.Boal, C.Krebs, J.M.Bollinger Jr.. Substrate-Triggered Formation of A Peroxo-FE2(III/III) Intermediate During Fatty Acid Decarboxylation By Unda. J.Am.Chem.Soc. V. 141 14510 2019.
ISSN: ESSN 1520-5126
PubMed: 31487162
DOI: 10.1021/JACS.9B06093