Iron in PDB 2uw1: Ivy Desaturase Structure

All present enzymatic activity of Ivy Desaturase Structure:
1.14.99.6;

The structure of Ivy Desaturase Structure, PDB code: 2uw1 was solved by J.E.Guy, E.Whittle, D.Kumaran, Y.Lindqvist, J.Shanklin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.122, 61.863, 201.002, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.9

The structure of Ivy Desaturase Structure also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Iron atom in the Ivy Desaturase Structure (pdb code 2uw1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ivy Desaturase Structure, PDB code: 2uw1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ivy Desaturase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ivy Desaturase Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1359 b:27.2 occ:1.00 O A:HOH2173 1.9 19.9 1.0 OE1 A:GLU138 2.1 22.9 1.0 OE1 A:GLU100 2.2 24.0 1.0 O1A A:GVM1362 2.3 22.0 1.0 ND1 A:HIS141 2.3 23.6 1.0 OE2 A:GLU100 2.3 24.9 1.0 CD A:GLU100 2.6 23.8 1.0 CD A:GLU138 3.1 24.4 1.0 CE1 A:HIS141 3.1 22.5 1.0 C1 A:GVM1362 3.1 22.0 1.0 FE A:FE1360 3.3 28.8 1.0 O1B A:GVM1362 3.3 19.9 1.0 OE2 A:GLU138 3.4 24.1 1.0 CG A:HIS141 3.4 21.9 1.0 OE2 A:GLU224 3.8 31.2 1.0 CB A:HIS141 3.8 22.7 1.0 O A:HOH2067 4.0 20.7 1.0 CG A:GLU100 4.1 24.2 1.0 O A:HOH2287 4.2 27.5 1.0 NE2 A:HIS141 4.3 22.1 1.0 O A:HOH2177 4.3 14.2 1.0 CG A:GLU138 4.4 23.6 1.0 CD2 A:HIS141 4.5 21.6 1.0 C2 A:GVM1362 4.5 22.7 1.0 CD A:GLU224 4.7 28.4 1.0 O A:GLU138 4.7 22.8 1.0 CB A:GLU138 4.7 23.1 1.0 CG2 A:ILE220 4.8 23.6 1.0 CG A:GLU224 4.8 25.8 1.0 CA A:GLU138 4.8 23.1 1.0 CB A:GLU100 4.8 23.4 1.0

Iron binding site 2 out of 4 in the Ivy Desaturase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ivy Desaturase Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1360 b:28.8 occ:1.00 O A:HOH2177 1.9 14.2 1.0 O A:HOH2173 2.0 19.9 1.0 O1B A:GVM1362 2.0 19.9 1.0 OE2 A:GLU138 2.0 24.1 1.0 OE1 A:GLU191 2.2 27.7 1.0 OE2 A:GLU191 2.3 26.2 1.0 CD A:GLU191 2.6 27.0 1.0 CD A:GLU138 2.9 24.4 1.0 C1 A:GVM1362 3.1 22.0 1.0 OE1 A:GLU138 3.2 22.9 1.0 FE A:FE1359 3.3 27.2 1.0 O1A A:GVM1362 3.5 22.0 1.0 CG A:GLU224 3.6 25.8 1.0 ND1 A:HIS227 3.7 24.6 1.0 CE1 A:HIS141 4.1 22.5 1.0 CG A:GLU191 4.1 25.2 1.0 OE2 A:GLU224 4.2 31.2 1.0 CG A:GLU138 4.2 23.6 1.0 NE1 A:TRP134 4.3 23.4 1.0 C2 A:GVM1362 4.4 22.7 1.0 ND1 A:HIS141 4.4 23.6 1.0 CG2 A:THR194 4.4 25.3 0.5 CZ2 A:TRP134 4.5 24.3 1.0 CD A:GLU224 4.5 28.4 1.0 OG1 A:THR194 4.5 25.0 0.5 CE1 A:HIS227 4.6 24.7 1.0 CB A:GLU224 4.6 23.4 1.0 C3 A:GVM1362 4.7 23.8 1.0 CE2 A:TRP134 4.7 24.2 1.0 CG A:HIS227 4.7 23.3 1.0 CA A:GLU224 4.7 23.6 1.0 O3 A:GVM1362 4.8 27.2 1.0 CB A:HIS227 4.9 23.1 1.0 CB A:GLU191 4.9 23.3 1.0

Iron binding site 3 out of 4 in the Ivy Desaturase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ivy Desaturase Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1359 b:28.1 occ:1.00 O B:HOH2179 1.9 20.3 1.0 OE1 B:GLU138 2.1 23.3 1.0 O1A B:GVM1362 2.2 22.4 1.0 OE1 B:GLU100 2.2 24.8 1.0 ND1 B:HIS141 2.3 21.4 1.0 OE2 B:GLU100 2.3 25.4 1.0 CD B:GLU100 2.6 24.6 1.0 CD B:GLU138 3.1 21.4 1.0 CE1 B:HIS141 3.1 23.0 1.0 C1 B:GVM1362 3.1 23.4 1.0 FE B:FE1360 3.2 28.6 1.0 OE2 B:GLU138 3.4 22.4 1.0 O1B B:GVM1362 3.4 22.7 1.0 CG B:HIS141 3.4 22.2 1.0 CB B:HIS141 3.8 23.0 1.0 OE2 B:GLU224 3.8 29.4 1.0 CG B:GLU100 4.1 23.8 1.0 O B:HOH2083 4.1 15.2 1.0 O B:HOH2259 4.2 35.2 1.0 NE2 B:HIS141 4.3 21.3 1.0 CG B:GLU138 4.4 22.3 1.0 CD2 B:HIS141 4.4 21.8 1.0 O B:HOH2183 4.5 19.6 1.0 C2 B:GVM1362 4.5 24.1 1.0 CG2 B:ILE220 4.6 23.4 1.0 CD B:GLU224 4.7 27.1 1.0 O B:GLU138 4.8 22.8 1.0 CB B:GLU138 4.8 22.2 1.0 CG B:GLU224 4.8 25.5 1.0 CA B:GLU138 4.8 22.3 1.0 CB B:GLU100 4.9 23.1 1.0

Iron binding site 4 out of 4 in the Ivy Desaturase Structure


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ivy Desaturase Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1360 b:28.6 occ:1.00 O B:HOH2183 1.9 19.6 1.0 O B:HOH2179 2.0 20.3 1.0 OE2 B:GLU138 2.0 22.4 1.0 O1B B:GVM1362 2.1 22.7 1.0 OE1 B:GLU191 2.3 25.9 1.0 OE2 B:GLU191 2.4 26.0 1.0 CD B:GLU191 2.6 25.9 1.0 CD B:GLU138 3.0 21.4 1.0 C1 B:GVM1362 3.1 23.4 1.0 FE B:FE1359 3.2 28.1 1.0 OE1 B:GLU138 3.3 23.3 1.0 O1A B:GVM1362 3.4 22.4 1.0 CG B:GLU224 3.6 25.5 1.0 ND1 B:HIS227 3.8 23.8 1.0 CE1 B:HIS141 4.1 23.0 1.0 CG B:GLU191 4.2 25.3 1.0 OE2 B:GLU224 4.2 29.4 1.0 NE1 B:TRP134 4.3 23.2 1.0 CG B:GLU138 4.3 22.3 1.0 ND1 B:HIS141 4.4 21.4 1.0 CZ2 B:TRP134 4.4 23.5 1.0 CG2 B:THR194 4.4 26.2 0.5 C2 B:GVM1362 4.4 24.1 1.0 CD B:GLU224 4.5 27.1 1.0 OG1 B:THR194 4.5 26.0 0.5 CE2 B:TRP134 4.6 23.5 1.0 CE1 B:HIS227 4.6 24.5 1.0 CB B:GLU224 4.7 23.8 1.0 C3 B:GVM1362 4.7 25.3 1.0 CA B:GLU224 4.7 23.9 1.0 CG B:HIS227 4.8 23.5 1.0 O3 B:GVM1362 4.8 28.1 1.0 CB B:HIS227 4.9 23.3 1.0

J.E.Guy, E.Whittle, D.Kumaran, Y.Lindqvist, J.Shanklin. The Crystal Structure of the Ivy {Delta}4-16:0-Acp Desaturase Reveals Structural Details of the Oxidized Active Site and Potential Determinants of Regioselectivity. J.Biol.Chem. V. 282 19863 2007.
ISSN: ISSN 0021-9258
PubMed: 17463003
DOI: 10.1074/JBC.M702520200