Iron in PDB 3pf7: Crystal Structure of Boxb with Malonate Bound to the Diiron Center

All present enzymatic activity of Crystal Structure of Boxb with Malonate Bound to the Diiron Center:
1.14.12.21;

The structure of Crystal Structure of Boxb with Malonate Bound to the Diiron Center, PDB code: 3pf7 was solved by T.Weinert, L.J.Rather, G.Fuchs, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.86 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	112.790, 213.490, 137.190, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.7

The structure of Crystal Structure of Boxb with Malonate Bound to the Diiron Center also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Crystal Structure of Boxb with Malonate Bound to the Diiron Center (pdb code 3pf7). 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 Boxb with Malonate Bound to the Diiron Center, PDB code: 3pf7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Boxb with Malonate Bound to the Diiron Center


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 Boxb with Malonate Bound to the Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1001 b:19.6 occ:1.00 O A:OH1003 2.0 17.0 1.0 OE1 A:GLU120 2.0 18.5 1.0 OE2 A:GLU150 2.0 20.9 1.0 O A:HOH975 2.2 18.6 1.0 O1A A:MLA1004 2.2 23.3 1.0 ND1 A:HIS153 2.2 23.1 1.0 CD A:GLU150 3.0 21.9 1.0 CD A:GLU120 3.0 21.1 1.0 CE1 A:HIS153 3.1 18.9 1.0 HE1 A:HIS153 3.1 22.7 1.0 C1 A:MLA1004 3.2 25.8 1.0 CG A:HIS153 3.3 19.3 1.0 OE1 A:GLU150 3.4 19.2 1.0 OE2 A:GLU120 3.4 23.9 1.0 FE A:FE1002 3.4 20.0 1.0 O1B A:MLA1004 3.5 23.9 1.0 HB2 A:HIS153 3.6 19.0 1.0 HB3 A:HIS153 3.7 19.0 1.0 HA A:GLU150 3.7 22.7 1.0 HE1 A:HIS243 3.7 21.5 1.0 CB A:HIS153 3.8 15.8 1.0 O3B A:MLA1004 4.0 29.3 1.0 OE2 A:GLU240 4.1 34.5 1.0 HA A:GLU120 4.2 25.4 1.0 NE2 A:HIS153 4.2 19.4 1.0 HB3 A:GLU120 4.3 28.9 1.0 CG A:GLU150 4.4 13.4 1.0 CG A:GLU120 4.4 19.5 1.0 CD2 A:HIS153 4.4 20.0 1.0 HB3 A:GLU150 4.4 20.3 1.0 C2 A:MLA1004 4.4 33.2 1.0 HE3 A:MET236 4.4 12.4 1.0 CE1 A:HIS243 4.5 17.9 1.0 OE1 A:GLU240 4.5 29.7 1.0 HD11 A:LEU218 4.5 22.0 1.0 CA A:GLU150 4.5 18.9 1.0 HE2 A:MET236 4.6 12.4 1.0 CD A:GLU240 4.6 33.7 1.0 HE22 A:GLN116 4.6 28.1 1.0 CB A:GLU150 4.7 16.9 1.0 ND1 A:HIS243 4.7 17.0 1.0 CB A:GLU120 4.7 24.1 1.0 C3 A:MLA1004 4.7 31.3 1.0 HC21 A:MLA1004 4.8 39.8 1.0 HG3 A:GLU120 4.8 23.4 1.0 HG2 A:GLU150 4.9 16.0 1.0 HE21 A:GLN116 4.9 28.1 1.0 CE A:MET236 4.9 10.3 1.0 CA A:GLU120 4.9 21.2 1.0 HG3 A:GLU150 5.0 16.0 1.0 HE2 A:HIS153 5.0 23.3 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Boxb with Malonate Bound to the Diiron Center


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 Boxb with Malonate Bound to the Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:20.0 occ:1.00 O A:OH1003 2.0 17.0 1.0 O1B A:MLA1004 2.1 23.9 1.0 OD2 A:ASP211 2.1 21.6 1.0 OE1 A:GLU150 2.1 19.2 1.0 OE1 A:GLU240 2.1 29.7 1.0 ND1 A:HIS243 2.2 17.0 1.0 CE1 A:HIS243 3.0 17.9 1.0 HE1 A:HIS243 3.0 21.5 1.0 C1 A:MLA1004 3.0 25.8 1.0 CG A:ASP211 3.1 21.1 1.0 CD A:GLU150 3.1 21.9 1.0 CD A:GLU240 3.2 33.7 1.0 HB3 A:ASP211 3.2 19.6 1.0 O1A A:MLA1004 3.3 23.3 1.0 CG A:HIS243 3.3 21.4 1.0 FE A:FE1001 3.4 19.6 1.0 OE2 A:GLU150 3.4 20.9 1.0 OE2 A:GLU240 3.5 34.5 1.0 CB A:ASP211 3.7 16.3 1.0 HB2 A:HIS243 3.7 26.1 1.0 HB3 A:HIS243 3.7 26.1 1.0 CB A:HIS243 3.8 21.8 1.0 HA A:GLU240 3.9 22.6 1.0 HA A:ASP211 4.0 22.6 1.0 OD1 A:ASP211 4.0 23.6 1.0 O A:HOH515 4.1 20.6 1.0 NE2 A:HIS243 4.2 18.1 1.0 HE1 A:HIS153 4.2 22.7 1.0 CD2 A:HIS243 4.4 17.2 1.0 CG A:GLU150 4.4 13.4 1.0 C2 A:MLA1004 4.4 33.2 1.0 CA A:ASP211 4.4 18.9 1.0 HB2 A:ASP211 4.5 19.6 1.0 HC22 A:MLA1004 4.5 39.8 1.0 CG A:GLU240 4.5 26.4 1.0 HG2 A:GLU150 4.6 16.0 1.0 O A:HOH975 4.6 18.6 1.0 HG3 A:GLU150 4.6 16.0 1.0 HG3 A:GLU240 4.6 31.6 1.0 HG13 A:VAL146 4.7 19.0 1.0 CA A:GLU240 4.8 18.9 1.0 CE1 A:HIS153 4.8 18.9 1.0 ND1 A:HIS153 4.9 23.1 1.0 HE2 A:HIS243 4.9 21.6 1.0 O A:ASP211 4.9 17.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Boxb with Malonate Bound to the Diiron Center


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 Boxb with Malonate Bound to the Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1001 b:21.2 occ:1.00 O B:OH1003 2.0 18.2 1.0 OE1 B:GLU120 2.0 23.3 1.0 OE2 B:GLU150 2.1 21.9 1.0 O3A B:MLA1004 2.1 26.1 1.0 O B:HOH882 2.2 20.2 1.0 ND1 B:HIS153 2.3 23.9 1.0 CD B:GLU120 3.0 25.7 1.0 CD B:GLU150 3.1 27.4 1.0 CE1 B:HIS153 3.1 22.1 1.0 HE1 B:HIS153 3.2 26.5 1.0 C3 B:MLA1004 3.2 31.3 1.0 OE2 B:GLU120 3.2 29.6 1.0 CG B:HIS153 3.4 16.5 1.0 OE1 B:GLU150 3.4 24.3 1.0 FE B:FE1002 3.5 24.3 1.0 HB2 B:HIS153 3.6 21.4 1.0 O3B B:MLA1004 3.6 31.6 1.0 HB3 B:HIS153 3.7 21.4 1.0 HA B:GLU150 3.7 28.0 1.0 CB B:HIS153 3.8 17.8 1.0 HE1 B:HIS243 3.8 37.9 1.0 OE2 B:GLU240 4.0 42.6 1.0 O1B B:MLA1004 4.0 31.1 1.0 HA B:GLU120 4.2 24.8 1.0 NE2 B:HIS153 4.3 22.9 1.0 HE3 B:MET236 4.4 21.0 1.0 CG B:GLU120 4.4 23.6 1.0 HB3 B:GLU120 4.4 25.7 1.0 C2 B:MLA1004 4.4 31.4 1.0 HB3 B:GLU150 4.4 27.5 1.0 CG B:GLU150 4.4 18.0 1.0 CD2 B:HIS153 4.4 19.4 1.0 HE2 B:MET236 4.5 21.0 1.0 CE1 B:HIS243 4.5 31.6 1.0 HD11 B:LEU218 4.5 24.4 1.0 HE22 B:GLN116 4.6 29.7 1.0 CA B:GLU150 4.6 23.3 1.0 OE1 B:GLU240 4.6 29.4 1.0 CD B:GLU240 4.7 39.8 1.0 HC22 B:MLA1004 4.7 37.6 1.0 CB B:GLU150 4.7 22.9 1.0 C1 B:MLA1004 4.7 35.1 1.0 ND1 B:HIS243 4.7 18.3 1.0 CB B:GLU120 4.8 21.4 1.0 CE B:MET236 4.8 17.5 1.0 HG3 B:GLU120 4.8 28.4 1.0 HE1 B:MET236 4.8 21.0 1.0 CA B:GLU120 4.9 20.7 1.0 HE21 B:GLN116 4.9 29.7 1.0 HG2 B:GLU150 4.9 21.6 1.0 HG2 B:GLU120 5.0 28.4 1.0 HG3 B:GLU150 5.0 21.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Boxb with Malonate Bound to the Diiron Center


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 Boxb with Malonate Bound to the Diiron Center within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1002 b:24.3 occ:1.00 OD2 B:ASP211 2.0 29.1 1.0 OE1 B:GLU150 2.1 24.3 1.0 O B:OH1003 2.1 18.2 1.0 ND1 B:HIS243 2.1 18.3 1.0 O3B B:MLA1004 2.2 31.6 1.0 OE1 B:GLU240 2.2 29.4 1.0 CE1 B:HIS243 2.9 31.6 1.0 HE1 B:HIS243 3.0 37.9 1.0 CD B:GLU240 3.0 39.8 1.0 CG B:ASP211 3.0 29.1 1.0 C3 B:MLA1004 3.0 31.3 1.0 CD B:GLU150 3.1 27.4 1.0 O3A B:MLA1004 3.2 26.1 1.0 OE2 B:GLU240 3.2 42.6 1.0 CG B:HIS243 3.3 23.1 1.0 HB3 B:ASP211 3.3 26.0 1.0 OE2 B:GLU150 3.4 21.9 1.0 FE B:FE1001 3.5 21.2 1.0 HB3 B:HIS243 3.6 26.0 1.0 HB2 B:HIS243 3.6 26.0 1.0 CB B:ASP211 3.7 21.7 1.0 CB B:HIS243 3.7 21.7 1.0 HA B:GLU240 3.9 25.1 1.0 OD1 B:ASP211 3.9 22.4 1.0 HA B:ASP211 4.0 28.9 1.0 NE2 B:HIS243 4.1 30.0 1.0 O B:HOH876 4.2 22.6 1.0 HE1 B:HIS153 4.2 26.5 1.0 CD2 B:HIS243 4.3 24.2 1.0 CG B:GLU150 4.4 18.0 1.0 C2 B:MLA1004 4.4 31.4 1.0 CG B:GLU240 4.4 30.0 1.0 CA B:ASP211 4.4 24.1 1.0 HG13 B:VAL146 4.4 18.7 1.0 HB2 B:ASP211 4.5 26.0 1.0 HC21 B:MLA1004 4.6 37.6 1.0 HG2 B:GLU150 4.6 21.6 1.0 HG3 B:GLU150 4.7 21.6 1.0 HG3 B:GLU240 4.7 36.0 1.0 O B:HOH882 4.7 20.2 1.0 CE1 B:HIS153 4.8 22.1 1.0 CA B:GLU240 4.8 20.9 1.0 ND1 B:HIS153 4.8 23.9 1.0 HE2 B:HIS243 4.9 36.0 1.0 O B:ASP211 5.0 20.8 1.0

L.J.Rather, T.Weinert, U.Demmer, E.Bill, W.Ismail, G.Fuchs, U.Ermler. Structure and Mechanism of the Diiron Benzoyl-Coenzyme A Epoxidase Boxb. J.Biol.Chem. V. 286 29241 2011.
ISSN: ISSN 0021-9258
PubMed: 21632537
DOI: 10.1074/JBC.M111.236893