Iron in PDB 8sm7: Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe

The structure of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm7 was solved by C.Liu, J.Rittle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.78 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	127.369, 127.369, 217.84, 90, 90, 90
R / Rfree (%)	19.9 / 24.2

The structure of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Iron atom in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe (pdb code 8sm7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe, PDB code: 8sm7:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:45.7 occ:0.55 NE2 A:HIS12 1.9 51.2 1.0 OE1 A:GLU242 2.0 46.2 1.0 OD2 A:ASP10 2.1 49.6 1.0 NE2 A:HIS185 2.2 47.4 1.0 OD1 A:ASP315 2.4 56.5 1.0 CE1 A:HIS12 2.7 46.5 1.0 CG A:ASP10 2.9 44.8 1.0 OD1 A:ASP10 3.0 44.9 1.0 CD2 A:HIS12 3.0 51.0 1.0 CE1 A:HIS185 3.1 46.1 1.0 CD A:GLU242 3.2 49.3 1.0 CD2 A:HIS185 3.3 40.2 1.0 CG A:ASP315 3.4 57.9 1.0 ND1 A:HIS12 3.8 47.4 1.0 OE2 A:GLU242 3.9 52.1 1.0 FE A:FE402 3.9 57.7 0.6 CG A:HIS12 4.0 50.7 1.0 OD2 A:ASP315 4.1 59.5 1.0 CB A:GLU242 4.3 39.9 1.0 ND1 A:HIS185 4.3 45.4 1.0 CB A:ASP10 4.3 43.3 1.0 CG A:GLU242 4.3 49.6 1.0 CG A:HIS185 4.4 41.3 1.0 CB A:ASP315 4.4 56.1 1.0 CG1 A:VAL241 4.6 40.0 1.0 CA A:ASP315 4.8 57.5 1.0 NE2 A:GLN286 4.9 53.4 1.0 OH A:TYR90 4.9 44.0 1.0 O A:ASP10 5.0 49.8 1.0

Iron binding site 2 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:57.7 occ:0.55 OE2 A:GLU242 2.1 52.1 1.0 ND1 A:HIS318 2.2 71.7 1.0 O A:HOH540 2.4 65.1 1.0 OD2 A:ASP315 2.4 59.5 1.0 CE1 A:HIS318 2.7 68.1 1.0 CD A:GLU242 3.0 49.3 1.0 CG A:HIS318 3.2 68.8 1.0 CG A:ASP315 3.2 57.9 1.0 OE1 A:GLU242 3.2 46.2 1.0 OD1 A:ASP315 3.3 56.5 1.0 NE2 A:HIS318 3.8 67.2 1.0 CB A:HIS318 3.8 67.7 1.0 FE A:FE401 3.9 45.7 0.6 CD2 A:HIS318 4.1 68.2 1.0 NE2 A:HIS12 4.2 51.2 1.0 O A:HOH535 4.2 48.9 1.0 OD1 A:ASP320 4.3 64.2 1.0 CD2 A:HIS12 4.4 51.0 1.0 CG A:GLU242 4.4 49.6 1.0 CB A:ASP315 4.7 56.1 1.0 CE1 A:HIS185 4.8 46.1 1.0 OE1 A:GLN286 4.9 61.2 1.0

Iron binding site 3 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:47.2 occ:0.61 OE1 B:GLU242 2.0 46.6 1.0 NE2 B:HIS12 2.0 49.1 1.0 OD2 B:ASP10 2.0 45.1 1.0 NE2 B:HIS185 2.2 46.6 1.0 OD1 B:ASP315 2.3 55.2 1.0 O B:HOH517 2.7 55.1 1.0 CE1 B:HIS12 2.8 48.1 1.0 CG B:ASP10 2.9 44.0 1.0 CE1 B:HIS185 3.0 47.3 1.0 OD1 B:ASP10 3.1 44.8 1.0 CD2 B:HIS12 3.1 49.9 1.0 CD B:GLU242 3.2 49.9 1.0 CD2 B:HIS185 3.2 44.0 1.0 CG B:ASP315 3.3 54.8 1.0 OE2 B:GLU242 3.8 52.6 1.0 OD2 B:ASP315 3.9 55.8 1.0 ND1 B:HIS12 4.0 49.2 1.0 CG B:HIS12 4.1 49.5 1.0 ND1 B:HIS185 4.2 45.4 1.0 FE B:FE402 4.2 64.5 0.6 CB B:GLU242 4.2 43.5 1.0 CB B:ASP10 4.3 42.0 1.0 CG B:GLU242 4.3 44.8 1.0 CG B:HIS185 4.3 42.8 1.0 CB B:ASP315 4.4 55.7 1.0 O B:HOH513 4.4 44.8 1.0 CG1 B:VAL241 4.5 40.6 1.0 ND1 B:HIS318 4.7 60.1 1.0 CA B:ASP315 4.8 54.4 1.0 CE1 B:HIS318 4.9 61.4 1.0 OE1 B:GLN286 4.9 51.4 1.0

Iron binding site 4 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:64.5 occ:0.60 O B:HOH517 1.9 55.1 1.0 OE2 B:GLU242 2.1 52.6 1.0 O B:HOH599 2.3 59.0 1.0 ND1 B:HIS318 2.5 60.1 1.0 OD2 B:ASP315 2.5 55.8 1.0 CD B:GLU242 3.1 49.9 1.0 CE1 B:HIS318 3.3 61.4 1.0 CG B:HIS318 3.4 69.9 1.0 CG B:ASP315 3.4 54.8 1.0 OE1 B:GLU242 3.5 46.6 1.0 OD1 B:ASP315 3.6 55.2 1.0 CB B:HIS318 3.7 66.9 1.0 OD1 B:ASP320 4.0 65.3 1.0 FE B:FE401 4.2 47.2 0.6 O B:HOH520 4.2 53.7 1.0 NE2 B:HIS318 4.4 67.8 1.0 CG B:GLU242 4.5 44.8 1.0 CD2 B:HIS318 4.5 69.7 1.0 O B:HOH598 4.6 60.1 1.0 NE2 B:HIS12 4.6 49.1 1.0 NE2 B:GLN286 4.7 53.8 1.0 CD2 B:HIS12 4.8 49.9 1.0 CB B:ASP315 4.8 55.7 1.0 CE1 B:HIS185 4.8 47.3 1.0 CG B:ASP320 5.0 62.6 1.0

Iron binding site 5 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:44.0 occ:0.63 OD2 D:ASP10 1.9 46.3 1.0 O D:HOH501 1.9 53.4 1.0 NE2 D:HIS12 2.0 53.5 1.0 OD1 D:ASP315 2.1 55.7 1.0 NE2 D:HIS185 2.2 44.6 1.0 OE1 D:GLU242 2.3 51.0 1.0 CG D:ASP10 2.7 47.6 1.0 CE1 D:HIS12 2.8 48.8 1.0 OD1 D:ASP10 2.9 46.8 1.0 CD2 D:HIS12 3.1 51.3 1.0 CE1 D:HIS185 3.2 40.4 1.0 CD2 D:HIS185 3.2 38.8 1.0 CG D:ASP315 3.3 61.4 1.0 CD D:GLU242 3.4 49.2 1.0 OD2 D:ASP315 4.0 62.2 1.0 ND1 D:HIS12 4.0 51.7 1.0 OE2 D:GLU242 4.1 55.4 1.0 CB D:ASP10 4.1 41.5 1.0 CG D:HIS12 4.2 53.5 1.0 FE D:FE402 4.2 60.6 0.5 O D:HOH517 4.3 47.7 1.0 ND1 D:HIS185 4.3 40.1 1.0 CG D:HIS185 4.3 42.6 1.0 CG1 D:VAL241 4.3 39.1 1.0 CB D:ASP315 4.4 56.2 1.0 CB D:GLU242 4.4 45.0 1.0 CG D:GLU242 4.5 48.0 1.0 CA D:ASP315 4.7 52.7 1.0 O D:ASP10 4.8 48.2 1.0 ND1 D:HIS318 4.9 66.7 1.0 OG1 D:THR86 4.9 45.1 1.0 OH D:TYR90 4.9 47.5 1.0 CE1 D:HIS318 5.0 64.6 1.0 OE1 D:GLN286 5.0 52.6 1.0

Iron binding site 6 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe402 b:60.6 occ:0.48 OE2 D:GLU242 2.1 55.4 1.0 ND1 D:HIS318 2.2 66.7 1.0 OD2 D:ASP315 2.4 62.2 1.0 O D:HOH501 2.4 53.4 1.0 O D:HOH575 2.5 56.7 1.0 CE1 D:HIS318 3.0 64.6 1.0 CD D:GLU242 3.0 49.2 1.0 OE1 D:GLU242 3.3 51.0 1.0 CG D:ASP315 3.3 61.4 1.0 CG D:HIS318 3.4 67.3 1.0 OD1 D:ASP315 3.5 55.7 1.0 CB D:HIS318 3.9 68.0 1.0 NE2 D:HIS318 4.2 72.1 1.0 FE D:FE401 4.2 44.0 0.6 O D:HOH558 4.2 42.6 1.0 CD2 D:HIS318 4.4 69.5 1.0 CG D:GLU242 4.4 48.0 1.0 OD1 D:ASP320 4.5 68.2 1.0 NE2 D:HIS12 4.5 53.5 1.0 CB D:ASP315 4.7 56.2 1.0 CE1 D:HIS185 4.7 40.4 1.0 CD2 D:HIS12 4.8 51.3 1.0 NE2 D:HIS185 5.0 44.6 1.0

Iron binding site 7 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe401 b:43.7 occ:0.67 OD2 G:ASP10 1.9 42.4 1.0 NE2 G:HIS185 2.0 42.5 1.0 NE2 G:HIS12 2.1 48.9 1.0 OE1 G:GLU242 2.2 49.5 1.0 OD1 G:ASP315 2.2 60.3 1.0 CE1 G:HIS12 2.8 45.8 1.0 CG G:ASP10 2.8 43.8 1.0 CD2 G:HIS185 3.0 37.1 1.0 CE1 G:HIS185 3.0 43.6 1.0 OD1 G:ASP10 3.2 42.0 1.0 CD2 G:HIS12 3.2 49.4 1.0 CG G:ASP315 3.3 59.5 1.0 CD G:GLU242 3.4 52.3 1.0 OD2 G:ASP315 3.9 63.0 1.0 FE G:FE402 3.9 77.1 0.6 ND1 G:HIS12 4.0 43.8 1.0 ND1 G:HIS185 4.1 42.1 1.0 CG G:HIS185 4.1 40.8 1.0 OE2 G:GLU242 4.2 56.5 1.0 O G:HOH536 4.2 51.5 1.0 CB G:ASP10 4.2 40.4 1.0 CB G:GLU242 4.2 45.9 1.0 CG G:HIS12 4.2 45.1 1.0 CG1 G:VAL241 4.4 33.0 1.0 CG G:GLU242 4.4 51.8 1.0 CB G:ASP315 4.4 59.9 1.0 OH G:TYR90 4.7 46.9 1.0 CA G:ASP315 4.8 53.4 1.0 OG1 G:THR86 5.0 42.5 1.0

Iron binding site 8 out of 8 in the Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Air-Oxidized G. Y4 Truffo Expressed From M9 Minimal Medium Supplemented with Fe within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe402 b:77.1 occ:0.63 ND1 G:HIS318 2.1 66.7 1.0 OD2 G:ASP315 2.2 63.0 1.0 OE2 G:GLU242 2.4 56.5 1.0 O G:HOH600 2.6 58.1 1.0 CE1 G:HIS318 2.8 66.2 1.0 CD G:GLU242 3.1 52.3 1.0 OE1 G:GLU242 3.1 49.5 1.0 CG G:ASP315 3.1 59.5 1.0 OD1 G:ASP315 3.3 60.3 1.0 CG G:HIS318 3.4 70.9 1.0 FE G:FE401 3.9 43.7 0.7 CB G:HIS318 3.9 69.8 1.0 NE2 G:HIS318 4.0 70.0 1.0 NE2 G:HIS12 4.2 48.9 1.0 CD2 G:HIS318 4.3 71.3 1.0 O G:HOH635 4.3 56.3 1.0 CD2 G:HIS12 4.5 49.4 1.0 CG G:GLU242 4.5 51.8 1.0 OD1 G:ASP320 4.5 69.8 1.0 CB G:ASP315 4.6 59.9 1.0 CE1 G:HIS185 4.6 43.6 1.0 NE2 G:HIS185 4.7 42.5 1.0

C.Liu, M.M.Powell, G.Rao, R.D.Britt, J.Rittle. Bioinformatic Discovery of A Cambialistic Monooxygenase. J.Am.Chem.Soc. V. 146 1783 2024.
ISSN: ESSN 1520-5126
PubMed: 38198693
DOI: 10.1021/JACS.3C12131