Iron in PDB 7ppt: Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose

The structure of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose, PDB code: 7ppt was solved by F.Lennartz, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.55 / 1.42
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	72.032, 72.032, 98.044, 90, 90, 120
R / Rfree (%)	18.5 / 20.8

The structure of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose (pdb code 7ppt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose, PDB code: 7ppt:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:17.6 occ:0.80 O B:OH401 1.8 15.9 1.0 OE2 A:GLU92 1.9 19.3 1.0 O A:HOH331 2.2 24.0 1.0 OE2 A:GLU126 2.2 14.4 1.0 OE1 A:GLU95 2.3 19.3 1.0 OE2 B:GLU53 2.3 14.9 1.0 HO B:OH401 2.4 19.0 1.0 CD A:GLU92 2.7 18.3 1.0 OE1 A:GLU92 2.8 18.2 1.0 CD A:GLU126 2.9 19.1 1.0 CD B:GLU53 3.2 14.7 1.0 HD1 A:HIS129 3.3 15.3 1.0 CD A:GLU95 3.3 18.9 1.0 FE B:FE404 3.4 16.0 1.0 OE1 B:GLU53 3.4 13.9 1.0 OE1 A:GLU126 3.4 17.9 1.0 HH B:TYR27 3.5 18.6 1.0 OE2 A:GLU95 3.6 19.0 1.0 HG3 A:GLU126 4.0 17.3 1.0 CG A:GLU126 4.0 14.4 1.0 HA A:GLU92 4.0 20.5 1.0 HE2 B:TYR27 4.1 16.6 1.0 HB3 A:GLU126 4.1 16.7 1.0 ND1 A:HIS129 4.1 12.7 1.0 CG A:GLU92 4.1 17.4 1.0 OH B:TYR27 4.3 15.5 1.0 HB1 B:ALA23 4.3 14.9 1.0 HA A:GLU126 4.4 14.4 1.0 HB2 B:ALA23 4.4 14.9 1.0 HG2 A:GLU92 4.4 20.8 1.0 OE2 B:GLU20 4.5 13.1 1.0 HG3 B:GLU53 4.5 16.7 1.0 CG B:GLU53 4.5 13.9 1.0 CB A:GLU126 4.5 13.9 1.0 HB2 A:GLU95 4.6 21.7 1.0 CG A:GLU95 4.6 18.4 1.0 OE1 B:GLU20 4.7 13.9 1.0 HG3 A:GLU92 4.7 20.8 1.0 CB B:ALA23 4.7 12.4 1.0 HB3 A:GLU92 4.7 20.2 1.0 HB2 A:HIS129 4.8 14.2 1.0 HB3 B:ALA23 4.8 14.9 1.0 HE1 A:HIS129 4.8 17.5 1.0 CB A:GLU92 4.8 16.8 1.0 HG2 A:GLU126 4.8 17.3 1.0 CA A:GLU92 4.8 17.1 1.0 CE2 B:TYR27 4.8 13.8 1.0 HE2 A:TYR100 4.9 20.6 1.0 CE1 A:HIS129 4.9 14.6 1.0 CD B:GLU20 4.9 13.3 1.0 HB3 A:GLU95 4.9 21.7 1.0 CB A:GLU95 5.0 18.1 1.0

Iron binding site 2 out of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:17.3 occ:1.00 OE1 B:GLU126 2.0 25.4 1.0 OE1 A:GLU53 2.1 15.5 1.0 O A:OH204 2.1 15.4 1.0 OE2 A:GLU20 2.1 14.0 1.0 OE1 A:GLU20 2.2 14.9 1.0 ND1 A:HIS56 2.2 13.8 1.0 CD A:GLU20 2.5 14.2 1.0 HO A:OH204 2.9 18.5 1.0 CD B:GLU126 2.9 22.8 1.0 CD A:GLU53 3.0 16.1 1.0 CE1 A:HIS56 3.0 14.2 1.0 HE1 A:HIS56 3.1 17.1 1.0 OE2 B:GLU126 3.2 23.8 1.0 CG A:HIS56 3.3 13.5 1.0 HA A:GLU53 3.3 17.9 1.0 FE B:FE403 3.4 20.4 0.9 HB2 A:HIS56 3.4 15.6 1.0 OE2 A:GLU53 3.5 17.0 1.0 HB3 A:HIS56 3.6 15.6 1.0 CB A:HIS56 3.7 13.0 1.0 HH B:TYR100 3.8 20.0 1.0 HE2 B:TYR100 3.9 20.0 1.0 CG A:GLU20 4.0 14.4 1.0 HE1 B:HIS129 4.1 20.5 1.0 HB3 A:GLU53 4.1 17.8 1.0 CA A:GLU53 4.2 14.9 1.0 NE2 A:HIS56 4.2 14.3 1.0 CG A:GLU53 4.2 15.2 1.0 CG B:GLU126 4.3 14.4 1.0 CD2 A:HIS56 4.3 13.8 1.0 HG B:LEU122 4.4 17.1 1.0 HG3 A:GLU20 4.4 17.4 1.0 HD1 B:HIS129 4.4 20.7 1.0 CB A:GLU53 4.4 14.8 1.0 HG2 A:GLU20 4.4 17.4 1.0 HG3 B:GLU126 4.4 17.3 1.0 HG2 B:GLU126 4.5 17.3 1.0 OE1 B:GLU95 4.5 20.6 1.0 HA A:GLU20 4.5 16.9 1.0 HB3 A:GLU20 4.6 16.9 1.0 OH B:TYR100 4.6 16.7 1.0 CE2 B:TYR100 4.7 16.7 1.0 CE1 B:HIS129 4.8 17.1 1.0 HG2 A:GLU53 4.8 18.3 1.0 CB A:GLU20 4.8 14.1 1.0 HD23 B:LEU122 4.8 20.6 1.0 HG3 A:GLU53 4.8 18.3 1.0 N A:GLU53 4.9 14.6 1.0 O A:GLY52 4.9 14.1 1.0 ND1 B:HIS129 4.9 17.3 1.0 O B:HOH503 4.9 37.3 1.0 HE2 A:HIS56 5.0 17.1 1.0

Iron binding site 3 out of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:20.4 occ:0.90 HO A:OH204 1.0 18.5 1.0 O A:OH204 1.9 15.4 1.0 OE1 B:GLU92 1.9 21.4 1.0 OE2 B:GLU126 2.1 23.8 1.0 O B:HOH503 2.2 37.3 1.0 OE2 A:GLU53 2.2 17.0 1.0 OE1 B:GLU95 2.2 20.6 1.0 CD B:GLU92 2.8 20.8 1.0 CD B:GLU126 2.9 22.8 1.0 OE2 B:GLU92 3.1 21.1 1.0 CD A:GLU53 3.1 16.1 1.0 CD B:GLU95 3.2 21.2 1.0 HD1 B:HIS129 3.3 20.7 1.0 FE A:FE203 3.4 17.3 1.0 OE1 A:GLU53 3.4 15.5 1.0 OE1 B:GLU126 3.4 25.4 1.0 HH A:TYR27 3.4 21.2 1.0 OE2 B:GLU95 3.5 21.9 1.0 HA B:GLU92 3.8 23.3 1.0 HG3 B:GLU126 4.0 17.3 1.0 CG B:GLU126 4.0 14.4 1.0 HB3 B:GLU126 4.0 19.2 1.0 ND1 B:HIS129 4.1 17.3 1.0 HE2 A:TYR27 4.2 19.2 1.0 CG B:GLU92 4.2 19.6 1.0 HB1 A:ALA23 4.2 17.1 1.0 OH A:TYR27 4.2 17.7 1.0 HA B:GLU126 4.4 17.9 1.0 HB2 A:ALA23 4.4 17.1 1.0 CB B:GLU126 4.5 16.0 1.0 CG A:GLU53 4.5 15.2 1.0 HG3 A:GLU53 4.5 18.3 1.0 HB2 B:GLU95 4.5 24.4 1.0 HG2 B:GLU92 4.5 23.6 1.0 OE2 A:GLU20 4.5 14.0 1.0 CG B:GLU95 4.6 21.0 1.0 CA B:GLU92 4.6 19.4 1.0 OE1 A:GLU20 4.6 14.9 1.0 HB3 B:GLU92 4.7 23.2 1.0 CB A:ALA23 4.7 14.2 1.0 CB B:GLU92 4.7 19.4 1.0 HE1 B:HIS129 4.8 20.5 1.0 HB3 A:ALA23 4.8 17.1 1.0 HG2 B:GLU126 4.8 17.3 1.0 HG3 B:GLU92 4.8 23.6 1.0 HB2 B:HIS129 4.9 21.1 1.0 HB3 B:GLU95 4.9 24.4 1.0 CE1 B:HIS129 4.9 17.1 1.0 CB B:GLU95 4.9 20.4 1.0 CE2 A:TYR27 4.9 16.0 1.0 CD A:GLU20 4.9 14.2 1.0 HE2 B:TYR100 5.0 20.0 1.0 CA B:GLU126 5.0 14.9 1.0

Iron binding site 4 out of 4 in the Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Dife-Sulerythrin at 0.26 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:16.0 occ:1.00 OE1 A:GLU126 2.0 17.9 1.0 OE1 B:GLU53 2.1 13.9 1.0 O B:OH401 2.1 15.9 1.0 OE2 B:GLU20 2.1 13.1 1.0 OE1 B:GLU20 2.2 13.9 1.0 ND1 B:HIS56 2.2 11.8 1.0 CD B:GLU20 2.5 13.3 1.0 HO B:OH401 2.5 19.0 1.0 CD A:GLU126 3.0 19.1 1.0 CD B:GLU53 3.0 14.7 1.0 CE1 B:HIS56 3.1 11.9 1.0 HE1 B:HIS56 3.2 14.3 1.0 OE2 A:GLU126 3.3 14.4 1.0 CG B:HIS56 3.3 12.3 1.0 FE A:FE202 3.4 17.6 0.8 HA B:GLU53 3.4 16.8 1.0 HB2 B:HIS56 3.4 14.6 1.0 OE2 B:GLU53 3.5 14.9 1.0 HB3 B:HIS56 3.6 14.6 1.0 CB B:HIS56 3.7 12.2 1.0 HH A:TYR100 3.8 20.6 1.0 HE2 A:TYR100 3.9 20.6 1.0 CG B:GLU20 4.0 14.0 1.0 HE1 A:HIS129 4.0 17.5 1.0 HB3 B:GLU53 4.2 16.6 1.0 HD1 A:HIS129 4.2 15.3 1.0 CA B:GLU53 4.2 14.0 1.0 CG B:GLU53 4.3 13.9 1.0 CG A:GLU126 4.3 14.4 1.0 NE2 B:HIS56 4.3 12.2 1.0 HG A:LEU122 4.4 14.7 1.0 HG3 B:GLU20 4.4 16.8 1.0 CD2 B:HIS56 4.4 12.5 1.0 HG2 B:GLU20 4.4 16.8 1.0 HG3 A:GLU126 4.4 17.3 1.0 CB B:GLU53 4.4 13.8 1.0 HG2 A:GLU126 4.5 17.3 1.0 HA B:GLU20 4.5 16.6 1.0 OE1 A:GLU95 4.6 19.3 1.0 HB3 B:GLU20 4.6 16.4 1.0 CE1 A:HIS129 4.6 14.6 1.0 OH A:TYR100 4.7 17.2 1.0 CE2 A:TYR100 4.7 17.1 1.0 ND1 A:HIS129 4.7 12.7 1.0 HD23 A:LEU122 4.7 16.6 1.0 O A:HOH331 4.8 24.0 1.0 HG2 B:GLU53 4.8 16.7 1.0 CB B:GLU20 4.8 13.7 1.0 HG3 B:GLU53 4.9 16.7 1.0 O B:GLY52 4.9 12.5 1.0 N B:GLU53 4.9 13.6 1.0

F.Lennartz, J.H.Jeoung, S.Ruenger, H.Dobbek, M.S.Weiss. Determining the Oxidation State of Elements By X-Ray Crystallography. Acta Crystallogr D Struct V. 78 238 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35102889
DOI: 10.1107/S2059798321013048