Iron in PDB 7ppv: Structure of Dife-Sulerythrin at 2.70 Mgy Total Absorbed Dose

The structure of Structure of Dife-Sulerythrin at 2.70 Mgy Total Absorbed Dose, PDB code: 7ppv 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 / 1.36
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	72.15, 72.15, 97.98, 90, 90, 120
R / Rfree (%)	18.1 / 19.9

The structure of Structure of Dife-Sulerythrin at 2.70 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 2.70 Mgy Total Absorbed Dose (pdb code 7ppv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Structure of Dife-Sulerythrin at 2.70 Mgy Total Absorbed Dose, PDB code: 7ppv:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Structure of Dife-Sulerythrin at 2.70 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 2.70 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:18.1 occ:0.62 FE A:FE202 0.0 18.1 0.6 HO A:OH204 1.7 42.9 1.0 FE A:FE202 1.9 13.7 0.4 OE2 A:GLU92 2.0 17.4 0.5 O A:OH204 2.0 35.8 1.0 O A:HOH362 2.1 22.2 1.0 OE2 A:GLU126 2.3 15.6 1.0 OE1 A:GLU92 2.3 16.1 0.5 OE2 B:GLU53 2.3 15.5 1.0 CD A:GLU92 2.5 16.4 0.5 OE2 A:GLU92 2.5 17.1 0.5 OE1 A:GLU95 2.6 18.0 0.4 OE1 A:GLU92 2.6 16.6 0.5 CD A:GLU92 2.8 16.4 0.5 CD A:GLU126 3.0 16.3 1.0 OE1 A:GLU95 3.2 18.1 0.6 CD B:GLU53 3.2 14.8 1.0 FE B:FE404 3.4 14.2 1.0 OE1 B:GLU53 3.5 14.0 1.0 OE1 A:GLU126 3.5 16.1 1.0 OE2 A:GLU95 3.6 17.4 0.6 CD A:GLU95 3.6 17.7 0.4 CD A:GLU95 3.7 17.7 0.6 HE2 B:TYR27 3.9 15.9 1.0 CG A:GLU92 3.9 15.6 0.5 ND1 A:HIS129 4.0 13.0 1.0 OH B:TYR27 4.0 16.5 1.0 OE2 A:GLU95 4.0 17.6 0.4 O A:HOH301 4.0 39.7 1.0 HG3 A:GLU126 4.0 19.3 1.0 CG A:GLU126 4.1 16.1 1.0 HA A:GLU92 4.1 19.0 0.5 HB3 A:GLU126 4.1 19.1 1.0 HA A:GLU92 4.1 19.0 0.5 CG A:GLU92 4.1 15.6 0.5 HG2 A:GLU92 4.2 18.6 0.5 HB1 B:ALA23 4.2 15.4 1.0 HG2 A:GLU92 4.3 18.7 0.5 HB2 B:ALA23 4.4 15.4 1.0 HA A:GLU126 4.4 19.1 1.0 HH B:TYR27 4.4 19.8 1.0 HG3 A:GLU92 4.4 18.6 0.5 HG3 B:GLU53 4.5 16.2 1.0 CG B:GLU53 4.6 13.5 1.0 CB A:GLU126 4.6 15.9 1.0 OE2 B:GLU20 4.6 12.8 1.0 CB B:ALA23 4.7 12.9 1.0 CE2 B:TYR27 4.7 13.3 1.0 HE1 A:HIS129 4.7 16.3 1.0 HB2 A:HIS129 4.7 16.0 1.0 HB3 B:ALA23 4.7 15.4 1.0 CE1 A:HIS129 4.8 13.7 1.0 HB2 A:GLU95 4.8 21.4 0.6 HB3 A:GLU92 4.8 18.6 0.5 HB2 A:GLU95 4.8 21.4 0.4 CB A:GLU92 4.8 15.6 0.5 HG3 A:GLU92 4.8 18.7 0.5 OE1 B:GLU20 4.8 14.4 1.0 CZ B:TYR27 4.8 14.4 1.0 HG2 A:GLU126 4.9 19.3 1.0 HB3 A:GLU92 4.9 18.6 0.5 CA A:GLU92 4.9 15.9 0.5 CB A:GLU92 4.9 15.6 0.5 CA A:GLU92 4.9 15.9 0.5 HB3 A:HIS129 4.9 16.0 1.0 CG A:GLU95 5.0 17.8 0.4 CG A:GLU95 5.0 17.8 0.6 CG A:HIS129 5.0 13.3 1.0

Iron binding site 2 out of 6 in the Structure of Dife-Sulerythrin at 2.70 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 2.70 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:13.7 occ:0.38 FE A:FE202 0.0 13.7 0.4 OE1 A:GLU92 1.8 16.1 0.5 FE A:FE202 1.9 18.1 0.6 OE2 A:GLU126 1.9 15.6 1.0 OE2 B:GLU53 2.0 15.5 1.0 ND1 A:HIS129 2.1 13.0 1.0 OE2 A:GLU92 2.3 17.1 0.5 OE1 A:GLU92 2.5 16.6 0.5 CD A:GLU92 2.7 16.4 0.5 CD A:GLU92 2.7 16.4 0.5 CD B:GLU53 2.9 14.8 1.0 CE1 A:HIS129 3.0 13.7 1.0 OE2 A:GLU92 3.0 17.4 0.5 OE1 B:GLU53 3.0 14.0 1.0 CD A:GLU126 3.0 16.3 1.0 HE1 A:HIS129 3.1 16.3 1.0 HO A:OH204 3.1 42.9 1.0 CG A:HIS129 3.2 13.3 1.0 O A:OH204 3.4 35.8 1.0 HB2 A:HIS129 3.4 16.0 1.0 HB3 A:HIS129 3.5 16.0 1.0 HA A:GLU126 3.5 19.1 1.0 OE1 A:GLU126 3.6 16.1 1.0 CB A:HIS129 3.6 13.4 1.0 HE2 B:TYR27 3.6 15.9 1.0 FE B:FE404 3.7 14.2 1.0 O A:HOH362 3.7 22.2 1.0 HG23 B:ILE49 3.9 14.8 1.0 CG A:GLU92 4.1 15.6 0.5 NE2 A:HIS129 4.1 14.8 1.0 HG3 A:GLU92 4.2 18.6 0.5 CG B:GLU53 4.2 13.5 1.0 OE1 A:GLU95 4.2 18.0 0.4 CG A:GLU92 4.2 15.6 0.5 CD2 A:HIS129 4.3 14.8 1.0 HB3 A:GLU126 4.3 19.1 1.0 CG A:GLU126 4.3 16.1 1.0 HG21 B:ILE49 4.3 14.8 1.0 HG22 B:ILE49 4.4 14.8 1.0 HG2 B:GLU53 4.4 16.2 1.0 HG3 B:GLU53 4.4 16.2 1.0 CG2 B:ILE49 4.4 12.4 1.0 CA A:GLU126 4.4 16.0 1.0 HE1 B:HIS56 4.5 15.2 1.0 OH B:TYR27 4.5 16.5 1.0 CB A:GLU126 4.5 15.9 1.0 CE2 B:TYR27 4.5 13.3 1.0 HG3 A:GLU92 4.5 18.7 0.5 HE2 A:PHE133 4.6 17.5 1.0 HG2 A:GLU92 4.6 18.6 0.5 HG2 A:GLU92 4.6 18.7 0.5 HG3 A:GLU126 4.7 19.3 1.0 OE1 A:GLU95 4.8 18.1 0.6 HB3 A:GLU92 4.8 18.6 0.5 HE2 A:HIS129 4.9 17.7 1.0 HB3 A:GLU92 4.9 18.6 0.5 HG2 A:GLU126 4.9 19.3 1.0 HA A:GLU92 5.0 19.0 0.5

Iron binding site 3 out of 6 in the Structure of Dife-Sulerythrin at 2.70 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 2.70 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:16.1 occ:1.00 OE1 B:GLU126 2.0 17.1 1.0 OE1 A:GLU53 2.1 16.4 1.0 OE2 A:GLU20 2.2 14.7 1.0 ND1 A:HIS56 2.2 14.7 1.0 OE1 A:GLU20 2.2 16.3 1.0 O B:OH401 2.2 35.8 1.0 CD A:GLU20 2.5 15.2 1.0 HO B:OH401 2.9 42.9 1.0 CD B:GLU126 3.0 18.2 1.0 CE1 A:HIS56 3.0 15.5 1.0 CD A:GLU53 3.0 16.9 1.0 HE1 A:HIS56 3.1 18.6 1.0 OE2 B:GLU126 3.2 18.2 1.0 CG A:HIS56 3.3 14.3 1.0 HA A:GLU53 3.3 18.0 1.0 HB2 A:HIS56 3.4 16.5 1.0 FE B:FE403 3.4 20.0 0.6 OE2 A:GLU53 3.5 18.1 1.0 HB3 A:HIS56 3.6 16.5 1.0 CB A:HIS56 3.7 13.8 1.0 FE B:FE403 3.7 16.3 0.4 OE1 B:GLU95 4.0 18.0 0.4 HH B:TYR100 4.0 19.2 1.0 CG A:GLU20 4.0 15.2 1.0 HE2 B:TYR100 4.0 19.7 1.0 HE1 B:HIS129 4.1 18.1 1.0 HB3 A:GLU53 4.2 17.8 1.0 NE2 A:HIS56 4.2 15.7 1.0 CA A:GLU53 4.2 15.1 1.0 CG A:GLU53 4.3 15.6 1.0 CG B:GLU126 4.3 18.0 1.0 CD2 A:HIS56 4.3 15.1 1.0 HG3 A:GLU20 4.4 18.2 1.0 HG B:LEU122 4.4 19.6 1.0 CB A:GLU53 4.4 14.9 1.0 HG2 A:GLU20 4.5 18.2 1.0 HG3 B:GLU126 4.5 21.6 1.0 HG2 B:GLU126 4.5 21.6 1.0 HA A:GLU20 4.5 17.3 1.0 OE1 B:GLU95 4.6 18.2 0.6 HB3 A:GLU20 4.6 17.2 1.0 OH B:TYR100 4.7 16.1 1.0 CE1 B:HIS129 4.8 15.1 1.0 HG2 A:GLU53 4.8 18.7 1.0 CE2 B:TYR100 4.8 16.4 1.0 HD23 B:LEU122 4.8 19.0 1.0 CB A:GLU20 4.8 14.4 1.0 HG3 A:GLU53 4.8 18.7 1.0 N A:GLU53 4.9 14.9 1.0 ND1 B:HIS129 4.9 14.2 1.0 O A:GLY52 4.9 15.0 1.0 HE2 A:HIS56 5.0 18.8 1.0 O B:HOH501 5.0 35.8 1.0

Iron binding site 4 out of 6 in the Structure of Dife-Sulerythrin at 2.70 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 2.70 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:20.0 occ:0.64 FE B:FE403 0.0 20.0 0.6 FE B:FE403 1.9 16.3 0.4 O B:OH401 1.9 35.8 1.0 OE2 B:GLU92 2.0 19.0 0.4 O B:HOH501 2.1 35.8 1.0 OE2 B:GLU126 2.2 18.2 1.0 OE1 B:GLU92 2.2 18.8 0.4 OE2 A:GLU53 2.2 18.1 1.0 HO B:OH401 2.3 42.9 1.0 CD B:GLU92 2.4 18.6 0.4 OE1 B:GLU95 2.5 18.2 0.6 OE2 B:GLU92 2.6 18.6 0.6 OE1 B:GLU92 2.8 19.1 0.6 CD B:GLU92 2.9 18.6 0.6 CD B:GLU126 2.9 18.2 1.0 CD A:GLU53 3.1 16.9 1.0 OE1 B:GLU95 3.1 18.0 0.4 FE A:FE203 3.4 16.1 1.0 OE1 B:GLU126 3.4 17.1 1.0 OE1 A:GLU53 3.4 16.4 1.0 CD B:GLU95 3.5 19.1 0.6 OE2 B:GLU95 3.8 19.7 0.6 CD B:GLU95 3.9 19.0 0.4 CG B:GLU92 3.9 17.9 0.4 HH A:TYR27 3.9 21.4 1.0 HA B:GLU92 3.9 22.1 0.6 HA B:GLU92 3.9 22.0 0.4 ND1 B:HIS129 4.0 14.2 1.0 CG B:GLU126 4.0 18.0 1.0 HE2 A:TYR27 4.0 18.4 1.0 HG3 B:GLU126 4.1 21.6 1.0 HB3 B:GLU126 4.1 23.0 1.0 OH A:TYR27 4.1 17.9 1.0 CG B:GLU92 4.2 18.0 0.6 HB1 A:ALA23 4.2 17.8 1.0 HG2 B:GLU92 4.2 21.5 0.6 HG2 B:GLU92 4.3 21.4 0.4 HA B:GLU126 4.4 24.1 1.0 HB2 A:ALA23 4.4 17.8 1.0 HG3 B:GLU92 4.4 21.4 0.4 OE2 B:GLU95 4.4 19.6 0.4 HG3 A:GLU53 4.5 18.7 1.0 CG A:GLU53 4.5 15.6 1.0 CB B:GLU126 4.5 19.2 1.0 OE2 A:GLU20 4.6 14.7 1.0 HB3 B:GLU92 4.6 21.8 0.4 CB A:ALA23 4.6 14.9 1.0 HG3 B:GLU95 4.6 23.2 0.4 CB B:GLU92 4.7 18.2 0.4 HB2 B:GLU95 4.7 22.5 0.6 HE1 B:HIS129 4.7 18.1 1.0 HB2 B:GLU95 4.7 22.5 0.4 CA B:GLU92 4.7 18.4 0.4 HB3 A:ALA23 4.7 17.8 1.0 HB2 B:HIS129 4.7 19.2 1.0 CA B:GLU92 4.7 18.4 0.6 CE2 A:TYR27 4.8 15.4 1.0 OE1 A:GLU20 4.8 16.3 1.0 CE1 B:HIS129 4.8 15.1 1.0 CG B:GLU95 4.8 19.4 0.4 HG2 B:GLU126 4.8 21.6 1.0 HG3 B:GLU92 4.8 21.5 0.6 CG B:GLU95 4.8 19.3 0.6 O B:HOH505 4.9 34.9 1.0 CB B:GLU92 4.9 18.3 0.6 CZ A:TYR27 4.9 16.2 1.0 HB3 B:GLU92 4.9 21.9 0.6 HB3 B:HIS129 5.0 19.2 1.0 CA B:GLU126 5.0 20.1 1.0

Iron binding site 5 out of 6 in the Structure of Dife-Sulerythrin at 2.70 Mgy Total Absorbed Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Dife-Sulerythrin at 2.70 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:16.3 occ:0.36 FE B:FE403 0.0 16.3 0.4 OE1 B:GLU92 1.8 18.8 0.4 OE2 B:GLU126 1.9 18.2 1.0 FE B:FE403 1.9 20.0 0.6 OE2 A:GLU53 2.0 18.1 1.0 ND1 B:HIS129 2.1 14.2 1.0 OE2 B:GLU92 2.2 18.6 0.6 OE1 B:GLU92 2.5 19.1 0.6 CD B:GLU92 2.6 18.6 0.4 CD B:GLU92 2.6 18.6 0.6 CD A:GLU53 2.9 16.9 1.0 OE2 B:GLU92 2.9 19.0 0.4 CE1 B:HIS129 3.0 15.1 1.0 CD B:GLU126 3.0 18.2 1.0 HE1 B:HIS129 3.1 18.1 1.0 OE1 A:GLU53 3.1 16.4 1.0 CG B:HIS129 3.2 15.8 1.0 O B:OH401 3.3 35.8 1.0 HB2 B:HIS129 3.4 19.2 1.0 HA B:GLU126 3.4 24.1 1.0 HB3 B:HIS129 3.5 19.2 1.0 OE1 B:GLU126 3.6 17.1 1.0 CB B:HIS129 3.6 16.1 1.0 FE A:FE203 3.7 16.1 1.0 O B:HOH501 3.7 35.8 1.0 HE2 A:TYR27 3.7 18.4 1.0 HO B:OH401 3.9 42.9 1.0 HG23 A:ILE49 3.9 18.4 1.0 CG B:GLU92 4.0 17.9 0.4 HG3 B:GLU92 4.0 21.4 0.4 HH A:TYR27 4.1 21.4 1.0 OE1 B:GLU95 4.1 18.2 0.6 NE2 B:HIS129 4.1 17.8 1.0 CG B:GLU92 4.1 18.0 0.6 HB3 B:GLU126 4.2 23.0 1.0 HG21 A:ILE49 4.2 18.4 1.0 CG A:GLU53 4.2 15.6 1.0 CG B:GLU126 4.2 18.0 1.0 CD2 B:HIS129 4.3 18.3 1.0 CA B:GLU126 4.3 20.1 1.0 HE1 A:HIS56 4.4 18.6 1.0 CG2 A:ILE49 4.4 15.4 1.0 HG22 A:ILE49 4.4 18.4 1.0 HG2 A:GLU53 4.4 18.7 1.0 CB B:GLU126 4.4 19.2 1.0 HG3 A:GLU53 4.4 18.7 1.0 HG2 B:GLU92 4.5 21.5 0.6 HG3 B:GLU92 4.5 21.5 0.6 OH A:TYR27 4.5 17.9 1.0 HB3 B:GLU92 4.5 21.8 0.4 HG2 B:GLU92 4.6 21.4 0.4 CE2 A:TYR27 4.6 15.4 1.0 HG3 B:GLU126 4.7 21.6 1.0 OE1 B:GLU95 4.7 18.0 0.4 HA B:GLU92 4.8 22.1 0.6 HE2 B:PHE133 4.8 18.6 1.0 CB B:GLU92 4.8 18.2 0.4 HA B:GLU92 4.8 22.0 0.4 HB3 B:GLU92 4.9 21.9 0.6 HE2 B:HIS129 4.9 21.3 1.0 HG2 B:GLU126 4.9 21.6 1.0 CE1 A:HIS56 5.0 15.5 1.0

Iron binding site 6 out of 6 in the Structure of Dife-Sulerythrin at 2.70 Mgy Total Absorbed Dose


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Structure of Dife-Sulerythrin at 2.70 Mgy Total Absorbed Dose within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe404 b:14.2 occ:1.00 OE1 A:GLU126 2.0 16.1 1.0 OE1 B:GLU53 2.1 14.0 1.0 OE2 B:GLU20 2.2 12.8 1.0 O A:OH204 2.2 35.8 1.0 ND1 B:HIS56 2.2 12.1 1.0 OE1 B:GLU20 2.2 14.4 1.0 CD B:GLU20 2.5 13.3 1.0 HO A:OH204 2.8 42.9 1.0 CD A:GLU126 2.9 16.3 1.0 CD B:GLU53 3.1 14.8 1.0 CE1 B:HIS56 3.1 12.8 1.0 HE1 B:HIS56 3.2 15.2 1.0 OE2 A:GLU126 3.3 15.6 1.0 CG B:HIS56 3.3 12.3 1.0 HA B:GLU53 3.4 16.0 1.0 HB2 B:HIS56 3.4 14.1 1.0 FE A:FE202 3.4 18.1 0.6 OE2 B:GLU53 3.5 15.5 1.0 FE A:FE202 3.7 13.7 0.4 HB3 B:HIS56 3.7 14.1 1.0 CB B:HIS56 3.7 11.8 1.0 HH A:TYR100 3.9 19.7 1.0 HE2 A:TYR100 3.9 17.8 1.0 HE1 A:HIS129 4.0 16.3 1.0 CG B:GLU20 4.0 14.1 1.0 OE1 A:GLU95 4.1 18.1 0.6 HB3 B:GLU53 4.2 15.8 1.0 CA B:GLU53 4.2 13.4 1.0 NE2 B:HIS56 4.2 13.1 1.0 CG A:GLU126 4.3 16.1 1.0 CG B:GLU53 4.3 13.5 1.0 CD2 B:HIS56 4.4 13.0 1.0 HG3 B:GLU20 4.4 16.8 1.0 HG3 A:GLU126 4.4 19.3 1.0 HG A:LEU122 4.4 16.2 1.0 HG2 A:GLU126 4.5 19.3 1.0 CB B:GLU53 4.5 13.2 1.0 HG2 B:GLU20 4.5 16.8 1.0 O A:HOH301 4.5 39.7 1.0 HA B:GLU20 4.5 17.0 1.0 HB3 B:GLU20 4.6 16.3 1.0 CE1 A:HIS129 4.7 13.7 1.0 OH A:TYR100 4.7 16.4 1.0 HD23 A:LEU122 4.7 17.3 1.0 OE1 A:GLU95 4.7 18.0 0.4 CE2 A:TYR100 4.7 14.9 1.0 ND1 A:HIS129 4.8 13.0 1.0 HG2 B:GLU53 4.8 16.2 1.0 CB B:GLU20 4.8 13.6 1.0 HG3 B:GLU53 4.9 16.2 1.0 O A:HOH362 4.9 22.2 1.0 N B:GLU53 4.9 13.1 1.0 O B:GLY52 5.0 13.2 1.0 OE2 A:GLU95 5.0 17.6 0.4 HE2 B:HIS56 5.0 15.7 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