Iron in PDB 7pfi: 20 Minute FE2+ Soaked Structure of Synftn Variant D65A

All present enzymatic activity of 20 Minute FE2+ Soaked Structure of Synftn Variant D65A:
1.16.3.2;

The structure of 20 Minute FE2+ Soaked Structure of Synftn Variant D65A, PDB code: 7pfi was solved by A.M.Hemmings, J.M.Bradley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.47 / 1.70
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	176.4, 176.4, 176.4, 90, 90, 90
R / Rfree (%)	17.3 / 19.4

The structure of 20 Minute FE2+ Soaked Structure of Synftn Variant D65A also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Iron atom in the 20 Minute FE2+ Soaked Structure of Synftn Variant D65A (pdb code 7pfi). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the 20 Minute FE2+ Soaked Structure of Synftn Variant D65A, PDB code: 7pfi:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the 20 Minute FE2+ Soaked Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 20 Minute FE2+ Soaked Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:29.0 occ:0.85 O A:HOH313 2.0 34.3 1.0 OE1 A:GLU66 2.0 30.7 1.0 OE1 A:GLU33 2.1 30.0 1.0 O A:HOH312 2.1 32.5 1.0 ND1 A:HIS69 2.2 28.2 1.0 CD A:GLU66 3.0 25.5 1.0 CD A:GLU33 3.0 34.3 1.0 CE1 A:HIS69 3.2 36.6 1.0 CG A:HIS69 3.2 27.7 1.0 OE2 A:GLU33 3.3 32.6 1.0 OE2 A:GLU66 3.4 31.5 1.0 FE A:FE202 3.5 36.8 0.3 CB A:HIS69 3.5 26.3 1.0 CG2 A:THR113 3.9 30.4 1.0 OE1 A:GLN143 4.1 33.7 1.0 CG A:GLU66 4.3 24.8 1.0 O A:HOH309 4.3 51.4 1.0 NE2 A:HIS69 4.3 30.7 1.0 CA A:GLU66 4.4 26.1 1.0 CD2 A:HIS69 4.4 28.4 1.0 CG A:GLU33 4.4 26.5 1.0 O A:HOH427 4.4 34.8 1.0 CB A:GLU66 4.5 24.5 1.0 O A:HOH391 4.6 32.7 1.0 CB A:GLU33 4.8 26.2 1.0 O A:GLU66 4.8 25.7 1.0 CD A:GLN143 4.9 29.2 1.0

Iron binding site 2 out of 3 in the 20 Minute FE2+ Soaked Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 20 Minute FE2+ Soaked Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:36.8 occ:0.30 OE2 A:GLU66 1.8 31.5 1.0 O A:HOH313 1.9 34.3 1.0 OE1 A:GLU110 2.0 34.1 1.0 O A:HOH309 2.1 51.4 1.0 O A:HOH391 2.3 32.7 1.0 O A:HOH311 2.7 38.6 1.0 CD A:GLU66 2.8 25.5 1.0 CD A:GLU110 2.8 33.5 1.0 OE2 A:GLU110 3.0 35.9 1.0 OE1 A:GLU66 3.2 30.7 1.0 FE A:FE201 3.5 29.0 0.8 OE1 A:GLN143 3.9 33.7 1.0 NE2 A:GLN143 4.1 28.0 1.0 CG A:GLU66 4.1 24.8 1.0 CG A:GLU110 4.2 34.9 1.0 OH A:TYR40 4.3 29.2 1.0 CE2 A:TYR40 4.4 26.0 1.0 CD A:GLN143 4.4 29.2 1.0 CG2 A:THR113 4.4 30.4 1.0 OG1 A:THR113 4.4 31.2 1.0 O A:HOH484 4.5 43.4 1.0 CB A:THR113 4.5 30.1 1.0 CA A:GLU110 4.7 28.1 1.0 O A:HOH312 4.7 32.5 1.0 O A:HOH335 4.7 36.0 1.0 CE1 A:HIS69 4.7 36.6 1.0 ND1 A:HIS69 4.7 28.2 1.0 CB A:GLU110 4.8 29.1 1.0 CZ A:TYR40 4.9 27.8 1.0

Iron binding site 3 out of 3 in the 20 Minute FE2+ Soaked Structure of Synftn Variant D65A


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 20 Minute FE2+ Soaked Structure of Synftn Variant D65A within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:29.2 occ:0.28 O A:HOH322 2.1 31.9 1.0 O A:HOH500 2.2 30.6 1.0 O A:HOH359 3.8 30.2 1.0 OD2 A:ASP137 4.1 30.0 1.0 CB A:ASP137 4.1 24.9 1.0 CG A:ASP137 4.4 27.4 1.0

J.M.Bradley, J.Fair, A.M.Hemmings, N.E.Le Brun. Key Carboxylate Residues For Iron Transit Through the Prokaryotic Ferritin Syn Ftn. Microbiology (Reading, V. 167 2021ENGL.).
ISSN: ESSN 1465-2080
PubMed: 34825885
DOI: 10.1099/MIC.0.001105