Iron in PDB 7pfk: 20 Minute FE2+ Soaked Structure of Synftn Variant E141D

All present enzymatic activity of 20 Minute FE2+ Soaked Structure of Synftn Variant E141D:
1.16.3.2;

The structure of 20 Minute FE2+ Soaked Structure of Synftn Variant E141D, PDB code: 7pfk 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)	40.51 / 1.55
Space group	F 4 3 2
Cell size a, b, c (Å), α, β, γ (°)	176.59, 176.59, 176.59, 90, 90, 90
R / Rfree (%)	15.3 / 18.6

The structure of 20 Minute FE2+ Soaked Structure of Synftn Variant E141D also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the 20 Minute FE2+ Soaked Structure of Synftn Variant E141D (pdb code 7pfk). 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 E141D, PDB code: 7pfk:
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 E141D


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 E141D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:28.7 occ:0.85 O A:HOH318 2.0 37.1 1.0 OE1 A:GLU33 2.0 30.8 1.0 OE1 A:GLU66 2.0 30.2 1.0 O A:HOH311 2.1 34.2 1.0 ND1 A:HIS69 2.2 29.1 1.0 CD A:GLU66 3.0 29.9 1.0 CD A:GLU33 3.0 31.7 1.0 CE1 A:HIS69 3.1 31.6 1.0 CG A:HIS69 3.2 28.2 1.0 OE2 A:GLU33 3.3 33.1 1.0 OE2 A:GLU66 3.4 33.4 1.0 FE A:FE202 3.5 41.7 0.5 CB A:HIS69 3.6 27.1 1.0 CG2 A:THR113 4.0 31.9 1.0 OE1 A:GLN143 4.1 32.0 1.0 NE2 A:HIS69 4.2 31.2 1.0 CG A:GLU66 4.3 26.7 1.0 CD2 A:HIS69 4.3 30.0 1.0 CA A:GLU66 4.4 24.2 1.0 O A:HOH417 4.4 34.4 1.0 CG A:GLU33 4.4 29.6 1.0 O A:HOH380 4.5 34.9 1.0 CB A:GLU66 4.5 25.0 1.0 CB A:GLU33 4.7 28.2 1.0 O A:GLU66 4.8 24.7 1.0 OE2 A:GLU110 5.0 37.4 1.0 O A:HOH358 5.0 48.7 1.0 CD A:GLN143 5.0 30.4 1.0

Iron binding site 2 out of 3 in the 20 Minute FE2+ Soaked Structure of Synftn Variant E141D


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 E141D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:41.7 occ:0.45 OE2 A:GLU66 1.9 33.4 1.0 O A:HOH318 1.9 37.1 1.0 OE2 A:GLU110 2.0 37.4 1.0 O A:HOH380 2.4 34.9 1.0 O A:HOH308 2.4 49.4 1.0 CD A:GLU110 2.6 37.2 1.0 OE1 A:GLU110 2.7 41.4 1.0 CD A:GLU66 2.9 29.9 1.0 OE1 A:GLU66 3.3 30.2 1.0 FE A:FE201 3.5 28.7 0.8 OE1 A:GLN143 3.7 32.0 1.0 CG A:GLU110 4.1 35.3 1.0 NE2 A:GLN143 4.1 30.3 1.0 CG A:GLU66 4.2 26.7 1.0 OG A:SER146 4.2 28.0 0.3 O A:HOH358 4.3 48.7 1.0 OH A:TYR40 4.4 31.9 1.0 CD A:GLN143 4.4 30.4 1.0 O A:HOH474 4.4 55.9 1.0 CE2 A:TYR40 4.4 28.2 1.0 CG2 A:THR113 4.5 31.9 1.0 OG1 A:THR113 4.6 31.3 1.0 CE1 A:HIS69 4.6 31.6 1.0 ND1 A:HIS69 4.7 29.1 1.0 CB A:THR113 4.7 30.6 1.0 O A:HOH311 4.7 34.2 1.0 CA A:GLU110 4.8 29.6 1.0 CB A:GLU110 4.8 31.9 1.0 OG A:SER146 4.9 28.1 0.7 CZ A:TYR40 4.9 29.5 1.0 CB A:SER146 4.9 27.3 0.3 CB A:SER146 4.9 27.2 0.7

Iron binding site 3 out of 3 in the 20 Minute FE2+ Soaked Structure of Synftn Variant E141D


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 E141D within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:38.1 occ:0.15 O A:HOH497 1.9 49.6 1.0 O A:HOH327 2.0 39.1 1.0 O A:HOH414 3.8 52.9 1.0 OD2 A:ASP137 4.1 32.8 1.0 CB A:ASP137 4.2 29.2 1.0 O A:HOH498 4.2 53.1 1.0 CG A:ASP137 4.5 31.3 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