Iron in PDB 2yeq: Structure of Phod

All present enzymatic activity of Structure of Phod:
3.1.3.1;

The structure of Structure of Phod, PDB code: 2yeq was solved by J.E.D.Lillington, F.Rodriguez, P.Roversi, S.J.Johnson, B.Berks, S.M.Lea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	135.64 / 1.93
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	147.318, 147.318, 347.646, 90.00, 90.00, 90.00
R / Rfree (%)	17.842 / 20.243

The structure of Structure of Phod also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Sodium	(Na)	6 atoms

The binding sites of Iron atom in the Structure of Phod (pdb code 2yeq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Phod, PDB code: 2yeq:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1524 b:17.6 occ:1.00 OH A:TYR154 2.0 16.3 1.0 OD2 A:ASP151 2.2 16.9 1.0 NE2 A:HIS382 2.2 16.8 1.0 O3 A:PO41527 2.3 19.7 1.0 O4 A:PO41527 2.3 18.8 1.0 SG A:CYS124 2.5 18.0 1.0 P A:PO41527 2.9 19.0 1.0 CZ A:TYR154 3.1 17.1 1.0 CE1 A:HIS382 3.1 17.7 1.0 CD2 A:HIS382 3.2 17.2 1.0 CG A:ASP151 3.2 16.4 1.0 CB A:CYS124 3.3 16.0 1.0 CB A:ASP151 3.6 15.3 1.0 CE2 A:TYR154 3.6 17.6 1.0 O2 A:PO41527 3.7 16.9 1.0 CA A:CA1525 3.9 18.4 1.0 O A:HOH2095 4.0 13.7 1.0 OG A:SER412 4.0 13.8 1.0 O1 A:PO41527 4.0 19.1 1.0 CA A:CYS124 4.1 15.6 1.0 O A:ASP380 4.1 20.6 1.0 CE1 A:TYR154 4.2 15.4 1.0 ND1 A:HIS382 4.3 16.4 1.0 CD2 A:HIS211 4.3 18.0 1.0 CG A:HIS382 4.3 16.7 1.0 OD1 A:ASP151 4.3 16.6 1.0 CB A:SER412 4.4 15.3 1.0 C A:ASP380 4.8 19.0 1.0 CA A:ASP380 4.8 18.1 1.0 NE2 A:HIS211 4.9 19.7 1.0 CD2 A:TYR154 5.0 17.9 1.0

Iron binding site 2 out of 2 in the Structure of Phod


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Phod within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1524 b:19.7 occ:1.00 OH B:TYR154 2.0 17.3 1.0 OD2 B:ASP151 2.2 18.9 1.0 NE2 B:HIS382 2.2 17.1 1.0 O3 B:PO41527 2.3 21.4 1.0 O4 B:PO41527 2.3 22.8 1.0 SG B:CYS124 2.5 20.3 1.0 P B:PO41527 2.9 21.9 1.0 CZ B:TYR154 3.1 18.8 1.0 CE1 B:HIS382 3.2 18.3 1.0 CG B:ASP151 3.2 19.7 1.0 CD2 B:HIS382 3.2 18.8 1.0 CB B:CYS124 3.3 20.2 1.0 CB B:ASP151 3.6 18.0 1.0 CE2 B:TYR154 3.6 19.1 1.0 O2 B:PO41527 3.8 20.1 1.0 CA B:CA1525 3.9 20.6 1.0 CA B:CYS124 4.0 19.1 1.0 O B:HOH2092 4.1 13.9 1.0 O1 B:PO41527 4.1 21.8 1.0 OG B:SER412 4.1 17.6 1.0 O B:ASP380 4.1 21.9 1.0 CE1 B:TYR154 4.2 17.0 1.0 CD2 B:HIS211 4.3 17.7 1.0 ND1 B:HIS382 4.3 17.5 1.0 OD1 B:ASP151 4.3 18.1 1.0 CG B:HIS382 4.4 18.9 1.0 CB B:SER412 4.4 17.1 1.0 CA B:ASP380 4.8 21.2 1.0 C B:ASP380 4.8 20.7 1.0 NE2 B:HIS211 4.9 17.6 1.0 CD2 B:TYR154 5.0 18.9 1.0 N B:CYS124 5.0 19.4 1.0

F.Rodriguez, J.Lillington, S.Johnson, C.R.Timmel, S.M.Lea, B.C.Berks. Crystal Structure of the Bacillus Subtilis Phosphodiesterase Phod Reveals An Iron and Calcium- Containing Active Site. J.Biol.Chem. V. 289 30889 2014.
ISSN: ISSN 0021-9258
PubMed: 25217636
DOI: 10.1074/JBC.M114.604892