Iron in PDB 5od5: Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst

The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5 was solved by A.K.Duhme-Klair, D.J.Raines, J.E.Clarke, E.V.Blagova, E.J.Dodson, K.S.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.42 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.692, 62.759, 68.195, 87.38, 76.90, 79.27
R / Rfree (%)	17.7 / 22.3

The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst also contains other interesting chemical elements:

Iridium

(Ir)

8 atoms

The binding sites of Iron atom in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst (pdb code 5od5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:31.3 occ:0.66 OAH A:95B403 2.0 34.7 1.0 OAF A:95B403 2.0 40.8 1.0 OAE A:95B403 2.0 43.6 1.0 OH A:TYR288 2.1 37.3 1.0 OAG A:95B403 2.1 38.1 1.0 CBA A:95B403 2.9 43.3 1.0 CAY A:95B403 2.9 43.1 1.0 CAX A:95B403 2.9 45.4 1.0 CAZ A:95B403 2.9 43.2 1.0 CZ A:TYR288 3.1 39.5 1.0 CE2 A:TYR288 3.7 37.2 1.0 NE2 A:GLN98 3.8 37.0 1.0 NH2 A:ARG249 3.9 45.4 1.0 CE1 A:TYR288 4.0 40.0 1.0 NE A:ARG249 4.0 44.2 1.0 NH2 A:ARG118 4.1 44.8 1.0 NE A:ARG118 4.2 40.2 1.0 CAL A:95B403 4.2 45.1 1.0 CBC A:95B403 4.3 50.3 1.0 CAK A:95B403 4.3 46.2 1.0 CBB A:95B403 4.3 46.2 1.0 NH1 A:ARG205 4.4 39.4 1.0 CZ A:ARG249 4.5 48.3 1.0 N A:95B403 4.6 53.6 1.0 NH2 A:ARG205 4.6 41.7 1.0 NAS A:95B403 4.6 47.1 1.0 CZ A:ARG118 4.6 46.2 1.0 CD2 A:TYR288 5.0 35.1 1.0 CAV A:95B403 5.0 51.2 1.0

Iron binding site 2 out of 3 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:65.2 occ:0.25 OH B:TYR288 3.3 71.2 1.0 NH1 B:ARG205 3.3 75.7 1.0 O B:HOH501 3.6 59.0 1.0 CD2 B:LEU191 4.0 50.6 1.0 CE1 B:TYR288 4.2 55.6 1.0 CZ B:TYR288 4.3 54.5 1.0 NE B:ARG249 4.4 66.2 1.0 CD B:ARG249 4.4 61.0 1.0 CZ B:ARG205 4.6 71.8 1.0 CZ B:ARG249 4.8 69.6 1.0 NH2 B:ARG205 4.9 80.6 1.0

Iron binding site 3 out of 3 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:28.7 occ:1.00 OAH C:95B404 2.0 28.6 1.0 OAF C:95B404 2.0 27.2 1.0 OAE C:95B404 2.0 34.2 1.0 OAG C:95B404 2.1 24.8 1.0 OH C:TYR288 2.1 27.9 1.0 O C:HOH515 2.2 40.9 1.0 CAX C:95B404 2.8 34.5 1.0 CBA C:95B404 2.9 26.2 1.0 CAY C:95B404 2.9 27.1 1.0 CAZ C:95B404 2.9 26.7 1.0 CZ C:TYR288 3.1 32.2 1.0 CE2 C:TYR288 3.7 30.5 1.0 NE2 C:GLN98 3.8 35.1 1.0 NH2 C:ARG249 4.1 35.8 1.0 NH2 C:ARG118 4.1 30.1 1.0 NE C:ARG118 4.1 27.1 1.0 CE1 C:TYR288 4.1 31.3 1.0 CAK C:95B404 4.1 32.4 1.0 O C:HOH555 4.2 37.6 1.0 CAL C:95B404 4.2 26.7 1.0 CBC C:95B404 4.2 29.4 1.0 NE C:ARG249 4.2 33.4 1.0 CBB C:95B404 4.3 30.1 1.0 NH1 C:ARG205 4.3 37.3 1.0 CZ C:ARG118 4.5 30.5 1.0 N C:95B404 4.6 32.5 1.0 CZ C:ARG249 4.6 39.6 1.0 NAS C:95B404 4.7 31.0 1.0 NH2 C:ARG205 4.7 32.1 1.0 CAW C:95B404 4.9 31.8 1.0 CD2 C:TYR288 5.0 28.9 1.0 CZ C:ARG205 5.0 31.3 1.0

A.D.J.Raines, J.E.Clarke, E.Blagova, E.J.Dodson, K.S.Wilson, A.K.Duhme-Klair. Redox-Switchable Siderophore Anchor Enables Reversible Artificial Metalloenzyme Assembly Nat Catal 2018.
DOI: 10.1038/S41929-018-0124-3