Iron in PDB 4hr4: R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor:
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor, PDB code: 4hr4 was solved by J.J.Griese, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 1.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.928, 97.709, 128.132, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.5

The structure of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor (pdb code 4hr4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor, PDB code: 4hr4:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:33.9 occ:1.00 O1 A:PLM404 1.7 31.6 1.0 OE2 A:GLU167 2.0 32.8 1.0 ND1 A:HIS205 2.0 31.5 1.0 OE1 A:GLU102 2.1 31.5 1.0 OE2 A:GLU202 2.2 33.0 1.0 OE1 A:GLU202 2.3 32.3 1.0 CD A:GLU202 2.5 38.4 1.0 CE1 A:HIS205 2.8 31.1 1.0 C1 A:PLM404 2.8 48.7 1.0 HE1 A:HIS205 2.9 37.4 1.0 CD A:GLU102 3.0 29.3 1.0 CD A:GLU167 3.1 40.5 1.0 CG A:HIS205 3.1 27.3 1.0 O2 A:PLM404 3.2 48.6 1.0 OE2 A:GLU102 3.2 28.4 1.0 HG2 A:GLU167 3.3 40.6 1.0 HB3 A:HIS205 3.4 36.4 1.0 HB2 A:HIS205 3.5 36.4 1.0 CB A:HIS205 3.6 30.3 1.0 MN A:MN401 3.6 30.9 1.0 HE2 A:PHE98 3.7 38.7 1.0 CG A:GLU167 3.8 33.8 1.0 HE2 A:TYR162 3.9 38.8 1.0 CE2 A:PHE98 4.0 32.2 1.0 OE1 A:GLU167 4.0 47.1 1.0 NE2 A:HIS205 4.0 32.5 1.0 HZ A:PHE98 4.0 37.8 1.0 CG A:GLU202 4.0 37.6 1.0 HA A:GLU202 4.0 40.7 1.0 CD2 A:HIS205 4.2 27.0 1.0 CZ A:PHE98 4.2 31.5 1.0 HG21 A:VAL72 4.2 33.0 1.0 HE1 A:HIS105 4.2 39.7 1.0 C2 A:PLM404 4.2 57.2 1.0 CG A:GLU102 4.4 32.9 1.0 O A:HOH567 4.4 48.5 1.0 HG3 A:GLU167 4.4 40.6 1.0 HG3 A:GLU202 4.4 45.1 1.0 HG2 A:GLU202 4.4 45.1 1.0 H21 A:PLM404 4.5 68.6 1.0 HB3 A:GLU167 4.5 36.9 1.0 HG2 A:GLU102 4.5 39.4 1.0 H22 A:PLM404 4.5 68.6 1.0 HG3 A:GLU102 4.6 39.4 1.0 HB3 A:GLU202 4.6 42.9 1.0 CD2 A:PHE98 4.7 28.4 1.0 CB A:GLU202 4.7 35.7 1.0 HE2 A:HIS205 4.7 39.0 1.0 CB A:GLU167 4.8 30.8 1.0 CE2 A:TYR162 4.8 32.3 1.0 CE1 A:HIS105 4.8 33.1 1.0 CA A:GLU202 4.8 33.9 1.0 ND1 A:HIS105 4.9 27.0 1.0 HB A:VAL72 4.9 36.0 1.0 HD2 A:PHE98 5.0 34.1 1.0 HG23 A:VAL72 5.0 33.0 1.0 CG2 A:VAL72 5.0 27.5 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of R2-Like Ligand-Binding Oxidase with Anaerobically Reconstituted Metal Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:66.9 occ:1.00 O A:HOH564 2.1 52.3 1.0 O A:HOH566 2.2 57.1 1.0 O A:HOH568 2.2 57.6 1.0 NE2 A:HIS130 2.3 49.1 1.0 CD2 A:HIS130 3.2 46.8 1.0 CE1 A:HIS130 3.3 52.4 1.0 HD2 A:HIS130 3.3 56.1 1.0 HE1 A:HIS130 3.5 62.8 1.0 O A:HOH573 4.0 51.1 1.0 OD2 A:ASP129 4.2 60.5 1.0 ND1 A:HIS130 4.4 50.8 1.0 CG A:HIS130 4.4 49.5 1.0 OD1 A:ASP129 4.4 50.5 1.0 O A:HOH569 4.7 59.6 1.0 CG A:ASP129 4.8 53.0 1.0 O A:HOH536 4.8 49.2 1.0 HA3 A:GLY240 4.9 49.9 1.0

J.J.Griese, K.Roos, N.Cox, H.S.Shafaat, R.M.M.Branca, J.Lehtio, A.Graslund, W.Lubitz, P.E.M.Siegbahn, M.Hogbom. Direct Observation of Structurally Encoded Metal Discrimination and Ether Bond Formation in A Heterodinuclear Metalloprotein Proc.Natl.Acad.Sci.Usa V. 110 17189 2013.
ISSN: ISSN 0027-8424
PubMed: 24101498
DOI: 10.1073/PNAS.1304368110