Iron in PDB 5omj: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor After Photoconversion

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

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor After Photoconversion, PDB code: 5omj 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)	48.66 / 2.01
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.625, 97.312, 127.984, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.4

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor After Photoconversion (pdb code 5omj). 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 Aerobically Reconstituted Metal Cofactor After Photoconversion, PDB code: 5omj:
Jump to Iron binding site number: 1; 2;

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


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 Aerobically Reconstituted Metal Cofactor After Photoconversion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:40.0 occ:1.00 O1 A:PLM403 1.9 45.1 1.0 ND1 A:HIS105 2.0 35.2 1.0 OE2 A:GLU69 2.1 44.8 1.0 OE2 A:GLU102 2.2 38.1 1.0 O A:HOH502 2.3 41.3 1.0 O A:HOH508 2.4 48.5 1.0 CE1 A:HIS105 2.8 42.5 1.0 C1 A:PLM403 2.8 39.3 1.0 HE1 A:HIS105 2.9 51.0 1.0 CD A:GLU69 3.1 47.1 1.0 CD A:GLU102 3.1 37.1 1.0 CG A:HIS105 3.2 41.8 1.0 FE A:FE402 3.3 43.0 1.0 OE1 A:GLU102 3.4 44.2 1.0 O2 A:PLM403 3.4 47.6 1.0 OE1 A:GLU69 3.4 49.4 1.0 HB3 A:HIS105 3.5 49.1 1.0 HB2 A:HIS105 3.6 49.1 1.0 CB A:HIS105 3.7 40.9 1.0 HA A:GLU102 3.7 48.8 1.0 OE1 A:GLU202 3.7 41.1 1.0 HE1 A:HIS205 3.9 47.9 1.0 NE2 A:HIS105 4.0 41.7 1.0 C2 A:PLM403 4.1 39.3 1.0 H31 A:PLM403 4.1 50.0 1.0 HA A:GLU69 4.1 50.0 1.0 H32 A:PLM403 4.2 50.0 1.0 CD2 A:HIS105 4.2 41.2 1.0 HG A:LEU198 4.3 51.0 1.0 C3 A:PLM403 4.4 41.7 1.0 CG A:GLU69 4.4 44.6 1.0 OH A:TYR175 4.5 45.4 1.0 CG A:GLU102 4.5 39.2 1.0 HH A:TYR175 4.5 54.5 1.0 CD A:GLU202 4.6 51.3 1.0 OE2 A:GLU202 4.6 51.6 1.0 CE1 A:HIS205 4.6 40.0 1.0 CA A:GLU102 4.6 40.7 1.0 HB3 A:GLU69 4.6 48.9 1.0 H22 A:PLM403 4.6 47.2 1.0 ND1 A:HIS205 4.7 40.5 1.0 CG2 A:VAL72 4.7 35.7 0.3 HB3 A:GLU102 4.7 46.2 1.0 HE2 A:HIS105 4.8 50.0 1.0 HG3 A:GLU69 4.8 53.5 1.0 HD23 A:LEU198 4.8 54.5 1.0 H21 A:PLM403 4.8 47.2 1.0 CB A:GLU102 4.9 38.5 1.0 CB A:GLU69 4.9 40.8 1.0 CA A:GLU69 4.9 41.7 1.0 HG2 A:GLU102 5.0 47.1 1.0

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


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 Aerobically Reconstituted Metal Cofactor After Photoconversion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:43.0 occ:1.00 OH A:TYR162 2.0 47.0 1.0 O2 A:PLM403 2.0 47.6 1.0 O A:HOH508 2.1 48.5 1.0 OE1 A:GLU102 2.1 44.2 1.0 OE2 A:GLU202 2.2 51.6 1.0 ND1 A:HIS205 2.2 40.5 1.0 C1 A:PLM403 2.9 39.3 1.0 CE1 A:HIS205 3.1 40.0 1.0 CD A:GLU202 3.1 51.3 1.0 CD A:GLU102 3.1 37.1 1.0 HE1 A:HIS205 3.1 47.9 1.0 CZ A:TYR162 3.2 53.9 1.0 O1 A:PLM403 3.3 45.1 1.0 CG A:HIS205 3.3 36.0 1.0 OE1 A:GLU202 3.3 41.1 1.0 FE A:FE401 3.3 40.0 1.0 HE2 A:TYR162 3.4 70.6 1.0 HB3 A:HIS205 3.5 39.9 1.0 OE2 A:GLU102 3.5 38.1 1.0 HB2 A:HIS205 3.7 39.9 1.0 CB A:HIS205 3.7 33.2 1.0 HB2 A:ABA167 3.7 56.1 1.0 CE2 A:TYR162 3.7 58.8 1.0 HE1 A:HIS105 3.9 51.0 1.0 HG1 A:ABA167 4.1 59.9 1.0 HA A:GLU202 4.1 47.9 1.0 HG3 A:ABA167 4.2 59.9 1.0 NE2 A:HIS205 4.2 34.0 1.0 HZ A:PHE98 4.2 52.1 1.0 C2 A:PLM403 4.3 39.3 1.0 CE1 A:TYR162 4.3 57.0 1.0 H22 A:PLM403 4.4 47.2 1.0 CD2 A:HIS205 4.4 33.8 1.0 CG A:GLU102 4.4 39.2 1.0 CZ A:PHE98 4.4 43.4 1.0 CG A:ABA167 4.4 49.9 1.0 HE1 A:TYR162 4.5 68.4 1.0 CG A:GLU202 4.5 52.6 1.0 CB A:ABA167 4.5 46.8 1.0 CE1 A:HIS105 4.5 42.5 1.0 HG2 A:GLU102 4.5 47.1 1.0 ND1 A:HIS105 4.6 35.2 1.0 HG3 A:GLU102 4.6 47.1 1.0 HG3 A:GLU202 4.6 63.1 1.0 H21 A:PLM403 4.7 47.2 1.0 O A:HOH502 4.7 41.3 1.0 HE1 A:PHE98 4.7 56.5 1.0 CE1 A:PHE98 4.7 47.0 1.0 CE2 A:PHE98 5.0 39.3 1.0 HB3 A:ABA167 5.0 56.1 1.0 HE2 A:HIS205 5.0 40.9 1.0

P.T.Maugeri, J.J.Griese, R.M.Branca, E.K.Miller, Z.R.Smith, J.Eirich, M.Hogbom, H.S.Shafaat. Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in A Heterobimetallic Oxidase. J. Am. Chem. Soc. V. 140 1471 2018.
ISSN: ESSN 1520-5126
PubMed: 29268610
DOI: 10.1021/JACS.7B11966