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

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

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor Before Photoconversion, PDB code: 5omk 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)	48.31 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.666, 96.624, 128.399, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 20.9

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor Before Photoconversion (pdb code 5omk). 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 Before Photoconversion, PDB code: 5omk:
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 Before 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 Before Photoconversion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:30.6 occ:1.00 OE2 A:GLU167 2.0 32.0 1.0 O2 A:PLM403 2.0 37.7 1.0 O A:HOH517 2.0 32.3 1.0 OE1 A:GLU102 2.1 29.2 1.0 OE2 A:GLU202 2.2 30.6 1.0 ND1 A:HIS205 2.2 29.5 1.0 HG2 A:GLU167 3.0 36.5 1.0 CD A:GLU167 3.0 34.6 1.0 CD A:GLU202 3.1 33.9 1.0 CD A:GLU102 3.1 27.8 1.0 C1 A:PLM403 3.1 36.0 1.0 CE1 A:HIS205 3.1 29.3 1.0 HE1 A:HIS205 3.2 35.1 1.0 CG A:HIS205 3.3 22.5 1.0 OE1 A:GLU202 3.4 34.5 1.0 HB3 A:HIS205 3.5 30.5 1.0 FE A:FE402 3.5 30.0 1.0 OE2 A:GLU102 3.5 28.3 1.0 CG A:GLU167 3.5 30.4 1.0 HB2 A:HIS205 3.6 30.5 1.0 HE2 A:PHE98 3.6 40.9 1.0 O1 A:PLM403 3.6 38.5 1.0 CB A:HIS205 3.7 25.4 1.0 HE1 A:HIS105 3.9 41.4 1.0 HE2 A:TYR162 4.0 42.9 1.0 HA A:GLU202 4.0 34.3 1.0 OE1 A:GLU167 4.1 31.2 1.0 CE2 A:PHE98 4.1 34.1 1.0 HG3 A:GLU167 4.2 36.5 1.0 HG21 A:VAL72 4.2 37.8 1.0 HB3 A:GLU167 4.2 37.5 1.0 NE2 A:HIS205 4.3 31.7 1.0 HZ A:PHE98 4.3 34.8 1.0 CD2 A:HIS205 4.4 26.4 1.0 CG A:GLU102 4.4 32.3 1.0 H22 A:PLM403 4.4 39.2 1.0 C2 A:PLM403 4.4 32.7 1.0 CG A:GLU202 4.5 33.9 1.0 CB A:GLU167 4.5 31.3 1.0 HG2 A:GLU102 4.5 38.7 1.0 CZ A:PHE98 4.5 29.0 1.0 HG3 A:GLU202 4.6 40.7 1.0 CE1 A:HIS105 4.6 34.5 1.0 HG3 A:GLU102 4.6 38.7 1.0 O A:HOH504 4.7 31.0 1.0 ND1 A:HIS105 4.7 25.5 1.0 H21 A:PLM403 4.8 39.2 1.0 CE2 A:TYR162 4.9 35.7 1.0 CA A:GLU202 4.9 28.6 1.0 HG11 A:VAL72 5.0 38.4 1.0 HH A:TYR175 5.0 39.6 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor Before 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 Before Photoconversion within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:30.0 occ:1.00 O1 A:PLM403 1.9 38.5 1.0 OE2 A:GLU69 2.0 29.6 1.0 O A:HOH517 2.0 32.3 1.0 ND1 A:HIS105 2.1 25.5 1.0 OE2 A:GLU102 2.1 28.3 1.0 O A:HOH504 2.2 31.0 1.0 C1 A:PLM403 2.8 36.0 1.0 CE1 A:HIS105 2.9 34.5 1.0 HE1 A:HIS105 2.9 41.4 1.0 CD A:GLU69 3.0 35.7 1.0 CD A:GLU102 3.1 27.8 1.0 O2 A:PLM403 3.2 37.7 1.0 CG A:HIS105 3.2 26.7 1.0 OE1 A:GLU69 3.3 33.6 1.0 OE1 A:GLU102 3.4 29.2 1.0 FE A:FE401 3.5 30.6 1.0 HB2 A:HIS105 3.5 35.5 1.0 HB3 A:HIS105 3.6 35.5 1.0 CB A:HIS105 3.7 29.6 1.0 HA A:GLU102 3.7 34.8 1.0 HG21 A:VAL72 3.8 37.8 1.0 OE1 A:GLU202 3.9 34.5 1.0 NE2 A:HIS105 4.1 30.3 1.0 HA A:GLU69 4.1 32.9 1.0 HG A:LEU198 4.1 38.8 1.0 HE1 A:HIS205 4.1 35.1 1.0 C2 A:PLM403 4.2 32.7 1.0 H31 A:PLM403 4.2 42.7 1.0 CD2 A:HIS105 4.2 30.5 1.0 H32 A:PLM403 4.3 42.7 1.0 HH A:TYR175 4.4 39.6 1.0 CG A:GLU69 4.4 27.6 1.0 OH A:TYR175 4.5 33.0 1.0 CG A:GLU102 4.5 32.3 1.0 C3 A:PLM403 4.5 35.6 1.0 HB3 A:GLU69 4.5 33.8 1.0 CG2 A:VAL72 4.6 31.5 1.0 HG23 A:VAL72 4.6 37.8 1.0 CA A:GLU102 4.6 29.0 1.0 OE2 A:GLU202 4.7 30.6 1.0 CD A:GLU202 4.7 33.9 1.0 HB3 A:GLU102 4.7 32.2 1.0 CE1 A:HIS205 4.7 29.3 1.0 H22 A:PLM403 4.8 39.2 1.0 HG22 A:VAL72 4.8 37.8 1.0 ND1 A:HIS205 4.8 29.5 1.0 H21 A:PLM403 4.8 39.2 1.0 HE2 A:HIS105 4.8 36.4 1.0 CB A:GLU69 4.8 28.1 1.0 CB A:GLU102 4.8 26.9 1.0 HG3 A:GLU69 4.8 33.1 1.0 CA A:GLU69 4.9 27.4 1.0 HD23 A:LEU198 4.9 38.4 1.0 HG2 A:GLU102 4.9 38.7 1.0 CG A:LEU198 5.0 32.3 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