Iron in PDB 5dco: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak)

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak):
1.17.4.1;

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak), PDB code: 5dco 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)	48.22 / 2.33
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	55.629, 96.695, 128.342, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 22.6

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak) (pdb code 5dco). 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 Diiron Cofactor (Short Soak), PDB code: 5dco:
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 Diiron Cofactor (Short Soak)


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 Diiron Cofactor (Short Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:41.3 occ:1.00 O1 A:PLM403 1.9 46.1 1.0 OE2 A:GLU102 2.2 36.5 1.0 OE2 A:GLU69 2.2 47.2 1.0 O A:HOH507 2.2 43.3 1.0 ND1 A:HIS105 2.3 37.3 1.0 O A:HOH506 2.5 39.4 1.0 C1 A:PLM403 2.7 43.2 1.0 O2 A:PLM403 3.1 44.1 1.0 CD A:GLU69 3.1 40.6 1.0 CE1 A:HIS105 3.1 35.2 1.0 HE1 A:HIS105 3.2 42.2 1.0 CD A:GLU102 3.2 37.6 1.0 OE1 A:GLU69 3.3 51.1 1.0 CG A:HIS105 3.3 41.1 1.0 FE A:FE402 3.5 40.9 1.0 HB2 A:HIS105 3.5 49.9 1.0 HB3 A:HIS105 3.6 49.9 1.0 OE1 A:GLU102 3.6 44.6 1.0 CB A:HIS105 3.7 41.5 1.0 HA A:GLU102 3.8 36.6 1.0 OE1 A:GLU202 3.9 49.6 1.0 HG21 A:VAL72 3.9 59.9 1.0 HG A:LEU198 4.0 43.6 1.0 HE1 A:HIS205 4.1 45.0 1.0 C2 A:PLM403 4.1 39.4 1.0 H31 A:PLM403 4.2 49.2 1.0 HA A:GLU69 4.2 43.9 1.0 H32 A:PLM403 4.3 49.2 1.0 NE2 A:HIS105 4.3 33.9 1.0 OH A:TYR175 4.4 52.5 1.0 CD2 A:HIS105 4.4 43.3 1.0 HH A:TYR175 4.4 63.0 1.0 CG A:GLU69 4.5 42.2 1.0 HB3 A:GLU69 4.5 51.3 1.0 C3 A:PLM403 4.5 41.0 1.0 CG A:GLU102 4.6 39.0 1.0 H22 A:PLM403 4.7 47.3 1.0 OE2 A:GLU202 4.7 42.5 1.0 CA A:GLU102 4.7 30.5 1.0 CD A:GLU202 4.7 43.5 1.0 HB3 A:GLU102 4.7 37.9 1.0 CG2 A:VAL72 4.7 49.9 1.0 CE1 A:HIS205 4.7 37.5 1.0 HG23 A:VAL72 4.8 59.9 1.0 ND1 A:HIS205 4.8 43.0 1.0 CB A:GLU69 4.8 42.7 1.0 H21 A:PLM403 4.8 47.3 1.0 HG3 A:GLU69 4.9 50.7 1.0 CB A:GLU102 4.9 31.5 1.0 CG A:LEU198 4.9 36.3 1.0 HD23 A:LEU198 4.9 45.8 1.0 HG22 A:VAL72 4.9 59.9 1.0 CA A:GLU69 5.0 36.6 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (Short Soak)


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 Diiron Cofactor (Short Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:40.9 occ:1.00 O2 A:PLM403 2.0 44.1 1.0 OE2 A:GLU167 2.0 29.7 1.0 O A:HOH507 2.0 43.3 1.0 ND1 A:HIS205 2.2 43.0 1.0 OE1 A:GLU102 2.2 44.6 1.0 OE2 A:GLU202 2.3 42.5 1.0 HG2 A:GLU167 2.8 38.6 1.0 CD A:GLU167 3.0 32.8 1.0 CE1 A:HIS205 3.0 37.5 1.0 C1 A:PLM403 3.1 43.2 1.0 HE1 A:HIS205 3.1 45.0 1.0 CD A:GLU102 3.1 37.6 1.0 CD A:GLU202 3.2 43.5 1.0 CG A:HIS205 3.2 34.6 1.0 OE2 A:GLU102 3.4 36.5 1.0 CG A:GLU167 3.4 32.2 1.0 OE1 A:GLU202 3.5 49.6 1.0 HB3 A:HIS205 3.5 30.0 1.0 FE A:FE401 3.5 41.3 1.0 HB2 A:HIS205 3.5 30.0 1.0 CB A:HIS205 3.7 25.0 1.0 HE2 A:PHE98 3.7 45.6 1.0 O1 A:PLM403 3.7 46.1 1.0 HE2 A:TYR162 3.9 52.9 1.0 HA A:GLU202 4.0 43.1 1.0 HG3 A:GLU167 4.0 38.6 1.0 OE1 A:GLU167 4.0 29.5 1.0 CE2 A:PHE98 4.1 38.0 1.0 HZ A:PHE98 4.2 37.2 1.0 NE2 A:HIS205 4.2 32.1 1.0 HG21 A:VAL72 4.2 59.9 1.0 HB3 A:GLU167 4.3 37.7 1.0 HE1 A:HIS105 4.3 42.2 1.0 CD2 A:HIS205 4.3 35.9 1.0 H22 A:PLM403 4.3 47.3 1.0 C2 A:PLM403 4.3 39.4 1.0 CZ A:PHE98 4.4 31.0 1.0 CB A:GLU167 4.5 31.4 1.0 CG A:GLU102 4.5 39.0 1.0 CG A:GLU202 4.6 38.5 1.0 H21 A:PLM403 4.6 47.3 1.0 HG2 A:GLU102 4.7 46.8 1.0 HG3 A:GLU202 4.7 46.2 1.0 HG3 A:GLU102 4.8 46.8 1.0 CE2 A:TYR162 4.8 44.1 1.0 CA A:GLU202 4.9 35.9 1.0 CE1 A:HIS105 4.9 35.2 1.0 HG11 A:VAL72 4.9 59.1 1.0 ND1 A:HIS105 4.9 37.3 1.0 HE2 A:HIS205 4.9 38.5 1.0 O A:HOH506 4.9 39.4 1.0 HH A:TYR175 5.0 63.0 1.0

J.J.Griese, R.Kositzki, P.Schrapers, R.M.Branca, A.Nordstrom, J.Lehtio, M.Haumann, M.Hogbom. Structural Basis For Oxygen Activation at A Heterodinuclear Manganese/Iron Cofactor. J.Biol.Chem. V. 290 25254 2015.
ISSN: ESSN 1083-351X
PubMed: 26324712
DOI: 10.1074/JBC.M115.675223