Iron in PDB 4xb9: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor, PDB code: 4xb9 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)	48.53 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.044, 97.053, 129.742, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 20.3

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron Cofactor (pdb code 4xb9). 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, PDB code: 4xb9:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:24.9 occ:1.00 O1 A:PLM403 1.7 40.6 1.0 OE2 A:GLU69 2.0 24.7 1.0 O A:HOH544 2.1 31.4 1.0 OE2 A:GLU102 2.1 24.8 1.0 ND1 A:HIS105 2.1 20.0 1.0 O A:HOH542 2.3 32.1 1.0 C1 A:PLM403 2.6 37.7 1.0 CE1 A:HIS105 3.0 21.1 1.0 CD A:GLU69 3.0 32.4 1.0 O2 A:PLM403 3.0 42.9 1.0 HE1 A:HIS105 3.1 25.4 1.0 CD A:GLU102 3.1 29.0 1.0 CG A:HIS105 3.2 21.6 1.0 OE1 A:GLU69 3.3 34.1 1.0 OE1 A:GLU102 3.4 26.8 1.0 HB2 A:HIS105 3.5 29.2 1.0 FE A:FE402 3.5 26.3 1.0 HB3 A:HIS105 3.6 29.2 1.0 CB A:HIS105 3.7 24.3 1.0 HA A:GLU102 3.7 26.1 1.0 HG21 A:VAL72 3.8 33.3 1.0 H32 A:PLM403 4.0 41.7 1.0 C2 A:PLM403 4.0 36.6 1.0 OE1 A:GLU202 4.0 33.0 1.0 H31 A:PLM403 4.1 41.7 1.0 NE2 A:HIS105 4.2 22.3 1.0 HG A:LEU198 4.2 29.0 1.0 HA A:GLU69 4.2 31.8 1.0 HE1 A:HIS205 4.2 27.2 1.0 C3 A:PLM403 4.3 34.8 1.0 CD2 A:HIS105 4.3 21.4 1.0 CG A:GLU69 4.4 23.7 1.0 OH A:TYR175 4.5 30.1 1.0 HH A:TYR175 4.5 36.1 1.0 CG A:GLU102 4.5 26.1 1.0 HB3 A:GLU69 4.5 29.4 1.0 H21 A:PLM403 4.5 43.9 1.0 CG2 A:VAL72 4.6 27.7 1.0 CA A:GLU102 4.6 21.7 1.0 HG23 A:VAL72 4.6 33.3 1.0 H22 A:PLM403 4.7 43.9 1.0 HB3 A:GLU102 4.7 26.3 1.0 HD23 A:LEU198 4.7 33.0 1.0 OE2 A:GLU202 4.7 27.7 1.0 CD A:GLU202 4.7 32.3 1.0 HG22 A:VAL72 4.8 33.3 1.0 HG3 A:GLU69 4.8 28.4 1.0 CB A:GLU69 4.8 24.5 1.0 CE1 A:HIS205 4.9 22.6 1.0 CB A:GLU102 4.9 21.9 1.0 ND1 A:HIS205 4.9 25.4 1.0 HE2 A:HIS105 4.9 26.8 1.0 HG2 A:GLU102 5.0 31.3 1.0 CA A:GLU69 5.0 26.5 1.0 HG2 A:GLU69 5.0 28.4 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Diiron 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 Aerobically Reconstituted Diiron Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:26.3 occ:1.00 O2 A:PLM403 1.9 42.9 1.0 O A:HOH544 2.0 31.4 1.0 OE2 A:GLU167 2.0 26.6 1.0 OE1 A:GLU102 2.1 26.8 1.0 OE2 A:GLU202 2.2 27.7 1.0 ND1 A:HIS205 2.2 25.4 1.0 C1 A:PLM403 3.0 37.7 1.0 CD A:GLU167 3.1 31.0 1.0 HG2 A:GLU167 3.1 32.7 1.0 CE1 A:HIS205 3.1 22.6 1.0 CD A:GLU202 3.1 32.3 1.0 CD A:GLU102 3.1 29.0 1.0 HE1 A:HIS205 3.2 27.2 1.0 CG A:HIS205 3.3 18.9 1.0 OE1 A:GLU202 3.4 33.0 1.0 HE2 A:PHE98 3.5 35.2 1.0 FE A:FE401 3.5 24.9 1.0 HB3 A:HIS205 3.5 28.9 1.0 OE2 A:GLU102 3.5 24.8 1.0 HB2 A:HIS205 3.5 28.9 1.0 CG A:GLU167 3.6 27.2 1.0 O1 A:PLM403 3.7 40.6 1.0 CB A:HIS205 3.7 24.1 1.0 HA A:GLU202 3.9 27.2 1.0 HE2 A:TYR162 4.0 45.5 1.0 HE1 A:HIS105 4.0 25.4 1.0 CE2 A:PHE98 4.1 29.3 1.0 OE1 A:GLU167 4.1 30.2 1.0 HB3 A:GLU167 4.2 34.0 1.0 C2 A:PLM403 4.2 36.6 1.0 H21 A:PLM403 4.3 43.9 1.0 NE2 A:HIS205 4.3 24.1 1.0 HG3 A:GLU167 4.3 32.7 1.0 HG21 A:VAL72 4.3 33.3 1.0 CD2 A:HIS205 4.4 20.6 1.0 HZ A:PHE98 4.4 30.8 1.0 CG A:GLU102 4.4 26.1 1.0 CG A:GLU202 4.5 27.2 1.0 H22 A:PLM403 4.5 43.9 1.0 CB A:GLU167 4.5 28.4 1.0 HG2 A:GLU102 4.5 31.3 1.0 HG3 A:GLU202 4.6 32.7 1.0 CZ A:PHE98 4.6 25.6 1.0 HG3 A:GLU102 4.7 31.3 1.0 CE1 A:HIS105 4.7 21.1 1.0 ND1 A:HIS105 4.8 20.0 1.0 CA A:GLU202 4.8 22.6 1.0 O A:HOH542 4.8 32.1 1.0 CE2 A:TYR162 4.9 38.0 1.0 CD2 A:PHE98 4.9 25.0 1.0 HD2 A:PHE98 4.9 30.0 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