Iron in PDB 5dcr: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak)

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

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak), PDB code: 5dcr 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 / 2.11
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.190, 97.339, 129.764, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 21.2

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak) also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak) (pdb code 5dcr). 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 Mn/Fe Cofactor (Short Soak), PDB code: 5dcr:
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 Mn/Fe 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 Mn/Fe Cofactor (Short Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:37.4 occ:1.00 O2 A:PLM403 2.0 47.0 1.0 O A:HOH512 2.1 45.1 1.0 OE2 A:GLU167 2.1 37.6 1.0 OE1 A:GLU102 2.1 38.4 1.0 OE2 A:GLU202 2.2 39.7 1.0 ND1 A:HIS205 2.2 32.0 1.0 HG2 A:GLU167 3.0 45.6 1.0 C1 A:PLM403 3.0 49.5 1.0 CD A:GLU167 3.1 41.4 1.0 CE1 A:HIS205 3.1 37.8 1.0 CD A:GLU102 3.1 38.0 1.0 CD A:GLU202 3.2 49.3 1.0 HE1 A:HIS205 3.2 45.4 1.0 CG A:HIS205 3.3 31.7 1.0 O1 A:PLM403 3.5 49.8 1.0 OE2 A:GLU102 3.5 33.3 1.0 OE1 A:GLU202 3.5 50.9 1.0 HB3 A:HIS205 3.5 39.0 1.0 MN A:MN3401 3.5 36.2 1.0 CG A:GLU167 3.6 38.0 1.0 HB2 A:HIS205 3.6 39.0 1.0 CB A:HIS205 3.7 32.5 1.0 HE2 A:PHE98 3.8 44.5 1.0 HA A:GLU202 4.0 39.7 1.0 HE2 A:TYR162 4.0 45.9 1.0 OE1 A:GLU167 4.1 45.4 1.0 HE1 A:HIS105 4.1 38.0 1.0 HG21 A:VAL72 4.2 44.5 1.0 HG3 A:GLU167 4.2 45.6 1.0 CE2 A:PHE98 4.2 37.1 1.0 NE2 A:HIS205 4.2 34.8 1.0 HB3 A:GLU167 4.3 37.6 1.0 CD2 A:HIS205 4.4 31.7 1.0 HZ A:PHE98 4.4 41.1 1.0 C2 A:PLM403 4.4 37.9 1.0 CG A:GLU102 4.5 28.9 1.0 H21 A:PLM403 4.5 45.5 1.0 CG A:GLU202 4.5 42.8 1.0 CB A:GLU167 4.6 31.3 1.0 CZ A:PHE98 4.6 34.3 1.0 HG2 A:GLU102 4.6 34.7 1.0 HG3 A:GLU202 4.6 51.4 1.0 HG3 A:GLU102 4.7 34.7 1.0 CE1 A:HIS105 4.8 31.6 1.0 H22 A:PLM403 4.8 45.5 1.0 O A:HOH502 4.8 44.1 1.0 CA A:GLU202 4.9 33.1 1.0 ND1 A:HIS105 4.9 26.3 1.0 CE2 A:TYR162 4.9 38.3 1.0

Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe 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 Mn/Fe Cofactor (Short Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe404 b:85.2 occ:0.84 HE2 A:HIS130 1.6 60.5 1.0 O A:HOH548 2.3 67.3 1.0 NE2 A:HIS130 2.4 50.4 1.0 HD2 A:HIS130 3.2 53.8 1.0 CD2 A:HIS130 3.2 44.8 1.0 CE1 A:HIS130 3.5 54.2 1.0 HE1 A:HIS130 3.8 65.1 1.0 CG A:HIS130 4.4 48.9 1.0 ND1 A:HIS130 4.6 49.0 1.0 OD1 A:ASP129 4.6 56.4 1.0 OD2 A:ASP129 4.7 65.1 1.0 HA3 A:GLY240 4.7 52.0 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