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

Enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak)

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

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak), PDB code: 5dcs 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) 38.91 / 2.01
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.058, 97.419, 129.320, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 21.7

Other elements in 5dcs:

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

Manganese (Mn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak) (pdb code 5dcs). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total only one binding site of Iron was determined in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long Soak), PDB code: 5dcs:

Iron binding site 1 out of 1 in 5dcs

Go back to Iron Binding Sites List in 5dcs
Iron binding site 1 out of 1 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Long 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 (Long Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:32.0
occ:1.00
 O2 A:PLM403 2.0 42.2 1.0
OE2 A:GLU167 2.0 33.3 1.0
O A:HOH521 2.0 33.5 1.0
OE1 A:GLU102 2.1 29.4 1.0
ND1 A:HIS205 2.2 28.9 1.0
OE2 A:GLU202 2.2 37.5 1.0
CE1 A:HIS205 3.1 30.0 1.0
CD A:GLU167 3.1 39.3 1.0
HG2 A:GLU167 3.1 40.6 1.0
C1 A:PLM403 3.1 48.2 1.0
CD A:GLU102 3.1 33.1 1.0
HE1 A:HIS205 3.2 36.0 1.0
CD A:GLU202 3.2 47.7 1.0
CG A:HIS205 3.2 23.6 1.0
HB3 A:HIS205 3.4 31.2 1.0
OE1 A:GLU202 3.5 42.9 1.0
HB2 A:HIS205 3.5 31.2 1.0
OE2 A:GLU102 3.5 30.0 1.0
MN A:MN3401 3.5 29.2 1.0
CG A:GLU167 3.6 33.8 1.0
HE2 A:PHE98 3.6 41.0 1.0
CB A:HIS205 3.6 26.0 1.0
O1 A:PLM403 3.7 47.2 1.0
HA A:GLU202 3.9 38.6 1.0
HE2 A:TYR162 4.0 51.6 1.0
HE1 A:HIS105 4.0 30.7 1.0
CE2 A:PHE98 4.1 34.2 1.0
OE1 A:GLU167 4.1 36.0 1.0
NE2 A:HIS205 4.2 28.2 1.0
HB3 A:GLU167 4.2 36.9 1.0
HG21 A:VAL72 4.3 37.6 1.0
HZ A:PHE98 4.3 38.2 1.0
HG3 A:GLU167 4.3 40.6 1.0
CD2 A:HIS205 4.3 26.3 1.0
C2 A:PLM403 4.4 41.6 1.0
H21 A:PLM403 4.4 50.0 1.0
CG A:GLU102 4.4 29.9 1.0
CZ A:PHE98 4.5 31.8 1.0
HG2 A:GLU102 4.5 35.8 1.0
CG A:GLU202 4.5 40.5 1.0
CB A:GLU167 4.6 30.8 1.0
H22 A:PLM403 4.6 50.0 1.0
HG3 A:GLU102 4.7 35.8 1.0
CE1 A:HIS105 4.7 25.6 1.0
HG3 A:GLU202 4.7 48.5 1.0
ND1 A:HIS105 4.8 24.1 1.0
CA A:GLU202 4.8 32.2 1.0
O A:HOH501 4.8 39.9 1.0
CE2 A:TYR162 4.9 43.0 1.0
CD2 A:PHE98 5.0 31.9 1.0
HE2 A:HIS205 5.0 33.8 1.0
HH A:TYR175 5.0 47.0 1.0

Reference:

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
Page generated: Tue Aug 5 20:43:58 2025

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