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

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

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

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution), PDB code: 5ekb 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) 48.61 / 2.07
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.041, 97.217, 128.279, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 24.4

Other elements in 5ekb:

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

Manganese (Mn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution) (pdb code 5ekb). 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 (Reconstituted in Solution), PDB code: 5ekb:

Iron binding site 1 out of 1 in 5ekb

Go back to Iron Binding Sites List in 5ekb
Iron binding site 1 out of 1 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Reconstituted in Solution)


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 (Reconstituted in Solution) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:47.2
occ:0.79
 OE2 A:GLU167 1.9 46.4 1.0
OE2 A:GLU102 2.1 55.6 1.0
ND1 A:HIS205 2.2 43.4 1.0
O2 A:PLM403 2.2 59.5 1.0
O A:HOH502 2.2 59.7 1.0
OE2 A:GLU202 2.2 52.5 1.0
HG2 A:GLU167 2.9 48.3 1.0
CD A:GLU167 2.9 44.6 1.0
CE1 A:HIS205 3.1 44.2 1.0
CD A:GLU202 3.1 55.4 1.0
CD A:GLU102 3.2 49.2 1.0
CG A:HIS205 3.2 38.8 1.0
HE1 A:HIS205 3.2 53.1 1.0
C1 A:PLM403 3.3 59.9 1.0
OE1 A:GLU202 3.4 53.1 1.0
HB3 A:HIS205 3.4 41.3 1.0
CG A:GLU167 3.4 40.3 1.0
HB2 A:HIS205 3.5 41.3 1.0
OE1 A:GLU102 3.6 45.7 1.0
CB A:HIS205 3.6 34.4 1.0
MN A:MN3401 3.6 45.9 0.8
HE2 A:PHE98 3.7 54.4 1.0
HE2 A:TYR162 3.7 69.0 1.0
HA A:GLU202 3.9 50.8 1.0
OE1 A:GLU167 3.9 47.2 1.0
O1 A:PLM403 4.0 61.2 1.0
HE1 A:HIS105 4.1 62.2 1.0
HG3 A:GLU167 4.1 48.3 1.0
HG21 A:VAL72 4.1 66.5 1.0
HB3 A:GLU167 4.1 50.5 1.0
CE2 A:PHE98 4.1 45.3 1.0
NE2 A:HIS205 4.2 44.9 1.0
HZ A:PHE98 4.3 51.1 1.0
CD2 A:HIS205 4.3 43.3 1.0
CB A:GLU167 4.4 42.1 1.0
H22 A:PLM403 4.4 66.9 1.0
CZ A:PHE98 4.5 42.6 1.0
CG A:GLU202 4.5 48.7 1.0
C2 A:PLM403 4.5 55.7 1.0
CG A:GLU102 4.5 44.8 1.0
HG3 A:GLU202 4.6 58.4 1.0
CE2 A:TYR162 4.6 57.5 1.0
HG2 A:GLU102 4.7 53.7 1.0
CE1 A:HIS105 4.7 51.8 1.0
HG3 A:GLU102 4.7 53.7 1.0
H21 A:PLM403 4.8 66.9 1.0
CA A:GLU202 4.8 42.4 1.0
ND1 A:HIS105 4.8 51.0 1.0
HG11 A:VAL72 4.9 67.9 1.0
CD2 A:PHE98 5.0 46.3 1.0
CG2 A:VAL72 5.0 55.5 1.0
HB2 A:GLU167 5.0 50.5 1.0

Reference:

Y.Kutin, V.Srinivas, M.Fritz, R.Kositzki, H.S.Shafaat, J.Birrell, E.Bill, M.Haumann, W.Lubitz, M.Hogbom, J.J.Griese, N.Cox. Divergent Assembly Mechanisms of the Manganese/Iron Cofactors in R2LOX and R2C Proteins. J.Inorg.Biochem. V. 162 164 2016.
ISSN: ISSN 0162-0134
PubMed: 27138102
DOI: 10.1016/J.JINORGBIO.2016.04.019
Page generated: Tue Aug 6 00:29:04 2024

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