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Iron in PDB 6f6m: R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6m 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) 43.52 / 1.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.300, 55.599, 69.970, 90.00, 113.97, 90.00
R / Rfree (%) 14.9 / 18.7

Other elements in 6f6m:

The structure of R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor 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 Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6m). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6m:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6f6m

Go back to Iron Binding Sites List in 6f6m
Iron binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe 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 Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:21.8
occ:1.00
 O2 A:PLM404 1.9 31.8 1.0
OE2 A:GLU102 2.0 21.4 1.0
OE2 A:GLU167 2.0 24.7 1.0
OE1 A:GLU202 2.1 22.3 1.0
ND1 A:HIS205 2.2 20.8 1.0
OE2 A:GLU202 2.3 21.0 1.0
CD A:GLU202 2.5 21.4 1.0
CD A:GLU102 3.0 18.5 1.0
CE1 A:HIS205 3.0 22.0 1.0
CD A:GLU167 3.0 30.7 1.0
C1 A:PLM404 3.1 39.0 1.0
HE1 A:HIS205 3.1 26.4 1.0
CG A:HIS205 3.2 20.8 1.0
OE1 A:GLU102 3.3 19.6 1.0
HG2 A:GLU167 3.3 34.0 1.0
HB3 A:HIS205 3.4 25.2 1.0
HB2 A:HIS205 3.5 25.2 1.0
MN A:MN403 3.6 20.1 1.0
CB A:HIS205 3.6 21.0 1.0
O1 A:PLM404 3.7 39.5 1.0
CG A:GLU167 3.8 28.3 1.0
HE2 A:PHE98 3.9 28.3 1.0
HE2 A:PHE162 3.9 25.2 1.0
HZ A:PHE98 3.9 26.1 1.0
OE1 A:GLU167 3.9 33.9 1.0
CE2 A:PHE98 4.0 23.6 1.0
CG A:GLU202 4.0 22.2 1.0
CZ A:PHE98 4.0 21.8 1.0
HA A:GLU202 4.1 25.1 1.0
HG21 A:VAL72 4.1 27.6 1.0
NE2 A:HIS205 4.2 19.8 1.0
CD2 A:HIS205 4.3 21.1 1.0
CG A:GLU102 4.3 18.5 1.0
HB3 A:GLU167 4.4 29.0 1.0
HE1 A:HIS105 4.4 24.2 1.0
HG3 A:GLU167 4.4 34.0 1.0
HG3 A:GLU202 4.4 26.6 1.0
HG2 A:GLU202 4.4 26.6 1.0
C2 A:PLM404 4.4 42.7 1.0
HG2 A:GLU102 4.4 22.1 1.0
O A:HOH501 4.4 29.5 1.0
H22 A:PLM404 4.5 51.3 1.0
HG3 A:GLU102 4.6 22.1 1.0
HB3 A:GLU202 4.6 26.2 1.0
CB A:GLU167 4.7 24.2 1.0
CD2 A:PHE98 4.7 21.8 1.0
H21 A:PLM404 4.7 51.3 1.0
HB A:VAL72 4.7 28.8 1.0
CB A:GLU202 4.7 21.8 1.0
CE1 A:PHE98 4.8 22.9 1.0
CE2 A:PHE162 4.8 21.0 1.0
HG11 A:VAL72 4.9 31.3 1.0
CA A:GLU202 4.9 20.9 1.0
CG2 A:VAL72 4.9 23.0 1.0
HE2 A:HIS205 4.9 23.8 1.0

Iron binding site 2 out of 4 in 6f6m

Go back to Iron Binding Sites List in 6f6m
Iron binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe 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 Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:54.9
occ:0.82
 O A:HOH604 2.1 55.4 1.0
O A:HOH562 2.1 65.5 1.0
O A:HOH594 2.1 58.9 1.0
NE2 A:HIS130 2.1 44.3 1.0
O A:HOH554 2.2 55.3 1.0
CE1 A:HIS130 3.1 40.9 1.0
CD2 A:HIS130 3.1 40.8 1.0
HE1 A:HIS130 3.2 49.1 1.0
HD2 A:HIS130 3.3 49.0 1.0
O A:HOH526 4.2 38.8 1.0
ND1 A:HIS130 4.2 39.1 1.0
CG A:HIS130 4.3 36.5 1.0
OD2 A:ASP129 4.3 45.4 1.0
OD1 A:ASP129 4.4 41.6 1.0
HA3 A:GLY240 4.7 36.6 1.0
CG A:ASP129 4.8 40.2 1.0
O A:HOH582 4.8 42.1 1.0
HA2 A:GLY240 4.9 36.6 1.0
HD1 A:HIS130 5.0 47.0 1.0

Iron binding site 3 out of 4 in 6f6m

Go back to Iron Binding Sites List in 6f6m
Iron binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:22.9
occ:1.00
 OE2 B:GLU167 1.9 24.8 1.0
O2 B:PLM404 1.9 34.0 1.0
OE2 B:GLU102 2.0 20.7 1.0
ND1 B:HIS205 2.2 20.6 1.0
OE1 B:GLU202 2.2 24.9 1.0
OE2 B:GLU202 2.3 22.2 1.0
CD B:GLU202 2.6 21.1 1.0
CD B:GLU167 3.0 27.3 1.0
C1 B:PLM404 3.0 35.9 1.0
CD B:GLU102 3.0 19.5 1.0
CE1 B:HIS205 3.1 21.6 1.0
HG2 B:GLU167 3.2 29.0 1.0
CG B:HIS205 3.2 19.8 1.0
HE1 B:HIS205 3.3 25.9 1.0
HB3 B:HIS205 3.3 24.3 1.0
OE1 B:GLU102 3.4 21.2 1.0
HB2 B:HIS205 3.5 24.3 1.0
MN B:MN403 3.5 21.9 1.0
CB B:HIS205 3.6 20.2 1.0
O1 B:PLM404 3.6 32.9 1.0
CG B:GLU167 3.6 24.2 1.0
HE2 B:PHE162 3.8 25.2 1.0
HE2 B:PHE98 3.9 26.4 1.0
OE1 B:GLU167 3.9 27.5 1.0
HZ B:PHE98 3.9 26.5 1.0
HG21 B:VAL72 4.0 26.7 1.0
CE2 B:PHE98 4.0 22.0 1.0
CZ B:PHE98 4.1 22.1 1.0
CG B:GLU202 4.1 22.4 1.0
HA B:GLU202 4.1 26.3 1.0
HG3 B:GLU167 4.2 29.0 1.0
NE2 B:HIS205 4.3 20.6 1.0
CG B:GLU102 4.3 19.8 1.0
C2 B:PLM404 4.3 43.2 1.0
CD2 B:HIS205 4.3 21.2 1.0
H22 B:PLM404 4.4 51.8 1.0
HB3 B:GLU167 4.4 27.2 1.0
HG2 B:GLU102 4.4 23.8 1.0
HE1 B:HIS105 4.4 22.6 1.0
O B:HOH501 4.4 37.0 1.0
HG3 B:GLU202 4.5 26.9 1.0
HG2 B:GLU202 4.5 26.9 1.0
HG3 B:GLU102 4.5 23.8 1.0
H21 B:PLM404 4.6 51.8 1.0
HB3 B:GLU202 4.6 28.3 1.0
HB B:VAL72 4.6 28.3 1.0
CB B:GLU167 4.7 22.7 1.0
HG11 B:VAL72 4.7 29.8 1.0
CE2 B:PHE162 4.8 21.0 1.0
CB B:GLU202 4.8 23.6 1.0
CD2 B:PHE98 4.8 20.1 1.0
CG2 B:VAL72 4.8 22.2 1.0
CE1 B:PHE98 4.8 21.1 1.0
CA B:GLU202 4.9 21.9 1.0
HG23 B:VAL72 4.9 26.7 1.0
ND1 B:HIS105 5.0 19.3 1.0

Iron binding site 4 out of 4 in 6f6m

Go back to Iron Binding Sites List in 6f6m
Iron binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of R2-Like Ligand-Binding Oxidase Y162F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:44.9
occ:0.67
 O B:HOH593 2.0 43.5 1.0
O B:HOH547 2.1 55.0 1.0
O B:HOH572 2.2 52.7 1.0
NE2 B:HIS130 2.2 40.9 1.0
O B:HOH534 2.2 58.9 1.0
CD2 B:HIS130 3.1 37.4 1.0
CE1 B:HIS130 3.2 39.2 1.0
HD2 B:HIS130 3.3 44.9 1.0
HE1 B:HIS130 3.4 47.0 1.0
O B:HOH544 4.1 42.0 1.0
OD1 B:ASP129 4.2 39.1 1.0
CG B:HIS130 4.3 33.1 1.0
ND1 B:HIS130 4.3 34.9 1.0
OD2 B:ASP129 4.3 42.7 1.0
HA3 B:GLY240 4.7 34.8 1.0
CG B:ASP129 4.7 38.8 1.0
O B:HOH566 4.8 37.3 1.0
O B:HOH521 4.9 39.9 1.0
HA2 B:GLY240 5.0 34.8 1.0

Reference:

J.J.Griese, R.Kositzki, M.Haumann, M.Hogbom. Assembly of A Heterodinuclear Mn/Fe Cofactor Is Coupled to Tyrosine-Valine Ether Cross-Link Formation in the R2-Like Ligand-Binding Oxidase. J. Biol. Inorg. Chem. V. 24 211 2019.
ISSN: ESSN 1432-1327
PubMed: 30689052
DOI: 10.1007/S00775-019-01639-4
Page generated: Tue Aug 6 18:05:30 2024

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