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Iron in PDB 6f6e: R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6e 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) 43.57 / 1.63
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.516, 55.654, 70.054, 90.00, 114.11, 90.00
R / Rfree (%) 17.5 / 20.1

Other elements in 6f6e:

The structure of R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6e). 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 V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6e:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6f6e

Go back to Iron Binding Sites List in 6f6e
Iron binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:22.6
occ:0.88
 OE2 A:GLU167 1.9 22.4 1.0
OE2 A:GLU102 2.0 23.9 1.0
ND1 A:HIS205 2.2 22.7 1.0
OE1 A:GLU202 2.2 25.9 1.0
OE2 A:GLU202 2.3 26.3 1.0
O1 A:PLM404 2.3 29.8 1.0
CD A:GLU202 2.5 27.7 1.0
CD A:GLU167 3.0 26.4 1.0
CD A:GLU102 3.0 26.0 1.0
CE1 A:HIS205 3.0 22.2 1.0
C1 A:PLM404 3.2 35.5 1.0
HE1 A:HIS205 3.2 26.7 1.0
HG2 A:GLU167 3.2 26.5 1.0
CG A:HIS205 3.2 19.6 1.0
OE1 A:GLU102 3.3 23.2 1.0
O2 A:PLM404 3.4 30.7 1.0
HB3 A:HIS205 3.4 27.5 1.0
MN A:MN403 3.5 21.4 1.0
HB2 A:HIS205 3.6 27.5 1.0
CB A:HIS205 3.6 22.9 1.0
CG A:GLU167 3.7 22.1 1.0
HE2 A:TYR162 3.7 26.6 1.0
OE1 A:GLU167 3.9 26.4 1.0
HE2 A:PHE98 3.9 26.4 1.0
HZ A:PHE98 3.9 28.8 1.0
CG A:GLU202 4.0 27.9 1.0
CE2 A:PHE98 4.1 22.0 1.0
CZ A:PHE98 4.1 24.0 1.0
HA A:GLU202 4.1 25.8 1.0
HE1 A:HIS105 4.2 28.2 1.0
NE2 A:HIS205 4.2 21.2 1.0
HG3 A:GLU167 4.2 26.5 1.0
CG A:GLU102 4.3 20.9 1.0
CD2 A:HIS205 4.3 23.1 1.0
HG2 A:GLU102 4.4 25.1 1.0
HG2 A:GLU202 4.4 33.4 1.0
HG3 A:GLU202 4.5 33.4 1.0
HG3 A:GLU102 4.5 25.1 1.0
HB1 A:ALA72 4.6 28.0 1.0
O A:HOH508 4.6 26.8 1.0
HB3 A:GLU167 4.6 27.6 1.0
CE2 A:TYR162 4.6 22.2 1.0
HB3 A:GLU202 4.6 26.2 1.0
C2 A:PLM404 4.7 30.2 1.0
CB A:GLU202 4.8 21.8 1.0
CB A:GLU167 4.8 23.0 1.0
CE1 A:HIS105 4.8 23.5 1.0
CD2 A:PHE98 4.8 24.4 1.0
CE1 A:PHE98 4.8 22.3 1.0
ND1 A:HIS105 4.9 19.5 1.0
H22 A:PLM404 4.9 36.2 1.0
CA A:GLU202 4.9 21.5 1.0
HE2 A:HIS205 5.0 25.4 1.0

Iron binding site 2 out of 4 in 6f6e

Go back to Iron Binding Sites List in 6f6e
Iron binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:55.5
occ:0.82
 O A:HOH602 2.1 45.8 1.0
O A:HOH554 2.1 53.5 1.0
O A:HOH579 2.2 50.6 1.0
NE2 A:HIS130 2.2 46.8 1.0
O A:HOH540 2.3 48.9 1.0
CD2 A:HIS130 3.2 46.9 1.0
CE1 A:HIS130 3.3 46.6 1.0
HD2 A:HIS130 3.3 56.2 1.0
HE1 A:HIS130 3.5 56.0 1.0
OD1 A:ASP129 4.3 41.8 1.0
CG A:HIS130 4.3 43.0 1.0
ND1 A:HIS130 4.3 39.7 1.0
OD2 A:ASP129 4.4 54.4 1.0
HA3 A:GLY240 4.8 41.6 1.0
CG A:ASP129 4.8 51.4 1.0
O A:HOH573 4.9 39.6 1.0

Iron binding site 3 out of 4 in 6f6e

Go back to Iron Binding Sites List in 6f6e
Iron binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:21.4
occ:0.91
 OE2 B:GLU167 2.0 23.0 1.0
OE2 B:GLU102 2.0 23.6 1.0
OE1 B:GLU202 2.2 22.7 1.0
OE2 B:GLU202 2.2 22.6 1.0
ND1 B:HIS205 2.2 25.0 1.0
CD B:GLU202 2.4 23.9 1.0
O1 B:PLM404 2.5 30.6 1.0
CD B:GLU167 2.9 25.0 1.0
CD B:GLU102 3.0 22.8 1.0
CE1 B:HIS205 3.1 23.1 1.0
HG2 B:GLU167 3.2 32.3 1.0
HE1 B:HIS205 3.2 27.7 1.0
CG B:HIS205 3.3 20.9 1.0
C1 B:PLM404 3.3 35.9 1.0
OE1 B:GLU102 3.3 21.2 1.0
HB3 B:HIS205 3.4 28.3 1.0
MN B:MN403 3.5 18.5 0.9
HB2 B:HIS205 3.5 28.3 1.0
O2 B:PLM404 3.6 29.9 1.0
CB B:HIS205 3.6 23.6 1.0
CG B:GLU167 3.6 26.9 1.0
HE2 B:TYR162 3.7 25.1 1.0
OE1 B:GLU167 3.8 26.2 1.0
HE2 B:PHE98 3.9 27.9 1.0
CG B:GLU202 3.9 23.2 1.0
HZ B:PHE98 4.0 28.9 1.0
CE2 B:PHE98 4.0 23.2 1.0
HA B:GLU202 4.1 27.0 1.0
CZ B:PHE98 4.1 24.1 1.0
HG3 B:GLU167 4.2 32.3 1.0
HE1 B:HIS105 4.3 24.5 1.0
NE2 B:HIS205 4.3 22.1 1.0
CG B:GLU102 4.3 21.6 1.0
HG2 B:GLU202 4.3 27.8 1.0
CD2 B:HIS205 4.4 22.4 1.0
HG3 B:GLU202 4.4 27.8 1.0
HG2 B:GLU102 4.4 26.0 1.0
O B:HOH517 4.5 25.8 1.0
HB3 B:GLU167 4.5 28.1 1.0
HG3 B:GLU102 4.6 26.0 1.0
H21 B:PLM404 4.6 43.2 1.0
HB3 B:GLU202 4.6 26.5 1.0
HB1 B:ALA72 4.6 27.1 1.0
CE2 B:TYR162 4.6 20.9 1.0
C2 B:PLM404 4.7 36.0 1.0
CB B:GLU202 4.7 22.1 1.0
CB B:GLU167 4.7 23.4 1.0
CD2 B:PHE98 4.8 22.9 1.0
CE1 B:PHE98 4.8 22.1 1.0
CE1 B:HIS105 4.8 20.4 1.0
CA B:GLU202 4.9 22.5 1.0
ND1 B:HIS105 4.9 21.4 1.0

Iron binding site 4 out of 4 in 6f6e

Go back to Iron Binding Sites List in 6f6e
Iron binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:54.1
occ:0.77
 O B:HOH585 1.9 47.8 1.0
O B:HOH595 2.0 57.6 1.0
O B:HOH540 2.1 53.4 1.0
NE2 B:HIS130 2.1 40.0 1.0
O B:HOH559 2.3 48.4 1.0
CE1 B:HIS130 3.1 41.5 1.0
CD2 B:HIS130 3.1 40.4 1.0
HD2 B:HIS130 3.3 48.5 1.0
HE1 B:HIS130 3.3 49.8 1.0
OD2 B:ASP129 4.2 50.9 1.0
O B:HOH523 4.2 43.2 1.0
ND1 B:HIS130 4.2 41.4 1.0
CG B:HIS130 4.2 37.7 1.0
OD1 B:ASP129 4.4 41.7 1.0
HA3 B:GLY240 4.7 40.2 1.0
CG B:ASP129 4.7 45.4 1.0
O B:HOH583 4.8 44.0 1.0
O B:HOH516 4.9 43.0 1.0
HA2 B:GLY240 5.0 40.2 1.0
HD1 B:HIS130 5.0 49.7 1.0

Reference:

J.J.Griese, R.M.M.Branca, V.Srinivas, M.Hogbom. Ether Cross-Link Formation in the R2-Like Ligand-Binding Oxidase. J. Biol. Inorg. Chem. V. 23 879 2018.
ISSN: ESSN 1432-1327
PubMed: 29946980
DOI: 10.1007/S00775-018-1583-3
Page generated: Tue Aug 6 18:02:35 2024

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