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Iron in PDB 6f6g: R2-Like Ligand-Binding Oxidase V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6g 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) 48.59 / 1.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 127.988, 98.467, 55.862, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24

Other elements in 6f6g:

The structure of R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6g). 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6g:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6f6g

Go back to Iron Binding Sites List in 6f6g
Iron binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:30.5
occ:1.00
 OE1 A:GLU102 1.9 32.7 1.0
OE2 A:GLU167 2.0 32.8 1.0
ND1 A:HIS205 2.1 29.0 1.0
O2 A:PLM404 2.1 44.5 1.0
OE2 A:GLU202 2.2 34.0 1.0
OE1 A:GLU202 2.4 47.7 1.0
CD A:GLU202 2.6 34.7 1.0
CD A:GLU102 2.9 27.9 1.0
CE1 A:HIS205 3.0 30.0 1.0
CD A:GLU167 3.0 61.4 1.0
HE1 A:HIS205 3.1 36.0 1.0
CG A:HIS205 3.2 28.4 1.0
OE2 A:GLU102 3.2 30.9 1.0
C1 A:PLM404 3.2 49.6 1.0
HB3 A:HIS205 3.4 35.2 1.0
HG2 A:GLU167 3.4 62.6 1.0
HB2 A:HIS205 3.5 35.2 1.0
MN A:MN401 3.5 30.5 1.0
HE2 A:TYR162 3.5 60.9 0.4
CB A:HIS205 3.6 29.3 1.0
O1 A:PLM404 3.8 68.4 1.0
CG A:GLU167 3.8 52.2 1.0
HZ A:PHE98 3.8 39.2 1.0
OE1 A:GLU167 3.9 55.4 1.0
CZ A:PHE98 4.0 32.7 1.0
HA A:GLU202 4.1 34.6 1.0
CG A:GLU202 4.1 37.5 1.0
NE2 A:HIS205 4.1 28.6 1.0
HE1 A:HIS105 4.1 44.5 1.0
CG A:GLU102 4.2 27.5 1.0
CD2 A:HIS205 4.3 27.6 1.0
HG12 A:ILE72 4.3 57.2 1.0
HG2 A:GLU102 4.3 33.0 1.0
CE2 A:PHE98 4.4 40.6 1.0
CE1 A:PHE98 4.4 40.6 1.0
HG3 A:GLU167 4.4 62.6 1.0
HG21 A:ILE72 4.4 52.8 1.0
CE2 A:TYR162 4.4 50.7 0.4
HG3 A:GLU102 4.5 33.0 1.0
HE2 A:PHE98 4.5 48.7 1.0
HE1 A:PHE98 4.5 48.7 1.0
HG2 A:GLU202 4.6 44.9 1.0
HG3 A:GLU202 4.6 44.9 1.0
HB3 A:GLU202 4.6 37.1 1.0
C2 A:PLM404 4.6 54.4 1.0
OH A:TYR162 4.7 50.6 0.4
HB3 A:GLU167 4.7 43.2 1.0
H21 A:PLM404 4.7 65.2 1.0
O A:HOH513 4.7 43.3 1.0
CE1 A:HIS105 4.8 37.1 1.0
CB A:GLU202 4.8 30.9 1.0
ND1 A:HIS105 4.8 34.2 1.0
HE1 A:TYR162 4.8 54.7 0.6
H22 A:PLM404 4.9 65.2 1.0
HE2 A:HIS205 4.9 34.3 1.0
CA A:GLU202 4.9 28.8 1.0
CB A:GLU167 4.9 36.0 1.0

Iron binding site 2 out of 4 in 6f6g

Go back to Iron Binding Sites List in 6f6g
Iron binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:69.8
occ:1.00
 O A:HOH521 2.1 59.4 1.0
O A:HOH554 2.2 56.1 1.0
NE2 A:HIS130 2.3 58.0 1.0
CD2 A:HIS130 3.1 49.7 1.0
HD2 A:HIS130 3.1 59.6 1.0
CE1 A:HIS130 3.4 56.7 1.0
HE1 A:HIS130 3.6 68.0 1.0
OD2 A:ASP129 4.1 61.5 1.0
OD1 A:ASP129 4.2 63.7 1.0
CG A:HIS130 4.3 50.1 1.0
ND1 A:HIS130 4.4 56.7 1.0
CG A:ASP129 4.6 60.9 1.0
HA3 A:GLY240 4.8 57.4 1.0
O A:HOH535 4.9 45.6 1.0

Iron binding site 3 out of 4 in 6f6g

Go back to Iron Binding Sites List in 6f6g
Iron binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:32.2
occ:1.00
 O1 B:PLM404 1.9 46.8 1.0
OE2 B:GLU167 1.9 36.0 1.0
ND1 B:HIS205 2.0 27.0 1.0
OE1 B:GLU102 2.1 34.7 1.0
OE2 B:GLU202 2.2 37.6 1.0
OE1 B:GLU202 2.5 41.9 1.0
CD B:GLU202 2.7 40.9 1.0
CD B:GLU167 2.9 46.2 1.0
CE1 B:HIS205 3.0 32.5 1.0
C1 B:PLM404 3.0 54.8 1.0
CD B:GLU102 3.0 32.9 1.0
HE1 B:HIS205 3.1 39.0 1.0
CG B:HIS205 3.1 34.5 1.0
HH B:TYR162 3.3 74.4 0.6
HB3 B:HIS205 3.3 38.0 1.0
OE2 B:GLU102 3.3 35.1 1.0
HB2 B:HIS205 3.4 38.0 1.0
HG2 B:GLU167 3.5 56.9 1.0
O2 B:PLM404 3.5 56.4 1.0
HE2 B:TYR162 3.5 67.2 0.6
CB B:HIS205 3.5 31.7 1.0
MN B:MN401 3.6 31.8 1.0
OE1 B:GLU167 3.7 48.5 1.0
HZ B:PHE98 3.7 38.5 1.0
CG B:GLU167 3.8 47.4 1.0
CZ B:PHE98 3.9 32.1 1.0
HA B:GLU202 4.0 37.9 1.0
OH B:TYR162 4.1 62.0 0.6
NE2 B:HIS205 4.1 33.3 1.0
HD13 B:ILE72 4.1 57.0 0.4
CG B:GLU202 4.1 40.5 1.0
CD2 B:HIS205 4.2 31.8 1.0
CE2 B:PHE98 4.3 35.3 1.0
O B:HOH501 4.3 48.2 1.0
CG B:GLU102 4.3 38.3 1.0
HG3 B:GLU167 4.3 56.9 1.0
CE1 B:PHE98 4.3 38.2 1.0
CE2 B:TYR162 4.3 56.0 0.6
HD12 B:ILE72 4.3 57.0 0.4
HG2 B:GLU102 4.4 45.9 1.0
HE2 B:PHE98 4.4 42.4 1.0
HE1 B:HIS105 4.4 38.0 1.0
C2 B:PLM404 4.4 60.2 1.0
HE1 B:PHE98 4.4 45.9 1.0
H21 B:PLM404 4.4 72.2 1.0
HG12 B:ILE72 4.5 55.7 0.6
HG21 B:ILE72 4.5 57.4 0.4
HG2 B:GLU202 4.5 48.6 1.0
HB3 B:GLU202 4.5 44.3 1.0
HG3 B:GLU102 4.6 45.9 1.0
HG21 B:ILE72 4.6 49.7 0.6
HE1 B:TYR162 4.6 68.6 0.4
HG3 B:GLU202 4.6 48.6 1.0
CD1 B:ILE72 4.7 47.5 0.4
CZ B:TYR162 4.7 64.5 0.6
CB B:GLU202 4.7 36.9 1.0
H22 B:PLM404 4.8 72.2 1.0
HB3 B:GLU167 4.8 43.3 1.0
CA B:GLU202 4.8 31.6 1.0
HE2 B:HIS205 4.9 39.9 1.0
CB B:GLU167 5.0 36.1 1.0
ND1 B:HIS105 5.0 28.4 1.0
CE1 B:HIS105 5.0 31.6 1.0
CD2 B:PHE98 5.0 37.0 1.0

Iron binding site 4 out of 4 in 6f6g

Go back to Iron Binding Sites List in 6f6g
Iron binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase V72I 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 V72I Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:75.7
occ:1.00
 O B:HOH537 2.0 49.4 1.0
O B:HOH550 2.0 54.6 1.0
NE2 B:HIS130 2.3 59.2 1.0
CD2 B:HIS130 3.2 47.3 1.0
HD2 B:HIS130 3.2 56.8 1.0
CE1 B:HIS130 3.3 49.5 1.0
HE1 B:HIS130 3.6 59.4 1.0
OD2 B:ASP129 4.1 70.4 1.0
OD1 B:ASP129 4.2 55.2 1.0
CG B:HIS130 4.3 45.4 1.0
ND1 B:HIS130 4.4 42.4 1.0
CG B:ASP129 4.6 69.3 1.0
O B:HOH533 4.6 51.7 1.0
HA3 B:GLY240 4.8 48.5 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 18:03:57 2024

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