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Iron in PDB 6f6k: R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6k 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 / 1.98
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.612, 55.655, 70.075, 90.00, 114.16, 90.00
R / Rfree (%) 19.8 / 26.3

Other elements in 6f6k:

The structure of R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6k). 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6k:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:25.7
occ:1.00
 ND1 A:HIS205 1.9 27.4 1.0
OE2 A:GLU102 2.0 29.0 1.0
OE1 A:GLU167 2.0 29.2 0.5
OE2 A:GLU167 2.0 24.0 0.5
OE2 A:GLU167 2.1 28.2 0.5
OE1 A:GLU202 2.1 36.2 1.0
OE2 A:GLU202 2.3 25.6 1.0
CD A:GLU167 2.3 25.1 0.5
CD A:GLU202 2.5 24.3 1.0
CE1 A:HIS205 2.7 31.1 1.0
HE1 A:HIS205 2.9 37.3 1.0
CD A:GLU102 3.0 29.8 1.0
CG A:HIS205 3.0 29.4 1.0
CD A:GLU167 3.1 27.7 0.5
HB3 A:HIS205 3.3 33.8 1.0
OE1 A:GLU102 3.3 23.3 1.0
HG2 A:GLU167 3.4 32.0 0.5
HB2 A:HIS205 3.5 33.8 1.0
CB A:HIS205 3.5 28.2 1.0
HZ A:PHE98 3.6 40.3 1.0
MN A:MN401 3.7 27.1 1.0
HE2 A:TYR162 3.7 32.4 1.0
HE2 A:PHE98 3.8 41.3 1.0
CZ A:PHE98 3.8 33.6 1.0
CG A:GLU167 3.8 26.6 0.5
CG A:GLU167 3.8 25.9 0.5
OE1 A:GLU167 3.9 23.5 0.5
CE2 A:PHE98 3.9 34.4 1.0
NE2 A:HIS205 3.9 22.8 1.0
CG A:GLU202 4.0 22.6 1.0
HG A:LEU72 4.0 40.4 1.0
HA A:GLU202 4.1 28.3 1.0
CD2 A:HIS205 4.1 22.5 1.0
O A:HOH549 4.2 36.5 1.0
HG3 A:GLU167 4.2 31.1 0.5
HG2 A:GLU167 4.2 31.1 0.5
HB3 A:GLU167 4.3 31.3 0.5
HE1 A:HIS105 4.3 42.5 1.0
HG2 A:GLU202 4.3 27.1 1.0
CG A:GLU102 4.4 30.3 1.0
O A:HOH514 4.4 36.6 1.0
HG3 A:GLU202 4.4 27.1 1.0
HB3 A:GLU167 4.5 31.2 0.5
HG2 A:GLU102 4.5 36.4 1.0
HG3 A:GLU167 4.5 32.0 0.5
CE1 A:PHE98 4.5 36.6 1.0
HD23 A:LEU72 4.6 40.1 1.0
CE2 A:TYR162 4.6 27.0 1.0
CD2 A:PHE98 4.7 29.5 1.0
HG3 A:GLU102 4.7 36.4 1.0
HE2 A:HIS205 4.7 27.4 1.0
CB A:GLU167 4.7 26.1 0.5
HB3 A:GLU202 4.8 31.8 1.0
OH A:TYR162 4.8 25.6 1.0
CB A:GLU202 4.8 26.5 1.0
CB A:GLU167 4.8 26.0 0.5
HD21 A:LEU72 4.8 40.1 1.0
HE1 A:PHE98 4.9 44.0 1.0
CA A:GLU202 4.9 23.6 1.0
CG A:LEU72 4.9 33.7 1.0
CE1 A:HIS105 4.9 35.4 1.0
HD2 A:HIS205 4.9 27.1 1.0

Iron binding site 2 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:65.1
occ:1.00
 O A:HOH560 2.0 46.1 1.0
NE2 A:HIS130 2.2 52.6 1.0
O A:HOH578 3.1 43.5 1.0
CE1 A:HIS130 3.1 36.8 1.0
CD2 A:HIS130 3.2 35.9 1.0
HE1 A:HIS130 3.2 44.1 1.0
HD2 A:HIS130 3.4 43.1 1.0
ND1 A:HIS130 4.2 44.0 1.0
CG A:HIS130 4.3 44.4 1.0
OD2 A:ASP129 4.4 43.6 1.0
HA3 A:GLY240 4.5 53.1 1.0
OD1 A:ASP129 4.7 51.9 1.0
HA2 A:GLY240 4.9 53.1 1.0
CG A:ASP129 5.0 51.7 1.0
HD1 A:HIS130 5.0 52.9 1.0

Iron binding site 3 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:30.6
occ:1.00
 OE2 B:GLU102 1.9 27.8 1.0
OE1 B:GLU167 2.0 26.6 0.5
OE2 B:GLU167 2.0 27.7 0.5
OE2 B:GLU167 2.1 29.4 0.5
OE1 B:GLU202 2.2 43.4 1.0
ND1 B:HIS205 2.2 29.6 1.0
CD B:GLU167 2.3 24.2 0.5
OE2 B:GLU202 2.4 39.5 1.0
CD B:GLU202 2.6 36.7 1.0
CD B:GLU102 2.9 25.2 1.0
CD B:GLU167 2.9 26.4 0.5
CE1 B:HIS205 3.1 30.3 1.0
CG B:HIS205 3.2 18.8 1.0
HG2 B:GLU167 3.2 36.4 0.5
HB3 B:HIS205 3.2 35.2 1.0
HE1 B:HIS205 3.3 36.3 1.0
OE1 B:GLU102 3.3 29.3 1.0
HB2 B:HIS205 3.5 35.2 1.0
CB B:HIS205 3.5 29.3 1.0
CG B:GLU167 3.6 30.4 0.5
HE2 B:PHE98 3.6 29.1 1.0
MN B:MN401 3.7 28.6 1.0
HE2 B:TYR162 3.8 23.0 1.0
OE1 B:GLU167 3.8 23.6 0.5
CG B:GLU167 3.8 30.7 0.5
HG B:LEU72 3.8 45.5 1.0
HZ B:PHE98 3.8 36.8 1.0
CE2 B:PHE98 3.9 24.3 1.0
CZ B:PHE98 4.0 30.7 1.0
HA B:GLU202 4.1 37.3 1.0
CG B:GLU202 4.1 39.6 1.0
HB3 B:GLU167 4.1 30.3 0.5
HG3 B:GLU167 4.2 36.8 0.5
O B:HOH521 4.2 36.6 1.0
HG2 B:GLU167 4.2 36.8 0.5
HG3 B:GLU167 4.3 36.4 0.5
NE2 B:HIS205 4.3 25.3 1.0
CG B:GLU102 4.3 20.9 1.0
CD2 B:HIS205 4.3 34.7 1.0
HE1 B:HIS105 4.3 44.0 1.0
HB3 B:GLU167 4.4 30.3 0.5
HG2 B:GLU102 4.4 25.1 1.0
HG3 B:GLU202 4.5 47.5 1.0
HG3 B:GLU102 4.5 25.1 1.0
CB B:GLU167 4.6 25.3 0.5
HG2 B:GLU202 4.6 47.5 1.0
O B:HOH559 4.6 35.8 1.0
CE2 B:TYR162 4.6 19.1 1.0
CB B:GLU167 4.6 25.3 0.5
HB3 B:GLU202 4.7 35.1 1.0
CD2 B:PHE98 4.7 31.1 1.0
HD23 B:LEU72 4.7 51.5 1.0
CG B:LEU72 4.7 37.9 1.0
HB3 B:LEU72 4.8 44.1 1.0
CB B:GLU202 4.8 29.2 1.0
CE1 B:PHE98 4.8 33.4 1.0
CA B:GLU202 4.9 31.1 1.0
CE1 B:HIS105 4.9 36.7 1.0
ND1 B:HIS105 4.9 24.8 1.0
HD2 B:PHE98 5.0 37.4 1.0
OH B:TYR162 5.0 26.0 1.0

Iron binding site 4 out of 4 in 6f6k

Go back to Iron Binding Sites List in 6f6k
Iron binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase V72L 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 V72L Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:61.9
occ:0.91
 NE2 B:HIS130 2.2 56.6 1.0
O B:HOH522 2.2 47.3 1.0
O B:HOH533 2.2 51.9 1.0
CE1 B:HIS130 2.9 47.0 1.0
HE1 B:HIS130 2.9 56.4 1.0
O B:HOH573 3.0 50.7 1.0
CD2 B:HIS130 3.3 48.0 1.0
HD2 B:HIS130 3.6 57.6 1.0
ND1 B:HIS130 4.1 54.8 1.0
CG B:HIS130 4.3 48.6 1.0
OD2 B:ASP129 4.4 59.1 1.0
OD1 B:ASP129 4.6 53.5 1.0
HA3 B:GLY240 4.7 54.6 1.0
O B:HOH516 4.7 43.2 1.0
O B:HOH531 4.7 46.5 1.0
HD1 B:HIS130 4.8 65.8 1.0
HA2 B:GLY240 4.9 54.6 1.0
CG B:ASP129 5.0 58.6 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 18:04:46 2024

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