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Iron in PDB 6f6h: R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor

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

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

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6h 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) 43.53 / 1.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.395, 55.783, 69.607, 90.00, 114.06, 90.00
R / Rfree (%) 18.3 / 23.5

Other elements in 6f6h:

The structure of R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6h). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6h:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6f6h

Go back to Iron Binding Sites List in 6f6h
Iron binding site 1 out of 2 in the R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically 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 Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:32.6
occ:1.00
OE2 A:GLU102 2.1 34.3 1.0
OE2 A:GLU167 2.1 29.0 1.0
O A:HOH512 2.1 39.1 1.0
O2 A:PLM404 2.3 51.9 1.0
OE2 A:GLU202 2.3 33.5 1.0
ND1 A:HIS205 2.3 35.5 1.0
HG2 A:GLU167 2.9 30.2 1.0
CD A:GLU167 3.1 32.7 1.0
CD A:GLU102 3.1 30.8 1.0
CD A:GLU202 3.2 35.1 1.0
CE1 A:HIS205 3.2 25.9 1.0
CG A:HIS205 3.3 24.0 1.0
HE1 A:HIS205 3.3 31.1 1.0
C1 A:PLM404 3.3 48.1 1.0
OE1 A:GLU202 3.4 37.6 1.0
HD23 A:LEU72 3.4 52.6 1.0
OE1 A:GLU102 3.4 32.0 1.0
HB3 A:HIS205 3.4 32.7 1.0
MN A:MN3402 3.5 34.0 1.0
CG A:GLU167 3.5 25.2 1.0
HB2 A:HIS205 3.5 32.7 1.0
HE2 A:PHE98 3.6 35.4 1.0
CB A:HIS205 3.7 27.3 1.0
O1 A:PLM404 3.8 53.3 1.0
HA A:GLU202 3.9 36.7 1.0
HE1 A:HIS105 4.0 36.8 1.0
HG3 A:GLU167 4.0 30.2 1.0
OE1 A:GLU167 4.1 33.0 1.0
CE2 A:PHE98 4.2 29.5 1.0
CD2 A:LEU72 4.2 43.8 1.0
HE2 A:TYR162 4.3 40.8 1.0
HD22 A:LEU72 4.3 52.6 1.0
HZ A:PHE98 4.3 32.2 1.0
NE2 A:HIS205 4.3 26.3 1.0
CG A:GLU102 4.4 28.1 1.0
CD2 A:HIS205 4.4 29.2 1.0
HG2 A:GLU102 4.4 33.8 1.0
HD21 A:LEU72 4.5 52.6 1.0
HB3 A:GLU167 4.5 41.0 1.0
CG A:GLU202 4.6 34.7 1.0
CZ A:PHE98 4.6 26.8 1.0
HG3 A:GLU102 4.6 33.8 1.0
CE1 A:HIS105 4.6 30.6 1.0
C2 A:PLM404 4.6 46.0 1.0
CB A:GLU167 4.7 34.1 1.0
HG3 A:GLU202 4.7 41.6 1.0
ND1 A:HIS105 4.7 31.9 1.0
H22 A:PLM404 4.8 55.2 1.0
H21 A:PLM404 4.8 55.2 1.0
CA A:GLU202 4.8 30.6 1.0
O A:HOH501 4.9 39.8 1.0
HH A:TYR175 5.0 43.6 1.0
HB3 A:LEU72 5.0 39.8 1.0

Iron binding site 2 out of 2 in 6f6h

Go back to Iron Binding Sites List in 6f6h
Iron binding site 2 out of 2 in the R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically 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 Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:34.5
occ:1.00
OE2 B:GLU167 2.0 29.3 1.0
O B:HOH501 2.0 39.3 1.0
OE2 B:GLU102 2.1 34.3 1.0
O1 B:PLM404 2.1 55.1 1.0
OE2 B:GLU202 2.1 30.4 1.0
ND1 B:HIS205 2.3 36.8 1.0
HG2 B:GLU167 2.8 38.6 1.0
CD B:GLU167 3.0 34.2 1.0
CD B:GLU202 3.1 38.6 1.0
CD B:GLU102 3.1 34.5 1.0
CE1 B:HIS205 3.1 30.2 1.0
HE1 B:HIS205 3.2 36.2 1.0
CG B:HIS205 3.3 30.7 1.0
OE1 B:GLU202 3.3 45.9 1.0
C1 B:PLM404 3.3 55.3 1.0
CG B:GLU167 3.4 32.2 1.0
HB3 B:HIS205 3.5 32.6 1.0
MN B:MN3401 3.5 35.3 1.0
OE1 B:GLU102 3.5 33.6 1.0
HE2 B:PHE98 3.6 42.8 1.0
HB2 B:HIS205 3.6 32.6 1.0
HD23 B:LEU72 3.6 51.5 1.0
CB B:HIS205 3.7 27.2 1.0
HA B:GLU202 3.9 37.8 1.0
HE1 B:HIS105 4.0 39.3 1.0
OE1 B:GLU167 4.0 35.4 1.0
HG3 B:GLU167 4.0 38.6 1.0
O2 B:PLM404 4.1 53.8 1.0
CE2 B:PHE98 4.1 35.7 1.0
HE2 B:TYR162 4.1 40.8 1.0
HZ B:PHE98 4.2 38.9 1.0
HB3 B:GLU167 4.3 34.2 1.0
NE2 B:HIS205 4.3 31.9 1.0
CG B:GLU202 4.4 36.6 1.0
CG B:GLU102 4.4 31.1 1.0
CD2 B:HIS205 4.4 34.6 1.0
CD2 B:LEU72 4.4 42.9 1.0
HG2 B:GLU102 4.5 37.4 1.0
CZ B:PHE98 4.5 32.4 1.0
CB B:GLU167 4.5 28.5 1.0
C2 B:PLM404 4.5 54.7 1.0
HD22 B:LEU72 4.5 51.5 1.0
HG3 B:GLU202 4.5 44.0 1.0
H21 B:PLM404 4.6 65.7 1.0
H22 B:PLM404 4.6 65.7 1.0
CE1 B:HIS105 4.6 32.7 1.0
HG3 B:GLU102 4.7 37.4 1.0
O B:HOH503 4.7 49.2 1.0
HD21 B:LEU72 4.7 51.5 1.0
ND1 B:HIS105 4.8 29.5 1.0
CA B:GLU202 4.8 31.5 1.0
HH B:TYR175 4.9 41.9 1.0
HB2 B:GLU202 5.0 45.3 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: Sun Dec 13 16:25:44 2020

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