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Iron in PDB 6qk0: R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk0 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) 48.60 / 2.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 160.808, 55.963, 98.059, 90.00, 126.23, 90.00
R / Rfree (%) 20.9 / 26.3

Other elements in 6qk0:

The structure of R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6qk0). 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk0:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qk0

Go back to Iron Binding Sites List in 6qk0
Iron binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:45.1
occ:1.00
 OE2 A:GLU167 2.0 41.0 1.0
OE2 A:GLU202 2.2 51.5 1.0
OE2 A:GLU102 2.2 39.7 1.0
O1 A:PLM403 2.3 49.4 1.0
ND1 A:HIS205 2.4 36.6 1.0
OE1 A:GLU202 2.5 50.4 1.0
CD A:GLU202 2.5 58.2 1.0
HG2 A:GLU167 2.8 53.4 1.0
CD A:GLU167 2.9 37.2 1.0
CD A:GLU102 3.2 39.2 1.0
CE1 A:HIS205 3.3 39.7 1.0
CG A:GLU167 3.3 44.5 1.0
HE1 A:HIS205 3.4 47.6 1.0
C1 A:PLM403 3.4 62.0 1.0
MN A:MN401 3.5 38.6 1.0
CG A:HIS205 3.5 40.6 1.0
OE1 A:GLU102 3.5 38.6 1.0
HB2 A:HIS205 3.6 37.1 1.0
HB3 A:HIS205 3.7 37.1 1.0
HE2 A:PHE98 3.8 48.6 1.0
CB A:HIS205 3.8 30.9 1.0
OE1 A:GLU167 3.9 41.8 1.0
HA A:GLU202 3.9 45.1 1.0
HE2 A:TYR162 3.9 52.0 1.0
CG A:GLU202 3.9 54.3 1.0
HG3 A:GLU167 4.0 53.4 1.0
HE1 A:HIS105 4.0 50.0 1.0
O2 A:PLM403 4.1 67.6 1.0
HG2 A:GLU202 4.1 65.1 1.0
HB3 A:GLU167 4.1 40.2 1.0
HH A:TYR162 4.3 54.9 1.0
CE2 A:PHE98 4.3 40.5 1.0
CB A:GLU167 4.4 33.5 1.0
H22 A:PLM403 4.4 66.7 1.0
NE2 A:HIS205 4.5 36.1 1.0
C2 A:PLM403 4.5 55.6 1.0
HB3 A:GLU202 4.5 49.6 1.0
HG21 A:VAL72 4.5 55.8 1.0
HG3 A:GLU202 4.6 65.1 1.0
CG A:GLU102 4.6 35.2 1.0
CD2 A:HIS205 4.6 35.5 1.0
HZ A:PHE98 4.6 54.2 1.0
CB A:GLU202 4.6 41.4 1.0
CE1 A:HIS105 4.6 41.6 1.0
ND1 A:HIS105 4.7 36.8 1.0
H21 A:PLM403 4.7 66.7 1.0
CA A:GLU202 4.7 37.6 1.0
HG2 A:GLU102 4.7 42.2 1.0
CZ A:PHE98 4.8 45.1 1.0
CE2 A:TYR162 4.8 43.4 1.0
HG3 A:GLU102 4.8 42.2 1.0
HB2 A:GLU167 5.0 40.2 1.0

Iron binding site 2 out of 4 in 6qk0

Go back to Iron Binding Sites List in 6qk0
Iron binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe404

b:78.2
occ:1.00
 NE2 A:HIS130 2.4 61.0 1.0
CE1 A:HIS130 3.3 59.1 1.0
CD2 A:HIS130 3.4 52.2 1.0
HE1 A:HIS130 3.4 70.9 1.0
HD2 A:HIS130 3.5 62.6 1.0
OD2 A:ASP129 3.8 70.6 1.0
ND1 A:HIS130 4.4 53.9 1.0
OD1 A:ASP129 4.5 57.7 1.0
CG A:HIS130 4.5 52.9 1.0
CG A:ASP129 4.6 55.4 1.0
O A:HOH501 4.7 52.0 1.0
HA3 A:GLY240 4.8 55.7 1.0

Iron binding site 3 out of 4 in 6qk0

Go back to Iron Binding Sites List in 6qk0
Iron binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:44.7
occ:0.61
 HD1 B:HIS205 1.8 44.3 1.0
OE2 B:GLU167 1.8 43.4 1.0
OE1 B:GLU202 2.2 59.7 1.0
OE2 B:GLU102 2.2 58.4 1.0
CD B:GLU202 2.3 57.9 1.0
OE2 B:GLU202 2.5 64.2 1.0
ND1 B:HIS205 2.6 37.0 1.0
HG2 B:GLU167 2.7 48.4 1.0
CD B:GLU167 2.7 41.0 1.0
MN B:MN401 3.1 62.0 0.9
HG3 B:GLU202 3.1 59.7 1.0
CG B:GLU167 3.2 40.4 1.0
CG B:GLU202 3.3 49.7 1.0
HE1 B:HIS205 3.3 46.9 1.0
CE1 B:HIS205 3.3 39.1 1.0
CD B:GLU102 3.4 47.0 1.0
CG B:HIS205 3.7 34.8 1.0
OE1 B:GLU167 3.8 41.6 1.0
HA B:GLU202 3.8 48.0 1.0
HG3 B:GLU167 3.8 48.4 1.0
HG2 B:GLU202 3.9 59.7 1.0
HB2 B:HIS205 3.9 39.8 1.0
HE2 B:PHE98 4.0 50.2 1.0
HE1 B:HIS105 4.0 55.6 1.0
HB3 B:HIS205 4.0 39.8 1.0
OE1 B:GLU102 4.1 62.7 1.0
CB B:HIS205 4.2 33.2 1.0
HB3 B:GLU167 4.2 39.5 1.0
HZ B:PHE98 4.3 42.5 1.0
OH B:TYR162 4.3 41.7 1.0
CE2 B:PHE98 4.3 41.8 1.0
CB B:GLU167 4.4 32.9 1.0
HH B:TYR162 4.4 50.0 1.0
CB B:GLU202 4.5 47.0 1.0
CG B:GLU102 4.5 51.1 1.0
ND1 B:HIS105 4.5 49.6 1.0
HG2 B:GLU102 4.5 61.4 1.0
CZ B:PHE98 4.5 35.5 1.0
CE1 B:HIS105 4.6 46.4 1.0
NE2 B:HIS205 4.6 38.8 1.0
CA B:GLU202 4.6 40.0 1.0
HG3 B:GLU102 4.6 61.4 1.0
O1 B:PLM403 4.8 64.5 1.0
CD2 B:HIS205 4.8 36.1 1.0
CZ B:TYR162 4.8 44.8 1.0
HB2 B:GLU167 4.9 39.5 1.0
HB2 B:GLU202 5.0 56.4 1.0

Iron binding site 4 out of 4 in 6qk0

Go back to Iron Binding Sites List in 6qk0
Iron binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase E69D 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 E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe404

b:76.8
occ:0.99
 NE2 B:HIS130 2.2 66.0 1.0
O B:HOH532 2.6 50.5 1.0
CD2 B:HIS130 3.0 57.4 1.0
HD2 B:HIS130 3.1 68.9 1.0
CE1 B:HIS130 3.3 64.3 1.0
OD2 B:ASP129 3.4 69.4 1.0
HE1 B:HIS130 3.5 77.2 1.0
CG B:HIS130 4.2 63.0 1.0
ND1 B:HIS130 4.3 66.3 1.0
CG B:ASP129 4.3 69.9 1.0
OD1 B:ASP129 4.4 65.7 1.0
HA3 B:GLY240 4.7 59.4 1.0

Reference:

J.J.Griese, M.Hogbom. R2-Like Ligand-Binding Oxidase E69D Mutant with Anaerobically Reconstituted Mn/Fe Cofactor To Be Published.
Page generated: Wed Aug 7 07:53:12 2024

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