Iron in PDB 6qk2: R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk2 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 / 1.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 129.119, 97.794, 55.994, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19

Other elements in 6qk2:

The structure of R2-Like Ligand-Binding Oxidase Y715F 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 Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor (pdb code 6qk2). 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 Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor, PDB code: 6qk2:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qk2

Go back to Iron Binding Sites List in 6qk2
Iron binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase Y715F 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 Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:22.6
occ:1.00
 O1 A:PLM404 1.8 22.5 1.0
OE2 A:GLU167 2.0 24.4 1.0
OE2 A:GLU102 2.0 22.6 1.0
ND1 A:HIS205 2.1 20.8 1.0
OE1 A:GLU202 2.1 24.8 1.0
OE2 A:GLU202 2.3 22.5 1.0
CD A:GLU202 2.5 23.0 1.0
C1 A:PLM404 3.0 30.2 1.0
CE1 A:HIS205 3.0 21.4 1.0
CD A:GLU102 3.0 20.0 1.0
CD A:GLU167 3.1 28.1 1.0
HE1 A:HIS205 3.1 25.7 1.0
CG A:HIS205 3.2 18.0 1.0
HB3 A:HIS205 3.4 27.3 1.0
OE1 A:GLU102 3.4 19.2 1.0
HG2 A:GLU167 3.5 31.6 1.0
HB2 A:HIS205 3.5 27.3 1.0
O2 A:PLM404 3.5 36.4 1.0
CB A:HIS205 3.6 22.8 1.0
MN A:MN403 3.7 18.4 1.0
HE2 A:PHE98 3.8 28.8 1.0
CG A:GLU167 3.8 26.4 1.0
HA A:GLU202 3.9 26.1 1.0
HZ A:PHE98 3.9 24.9 1.0
HE2 A:TYR162 3.9 26.1 1.0
OE1 A:GLU167 4.0 34.5 1.0
CE2 A:PHE98 4.0 24.0 1.0
CG A:GLU202 4.0 24.7 1.0
CZ A:PHE98 4.0 20.7 1.0
NE2 A:HIS205 4.2 18.9 1.0
CD2 A:HIS205 4.3 18.3 1.0
CG A:GLU102 4.3 16.0 1.0
HE1 A:HIS105 4.3 24.6 1.0
HG2 A:GLU102 4.3 19.2 1.0
HB3 A:GLU167 4.4 27.0 1.0
HG21 A:VAL72 4.4 24.9 1.0
C2 A:PLM404 4.4 44.0 1.0
HG2 A:GLU202 4.4 29.7 1.0
HG3 A:GLU202 4.5 29.7 1.0
HG3 A:GLU102 4.5 19.2 1.0
HG3 A:GLU167 4.6 31.6 1.0
H22 A:PLM404 4.6 52.9 1.0
H21 A:PLM404 4.7 52.9 1.0
HB3 A:GLU202 4.7 24.7 1.0
CD2 A:PHE98 4.7 20.8 1.0
CB A:GLU167 4.7 22.5 1.0
CA A:GLU202 4.7 21.7 1.0
CB A:GLU202 4.7 20.6 1.0
CE2 A:TYR162 4.8 21.8 1.0
CE1 A:PHE98 4.8 23.0 1.0
CE1 A:HIS105 4.9 20.5 1.0
HE2 A:HIS205 4.9 22.7 1.0
O A:HOH502 5.0 28.0 1.0
ND1 A:HIS105 5.0 17.3 1.0

Iron binding site 2 out of 4 in 6qk2

Go back to Iron Binding Sites List in 6qk2
Iron binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase Y715F 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 Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:37.7
occ:0.66
 O A:HOH612 1.9 45.6 1.0
O A:HOH561 1.9 39.1 1.0
O A:HOH584 2.0 40.8 1.0
O A:HOH573 2.0 43.2 1.0
NE2 A:HIS130 2.1 28.8 1.0
CE1 A:HIS130 3.1 32.5 1.0
CD2 A:HIS130 3.1 32.5 1.0
HE1 A:HIS130 3.2 39.0 1.0
HD2 A:HIS130 3.3 39.0 1.0
O A:HOH533 4.1 38.4 1.0
OD2 A:ASP129 4.2 43.2 1.0
ND1 A:HIS130 4.2 32.1 1.0
CG A:HIS130 4.3 29.2 1.0
OD1 A:ASP129 4.3 35.3 1.0
O A:HOH636 4.4 51.3 1.0
HA3 A:GLY240 4.7 34.9 1.0
CG A:ASP129 4.7 34.5 1.0
O A:HOH596 4.8 36.2 1.0
HD1 A:HIS130 5.0 38.5 1.0
O A:HOH529 5.0 37.5 1.0

Iron binding site 3 out of 4 in 6qk2

Go back to Iron Binding Sites List in 6qk2
Iron binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase Y715F 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 Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:37.6
occ:0.69
 O B:HOH613 2.0 39.2 1.0
O B:HOH595 2.1 41.2 1.0
O B:HOH583 2.1 39.9 1.0
O B:HOH651 2.2 43.2 1.0
NE2 B:HIS130 2.2 26.9 1.0
CE1 B:HIS130 3.1 33.8 1.0
CD2 B:HIS130 3.1 33.2 1.0
HE1 B:HIS130 3.3 40.6 1.0
HD2 B:HIS130 3.3 39.8 1.0
O B:HOH563 4.1 36.1 1.0
ND1 B:HIS130 4.2 30.7 1.0
CG B:HIS130 4.3 27.1 1.0
OD1 B:ASP129 4.3 32.3 1.0
OD2 B:ASP129 4.3 44.5 1.0
HA3 B:GLY240 4.7 32.2 1.0
CG B:ASP129 4.8 35.5 1.0
O B:HOH593 5.0 39.0 1.0

Iron binding site 4 out of 4 in 6qk2

Go back to Iron Binding Sites List in 6qk2
Iron binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase Y715F 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 Y715F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:22.8
occ:1.00
 O1 B:PLM404 1.9 28.9 1.0
OE2 B:GLU167 2.0 24.8 1.0
OE2 B:GLU102 2.1 21.4 1.0
ND1 B:HIS205 2.1 21.9 1.0
OE1 B:GLU202 2.1 24.0 1.0
OE2 B:GLU202 2.2 22.0 1.0
CD B:GLU202 2.5 20.5 1.0
C1 B:PLM404 3.0 31.0 1.0
CD B:GLU167 3.0 28.0 1.0
CE1 B:HIS205 3.0 21.1 1.0
CD B:GLU102 3.1 21.1 1.0
CG B:HIS205 3.2 20.2 1.0
HE1 B:HIS205 3.2 25.3 1.0
HB3 B:HIS205 3.3 28.4 1.0
O2 B:PLM404 3.4 33.6 1.0
HB2 B:HIS205 3.4 28.4 1.0
OE1 B:GLU102 3.4 20.4 1.0
HG2 B:GLU167 3.4 30.8 1.0
CB B:HIS205 3.5 23.6 1.0
MN B:MN403 3.6 18.1 1.0
HE2 B:PHE98 3.7 27.4 1.0
CG B:GLU167 3.8 25.6 1.0
HA B:GLU202 3.9 23.1 1.0
OE1 B:GLU167 3.9 34.3 1.0
CE2 B:PHE98 4.0 22.8 1.0
CG B:GLU202 4.0 23.4 1.0
HE2 B:TYR162 4.0 26.7 1.0
HZ B:PHE98 4.0 30.9 1.0
CZ B:PHE98 4.2 25.7 1.0
NE2 B:HIS205 4.2 19.3 1.0
CD2 B:HIS205 4.3 19.4 1.0
HB3 B:GLU167 4.3 25.9 1.0
CG B:GLU102 4.3 16.3 1.0
HG21 B:VAL72 4.4 24.6 1.0
HE1 B:HIS105 4.4 20.5 1.0
HG2 B:GLU202 4.4 28.1 1.0
HG2 B:GLU102 4.4 19.5 1.0
HG3 B:GLU202 4.4 28.1 1.0
C2 B:PLM404 4.5 38.1 1.0
HG3 B:GLU167 4.5 30.8 1.0
HG3 B:GLU102 4.6 19.5 1.0
HB3 B:GLU202 4.6 28.0 1.0
CB B:GLU167 4.7 21.6 1.0
CB B:GLU202 4.7 23.3 1.0
H22 B:PLM404 4.7 45.8 1.0
H21 B:PLM404 4.7 45.8 1.0
CD2 B:PHE98 4.7 21.4 1.0
CA B:GLU202 4.7 19.3 1.0
O B:HOH501 4.8 25.3 1.0
CE2 B:TYR162 4.9 22.2 1.0
CE1 B:HIS105 5.0 17.0 1.0
HE2 B:HIS205 5.0 23.2 1.0
HD2 B:PHE98 5.0 25.6 1.0
ND1 B:HIS105 5.0 17.2 1.0
CE1 B:PHE98 5.0 23.4 1.0

Reference:

J.J.Griese, M.Hogbom. R2-Like Ligand-Binding Oxidase Y175F Mutant with Anaerobically Reconstituted Mn/Fe Cofactor To Be Published.
Page generated: Sun Dec 13 16:51:50 2020

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