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Manganese in PDB 6f6l: R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6l 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) 43.46 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.748, 55.730, 69.456, 90.00, 113.92, 90.00
R / Rfree (%) 16.6 / 20.4

Other elements in 6f6l:

The structure of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6l:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6f6l

Go back to Manganese Binding Sites List in 6f6l
Manganese binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:32.4
occ:1.00
 O1 A:PLM404 1.7 45.8 1.0
OE1 A:GLU102 2.1 32.6 1.0
OE1 A:GLU69 2.1 34.5 1.0
ND1 A:HIS105 2.1 29.0 1.0
O A:HOH521 2.2 39.2 1.0
O A:HOH501 2.3 43.0 1.0
C1 A:PLM404 2.9 45.1 1.0
CE1 A:HIS105 3.0 32.4 1.0
CD A:GLU69 3.0 41.5 1.0
HE1 A:HIS105 3.1 38.9 1.0
CD A:GLU102 3.1 35.0 1.0
CG A:HIS105 3.2 29.7 1.0
OE2 A:GLU69 3.3 42.9 1.0
O2 A:PLM404 3.4 53.2 1.0
FE A:FE403 3.4 38.5 1.0
OE2 A:GLU102 3.5 37.0 1.0
HB2 A:HIS105 3.5 35.7 1.0
HB3 A:HIS105 3.5 35.7 1.0
CB A:HIS105 3.7 29.8 1.0
HA A:GLU102 3.7 35.0 1.0
OE1 A:GLU202 3.9 47.7 1.0
HG21 A:VAL72 3.9 42.4 1.0
HG A:LEU198 4.0 33.6 1.0
HE1 A:HIS205 4.1 37.8 1.0
HA A:GLU69 4.2 42.9 1.0
NE2 A:HIS105 4.2 34.4 1.0
C2 A:PLM404 4.2 42.2 1.0
H31 A:PLM404 4.2 51.2 1.0
CD2 A:HIS105 4.3 31.1 1.0
H32 A:PLM404 4.3 51.2 1.0
CG A:GLU69 4.4 39.1 1.0
HH A:TYR175 4.4 48.8 1.0
CG A:GLU102 4.5 34.6 1.0
OH A:TYR175 4.5 40.7 1.0
HB3 A:GLU69 4.5 40.7 1.0
C3 A:PLM404 4.5 42.7 1.0
OE2 A:GLU202 4.6 38.7 1.0
HB3 A:GLU102 4.6 38.6 1.0
CA A:GLU102 4.6 29.1 1.0
CD A:GLU202 4.6 45.0 1.0
CG2 A:VAL72 4.7 35.4 1.0
HD23 A:LEU198 4.7 38.6 1.0
HG23 A:VAL72 4.7 42.4 1.0
CE1 A:HIS205 4.8 31.5 1.0
ND1 A:HIS205 4.8 37.6 1.0
CB A:GLU102 4.8 32.2 1.0
H21 A:PLM404 4.8 50.6 1.0
HG3 A:GLU69 4.8 46.9 1.0
H22 A:PLM404 4.8 50.6 1.0
CB A:GLU69 4.8 33.9 1.0
HG22 A:VAL72 4.9 42.4 1.0
HG2 A:GLU102 4.9 41.5 1.0
CG A:LEU198 4.9 28.0 1.0
HE2 A:HIS105 4.9 41.3 1.0
CA A:GLU69 4.9 35.7 1.0
HD21 A:LEU198 5.0 38.6 1.0

Manganese binding site 2 out of 4 in 6f6l

Go back to Manganese Binding Sites List in 6f6l
Manganese binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:76.3
occ:0.75
 NE2 A:HIS130 2.2 56.6 1.0
CD2 A:HIS130 3.2 52.1 1.0
CE1 A:HIS130 3.2 56.5 1.0
HD2 A:HIS130 3.3 62.5 1.0
HE1 A:HIS130 3.4 67.8 1.0
O A:HOH544 4.2 51.8 1.0
CG A:HIS130 4.3 52.4 1.0
ND1 A:HIS130 4.3 57.1 1.0
OD1 A:ASP129 4.3 61.9 1.0
OD2 A:ASP129 4.5 84.0 1.0
HA3 A:GLY240 4.8 54.7 1.0
CG A:ASP129 4.9 73.3 1.0
O A:HOH529 4.9 53.0 1.0

Manganese binding site 3 out of 4 in 6f6l

Go back to Manganese Binding Sites List in 6f6l
Manganese binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:37.2
occ:1.00
 O1 B:PLM404 2.0 58.0 1.0
OE1 B:GLU102 2.1 34.4 1.0
OE1 B:GLU69 2.1 38.9 1.0
O B:HOH501 2.2 48.9 1.0
ND1 B:HIS105 2.3 31.7 1.0
OE1 B:GLU202 2.7 47.1 1.0
C1 B:PLM404 2.8 47.1 1.0
O2 B:PLM404 3.1 50.4 1.0
CE1 B:HIS105 3.1 31.6 1.0
CD B:GLU69 3.1 42.8 1.0
CD B:GLU102 3.2 37.0 1.0
HE1 B:HIS105 3.2 38.0 1.0
CG B:HIS105 3.3 33.3 1.0
OE2 B:GLU69 3.4 47.7 1.0
FE B:FE403 3.4 40.8 1.0
HB2 B:HIS105 3.5 39.8 1.0
OE2 B:GLU102 3.5 38.6 1.0
HB3 B:HIS105 3.6 39.8 1.0
HA B:GLU102 3.7 37.1 1.0
CB B:HIS105 3.7 33.1 1.0
CD B:GLU202 3.8 52.8 1.0
HG21 B:VAL72 3.8 46.8 1.0
HH B:TYR175 4.0 59.0 1.0
HE1 B:HIS205 4.0 44.3 1.0
C2 B:PLM404 4.1 43.1 1.0
H31 B:PLM404 4.1 58.7 1.0
HG B:LEU198 4.2 50.5 1.0
HA B:GLU69 4.3 40.6 1.0
NE2 B:HIS105 4.3 35.9 1.0
OH B:TYR175 4.4 49.2 1.0
HG2 B:GLU202 4.4 63.5 1.0
CD2 B:HIS105 4.4 32.2 1.0
OE2 B:GLU202 4.5 37.0 1.0
CG B:GLU69 4.5 34.9 1.0
CG B:GLU102 4.5 39.5 1.0
HG23 B:VAL72 4.5 46.8 1.0
H32 B:PLM404 4.5 58.7 1.0
C3 B:PLM404 4.6 48.9 1.0
CG2 B:VAL72 4.6 39.0 1.0
HB3 B:GLU69 4.6 43.4 1.0
H21 B:PLM404 4.6 51.7 1.0
CA B:GLU102 4.6 30.9 1.0
HB3 B:GLU102 4.6 42.3 1.0
CE1 B:HIS205 4.7 36.9 1.0
HD23 B:LEU198 4.7 47.0 1.0
CG B:GLU202 4.7 52.9 1.0
ND1 B:HIS205 4.8 36.6 1.0
HG22 B:VAL72 4.8 46.8 1.0
CB B:GLU102 4.8 35.3 1.0
H22 B:PLM404 4.9 51.7 1.0
CB B:GLU69 4.9 36.2 1.0
HG3 B:GLU69 4.9 41.9 1.0
HG2 B:GLU102 5.0 47.5 1.0

Manganese binding site 4 out of 4 in 6f6l

Go back to Manganese Binding Sites List in 6f6l
Manganese binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of R2-Like Ligand-Binding Oxidase Y162F Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:83.8
occ:0.84
 NE2 B:HIS130 2.2 53.4 1.0
CD2 B:HIS130 3.1 49.2 1.0
HD2 B:HIS130 3.2 59.1 1.0
CE1 B:HIS130 3.3 53.7 1.0
HE1 B:HIS130 3.5 64.4 1.0
OD2 B:ASP129 4.2 69.6 1.0
CG B:HIS130 4.3 52.8 1.0
ND1 B:HIS130 4.4 53.0 1.0
OD1 B:ASP129 4.5 63.9 1.0
HA3 B:GLY240 4.8 57.5 1.0
CG B:ASP129 4.8 60.5 1.0
HA2 B:GLY240 5.0 57.5 1.0

Reference:

J.J.Griese, R.Kositzki, M.Haumann, M.Hogbom. Assembly of A Heterodinuclear Mn/Fe Cofactor Is Coupled to Tyrosine-Valine Ether Cross-Link Formation in the R2-Like Ligand-Binding Oxidase. J. Biol. Inorg. Chem. V. 24 211 2019.
ISSN: ESSN 1432-1327
PubMed: 30689052
DOI: 10.1007/S00775-019-01639-4
Page generated: Sun Oct 6 04:33:26 2024

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