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Manganese 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:

Iron (Fe) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the R2-Like Ligand-Binding Oxidase V72L Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6h:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6f6h

Go back to Manganese Binding Sites List in 6f6h
Manganese binding site 1 out of 4 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 Manganese with other atoms in the Mn 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:Mn401

b:68.1
occ:0.67
 O A:HOH554 2.2 60.9 1.0
NE2 A:HIS130 2.3 48.1 1.0
CD2 A:HIS130 3.1 49.4 1.0
HD2 A:HIS130 3.2 59.3 1.0
CE1 A:HIS130 3.3 53.2 1.0
HE1 A:HIS130 3.6 63.9 1.0
O A:HOH552 4.1 43.4 1.0
OD2 A:ASP129 4.1 67.6 1.0
OD1 A:ASP129 4.2 52.0 1.0
CG A:HIS130 4.3 50.9 1.0
ND1 A:HIS130 4.4 52.5 1.0
O A:HOH539 4.5 46.9 1.0
CG A:ASP129 4.6 61.1 1.0
HA3 A:GLY240 4.7 53.7 1.0

Manganese binding site 2 out of 4 in 6f6h

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Manganese binding site 2 out of 4 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 Manganese with other atoms in the Mn 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
A:Mn402

b:34.0
occ:1.00
 O1 A:PLM404 1.8 53.3 1.0
OE1 A:GLU69 2.1 30.0 1.0
OE1 A:GLU102 2.1 32.0 1.0
O A:HOH512 2.1 39.1 1.0
ND1 A:HIS105 2.3 31.9 1.0
O A:HOH501 2.3 39.8 1.0
C1 A:PLM404 2.6 48.1 1.0
O2 A:PLM404 3.0 51.9 1.0
CD A:GLU69 3.0 40.4 1.0
CE1 A:HIS105 3.2 30.6 1.0
CD A:GLU102 3.2 30.8 1.0
HE1 A:HIS105 3.2 36.8 1.0
OE2 A:GLU69 3.3 37.9 1.0
CG A:HIS105 3.3 31.8 1.0
FE A:FE403 3.5 32.6 1.0
OE2 A:GLU102 3.5 34.3 1.0
HB3 A:HIS105 3.5 33.2 1.0
HB2 A:HIS105 3.6 33.2 1.0
CB A:HIS105 3.7 27.6 1.0
HA A:GLU102 3.8 30.2 1.0
HA A:GLU69 4.0 38.6 1.0
C2 A:PLM404 4.0 46.0 1.0
OE1 A:GLU202 4.0 37.6 1.0
HG A:LEU198 4.1 31.9 1.0
H32 A:PLM404 4.2 51.6 1.0
H31 A:PLM404 4.2 51.6 1.0
HD22 A:LEU72 4.2 52.6 1.0
NE2 A:HIS105 4.3 32.8 1.0
HE1 A:HIS205 4.4 31.1 1.0
C3 A:PLM404 4.4 43.0 1.0
CD2 A:HIS105 4.4 30.7 1.0
CG A:GLU69 4.4 37.2 1.0
HD23 A:LEU72 4.5 52.6 1.0
HH A:TYR175 4.5 43.6 1.0
H22 A:PLM404 4.5 55.2 1.0
CG A:GLU102 4.5 28.1 1.0
OH A:TYR175 4.5 36.3 1.0
HB3 A:GLU69 4.6 37.6 1.0
HB3 A:GLU102 4.6 31.0 1.0
H21 A:PLM404 4.6 55.2 1.0
CA A:GLU102 4.7 25.2 1.0
HD23 A:LEU198 4.7 36.0 1.0
OE2 A:GLU202 4.8 33.5 1.0
CA A:GLU69 4.8 32.2 1.0
CD A:GLU202 4.8 35.1 1.0
CD2 A:LEU72 4.8 43.8 1.0
HG3 A:GLU69 4.8 44.6 1.0
CB A:GLU69 4.8 31.3 1.0
CB A:GLU102 4.9 25.8 1.0
HG2 A:GLU102 4.9 33.8 1.0
HB2 A:LEU72 4.9 39.8 1.0
HD21 A:LEU198 4.9 36.0 1.0
ND1 A:HIS205 4.9 35.5 1.0
CG A:LEU198 5.0 26.5 1.0

Manganese binding site 3 out of 4 in 6f6h

Go back to Manganese Binding Sites List in 6f6h
Manganese binding site 3 out of 4 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 Manganese with other atoms in the Mn binding site number 3 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:Mn401

b:35.3
occ:1.00
 O2 B:PLM404 1.8 53.8 1.0
OE1 B:GLU69 2.1 33.0 1.0
O B:HOH501 2.1 39.3 1.0
OE1 B:GLU102 2.1 33.6 1.0
O B:HOH503 2.3 49.2 1.0
ND1 B:HIS105 2.3 29.5 1.0
C1 B:PLM404 2.3 55.3 1.0
O1 B:PLM404 2.6 55.1 1.0
CD B:GLU69 3.0 39.7 1.0
CD B:GLU102 3.1 34.5 1.0
CE1 B:HIS105 3.1 32.7 1.0
HE1 B:HIS105 3.2 39.3 1.0
OE2 B:GLU69 3.3 40.1 1.0
CG B:HIS105 3.4 27.6 1.0
OE2 B:GLU102 3.4 34.3 1.0
FE B:FE403 3.5 34.5 1.0
HB2 B:HIS105 3.5 37.4 1.0
HB3 B:HIS105 3.6 37.4 1.0
CB B:HIS105 3.7 31.1 1.0
HA B:GLU102 3.8 28.9 1.0
C2 B:PLM404 3.8 54.7 1.0
OE1 B:GLU202 3.9 45.9 1.0
HA B:GLU69 4.0 37.1 1.0
H22 B:PLM404 4.1 65.7 1.0
H31 B:PLM404 4.3 53.8 1.0
HD22 B:LEU72 4.3 51.5 1.0
HE1 B:HIS205 4.3 36.2 1.0
HG B:LEU198 4.3 43.1 1.0
NE2 B:HIS105 4.3 32.4 1.0
H32 B:PLM404 4.3 53.8 1.0
CG B:GLU69 4.4 34.5 1.0
HB3 B:GLU69 4.4 40.5 1.0
OH B:TYR175 4.4 34.9 1.0
C3 B:PLM404 4.4 44.8 1.0
CD2 B:HIS105 4.4 33.5 1.0
CG B:GLU102 4.4 31.1 1.0
HH B:TYR175 4.5 41.9 1.0
HD23 B:LEU72 4.5 51.5 1.0
H21 B:PLM404 4.5 65.7 1.0
HB3 B:GLU102 4.6 31.9 1.0
CA B:GLU102 4.6 24.1 1.0
HD23 B:LEU198 4.6 45.1 1.0
OE2 B:GLU202 4.7 30.4 1.0
CD B:GLU202 4.7 38.6 1.0
CB B:GLU69 4.8 33.8 1.0
CB B:GLU102 4.8 26.6 1.0
CA B:GLU69 4.8 30.9 1.0
HG3 B:GLU69 4.8 41.4 1.0
CD2 B:LEU72 4.8 42.9 1.0
HB2 B:LEU72 4.9 41.5 1.0
HG2 B:GLU102 4.9 37.4 1.0
CE1 B:HIS205 4.9 30.2 1.0
ND1 B:HIS205 4.9 36.8 1.0
HG2 B:GLU167 5.0 38.6 1.0

Manganese binding site 4 out of 4 in 6f6h

Go back to Manganese Binding Sites List in 6f6h
Manganese binding site 4 out of 4 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 Manganese with other atoms in the Mn binding site number 4 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:Mn402

b:75.5
occ:0.79
 O B:HOH550 2.2 55.9 1.0
NE2 B:HIS130 2.3 48.8 1.0
CE1 B:HIS130 3.2 48.8 1.0
CD2 B:HIS130 3.3 48.0 1.0
HE1 B:HIS130 3.4 58.6 1.0
HD2 B:HIS130 3.4 57.6 1.0
O B:HOH515 4.2 50.3 1.0
ND1 B:HIS130 4.3 51.6 1.0
CG B:HIS130 4.4 46.6 1.0
OD2 B:ASP129 4.4 60.0 1.0
OD1 B:ASP129 4.4 51.9 1.0
O B:HOH546 4.8 44.4 1.0
HA3 B:GLY240 4.8 61.0 1.0
CG B:ASP129 4.9 53.6 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: Sun Oct 6 04:33:21 2024

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