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Manganese in PDB 6f6c: R2-Like Ligand-Binding Oxidase V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6c 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) 43.57 / 1.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.462, 55.818, 69.741, 90.00, 114.09, 90.00
R / Rfree (%) 18 / 22.3

Other elements in 6f6c:

The structure of R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor (pdb code 6f6c). 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor, PDB code: 6f6c:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6f6c

Go back to Manganese Binding Sites List in 6f6c
Manganese binding site 1 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:61.8
occ:0.63
 NE2 A:HIS130 2.2 48.9 1.0
O A:HOH549 2.4 59.0 1.0
CD2 A:HIS130 3.1 47.8 1.0
HD2 A:HIS130 3.2 57.3 1.0
CE1 A:HIS130 3.3 50.9 1.0
HE1 A:HIS130 3.5 61.1 1.0
OD2 A:ASP129 4.2 63.2 1.0
O A:HOH562 4.2 45.2 1.0
OD1 A:ASP129 4.2 47.2 1.0
CG A:HIS130 4.3 46.9 1.0
ND1 A:HIS130 4.3 45.9 1.0
CG A:ASP129 4.7 50.4 1.0
O A:HOH545 4.7 47.4 1.0
HA3 A:GLY240 4.8 49.8 1.0

Manganese binding site 2 out of 4 in 6f6c

Go back to Manganese Binding Sites List in 6f6c
Manganese binding site 2 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:29.4
occ:1.00
 O1 A:PLM404 1.8 41.6 1.0
OE1 A:GLU69 2.1 30.1 1.0
OE1 A:GLU102 2.1 31.2 1.0
ND1 A:HIS105 2.2 21.6 1.0
O A:HOH501 2.4 40.3 1.0
O A:HOH502 2.4 37.8 1.0
C1 A:PLM404 2.9 42.6 1.0
CE1 A:HIS105 3.0 29.3 1.0
HE1 A:HIS105 3.0 35.1 1.0
CD A:GLU69 3.1 36.6 1.0
CD A:GLU102 3.2 31.8 1.0
CG A:HIS105 3.3 27.8 1.0
OE2 A:GLU69 3.4 36.3 1.0
FE A:FE403 3.4 33.7 1.0
H32 A:PLM404 3.4 44.6 1.0
OE2 A:GLU102 3.5 30.9 1.0
HB2 A:HIS105 3.6 31.7 1.0
O2 A:PLM404 3.6 51.8 1.0
HB3 A:HIS105 3.6 31.7 1.0
HA A:GLU102 3.7 33.6 1.0
CB A:HIS105 3.7 26.4 1.0
C2 A:PLM404 3.9 44.1 1.0
OE1 A:GLU202 3.9 42.3 1.0
HG A:LEU198 4.1 35.2 1.0
H21 A:PLM404 4.1 52.9 1.0
HA A:GLU69 4.2 34.0 1.0
NE2 A:HIS105 4.2 28.2 1.0
C3 A:PLM404 4.2 37.1 1.0
HE1 A:HIS205 4.3 35.2 1.0
CD2 A:HIS105 4.3 27.0 1.0
OE2 A:GLU202 4.3 34.3 1.0
CG A:GLU69 4.4 34.0 1.0
HH A:TYR175 4.5 46.1 1.0
OH A:TYR175 4.5 38.4 1.0
CD A:GLU202 4.5 39.9 1.0
CG A:GLU102 4.5 27.5 1.0
CA A:GLU102 4.6 28.0 1.0
HB3 A:GLU69 4.6 34.5 1.0
HB3 A:ALA72 4.6 37.3 1.0
HB3 A:GLU102 4.6 30.3 1.0
H31 A:PLM404 4.7 44.6 1.0
HB1 A:ALA72 4.8 37.3 1.0
HG3 A:GLU69 4.8 40.8 1.0
HD23 A:LEU198 4.8 35.1 1.0
CB A:GLU102 4.8 25.2 1.0
CE1 A:HIS205 4.9 29.4 1.0
H22 A:PLM404 4.9 52.9 1.0
ND1 A:HIS205 4.9 37.9 1.0
CB A:GLU69 4.9 28.7 1.0
HE2 A:HIS105 4.9 33.8 1.0
CG A:LEU198 5.0 29.3 1.0
CA A:GLU69 5.0 28.3 1.0
HB2 A:ALA72 5.0 37.3 1.0
HG2 A:GLU102 5.0 33.0 1.0

Manganese binding site 3 out of 4 in 6f6c

Go back to Manganese Binding Sites List in 6f6c
Manganese binding site 3 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:31.6
occ:1.00
 O1 B:PLM404 1.7 56.1 1.0
OE1 B:GLU69 2.1 33.0 1.0
OE1 B:GLU102 2.1 34.2 1.0
O B:HOH524 2.1 34.4 1.0
ND1 B:HIS105 2.2 26.6 1.0
O B:HOH501 2.3 40.0 1.0
C1 B:PLM404 2.7 42.1 1.0
CE1 B:HIS105 3.0 29.3 1.0
HE1 B:HIS105 3.1 35.1 1.0
CD B:GLU102 3.1 28.9 1.0
CD B:GLU69 3.1 34.5 1.0
O2 B:PLM404 3.2 52.3 1.0
CG B:HIS105 3.3 27.5 1.0
FE B:FE403 3.4 35.2 1.0
OE2 B:GLU102 3.5 31.4 1.0
OE2 B:GLU69 3.5 38.1 1.0
HB2 B:HIS105 3.5 36.6 1.0
HB3 B:HIS105 3.6 36.6 1.0
HA B:GLU102 3.7 27.1 1.0
CB B:HIS105 3.7 30.5 1.0
OE1 B:GLU202 3.9 53.5 1.0
C2 B:PLM404 3.9 39.3 1.0
H21 B:PLM404 3.9 47.2 1.0
H32 B:PLM404 4.2 51.6 1.0
HA B:GLU69 4.2 33.6 1.0
NE2 B:HIS105 4.2 30.8 1.0
HE1 B:HIS205 4.2 38.7 1.0
HG B:LEU198 4.2 44.2 1.0
CD2 B:HIS105 4.4 25.8 1.0
CG B:GLU102 4.5 27.6 1.0
CG B:GLU69 4.5 31.0 1.0
OE2 B:GLU202 4.5 33.3 1.0
HH B:TYR175 4.5 48.4 1.0
OH B:TYR175 4.5 40.3 1.0
CD B:GLU202 4.5 43.1 1.0
HB3 B:GLU69 4.5 35.3 1.0
CA B:GLU102 4.6 22.6 1.0
HB3 B:GLU102 4.6 27.6 1.0
C3 B:PLM404 4.6 43.0 1.0
HD23 B:LEU198 4.7 39.8 1.0
HB3 B:ALA72 4.7 36.6 1.0
H22 B:PLM404 4.7 47.2 1.0
CB B:GLU102 4.8 23.0 1.0
HG3 B:GLU69 4.8 37.2 1.0
ND1 B:HIS205 4.8 34.9 1.0
CE1 B:HIS205 4.8 32.3 1.0
HB1 B:ALA72 4.9 36.6 1.0
CB B:GLU69 4.9 29.4 1.0
HG2 B:GLU102 4.9 33.2 1.0
HE2 B:HIS105 5.0 36.9 1.0
CA B:GLU69 5.0 28.0 1.0
HG2 B:GLU167 5.0 35.6 1.0

Manganese binding site 4 out of 4 in 6f6c

Go back to Manganese Binding Sites List in 6f6c
Manganese binding site 4 out of 4 in the R2-Like Ligand-Binding Oxidase V72A 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 V72A Mutant with Aerobically Reconstituted Mn/Fe Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:64.2
occ:0.72
 NE2 B:HIS130 2.2 47.2 1.0
O B:HOH571 2.2 54.1 1.0
O B:HOH511 2.4 50.5 1.0
CE1 B:HIS130 3.1 49.0 1.0
CD2 B:HIS130 3.2 46.1 1.0
HE1 B:HIS130 3.3 58.8 1.0
HD2 B:HIS130 3.3 55.4 1.0
O B:HOH534 4.0 41.5 1.0
ND1 B:HIS130 4.3 46.0 1.0
CG B:HIS130 4.3 43.1 1.0
OD1 B:ASP129 4.3 50.4 1.0
OD2 B:ASP129 4.3 54.7 1.0
HA3 B:GLY240 4.7 49.6 1.0
O B:HOH560 4.7 44.6 1.0
CG B:ASP129 4.8 53.3 1.0
HA2 B:GLY240 5.0 49.6 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 04:32:28 2024

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