Atomistry » Manganese » PDB 6f4q-6fxr » 6f6h
Atomistry »
  Manganese »
    PDB 6f4q-6fxr »
      6f6h »

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

Go back to Manganese Binding Sites List in 6f6h
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy