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Manganese in PDB 5dcr: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak)

Enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak)

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak):
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak), PDB code: 5dcr 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) 48.66 / 2.11
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.190, 97.339, 129.764, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 21.2

Other elements in 5dcr:

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak) 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 with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak) (pdb code 5dcr). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak), PDB code: 5dcr:

Manganese binding site 1 out of 1 in 5dcr

Go back to Manganese Binding Sites List in 5dcr
Manganese binding site 1 out of 1 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak)


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 with Aerobically Reconstituted Mn/Fe Cofactor (Short Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:36.2
occ:1.00
 O1 A:PLM403 1.7 49.8 1.0
OE2 A:GLU69 2.2 39.6 1.0
ND1 A:HIS105 2.2 26.3 1.0
OE2 A:GLU102 2.2 33.3 1.0
O A:HOH512 2.3 45.1 1.0
O A:HOH502 2.3 44.1 1.0
C1 A:PLM403 2.7 49.5 1.0
CE1 A:HIS105 3.0 31.6 1.0
HE1 A:HIS105 3.1 38.0 1.0
CD A:GLU69 3.1 42.0 1.0
CD A:GLU102 3.2 38.0 1.0
O2 A:PLM403 3.3 47.0 1.0
CG A:HIS105 3.3 32.7 1.0
OE1 A:GLU69 3.4 51.0 1.0
HB2 A:HIS105 3.5 39.4 1.0
FE A:FE402 3.5 37.4 1.0
OE1 A:GLU102 3.5 38.4 1.0
HB3 A:HIS105 3.6 39.4 1.0
CB A:HIS105 3.7 32.8 1.0
HA A:GLU102 3.8 37.4 1.0
OE1 A:GLU202 4.0 50.9 1.0
HG21 A:VAL72 4.0 44.5 1.0
C2 A:PLM403 4.1 37.9 1.0
H32 A:PLM403 4.1 56.6 1.0
HE1 A:HIS205 4.1 45.4 1.0
HG A:LEU198 4.1 42.2 1.0
HA A:GLU69 4.2 43.7 1.0
NE2 A:HIS105 4.2 33.1 1.0
H31 A:PLM403 4.3 56.6 1.0
CD2 A:HIS105 4.3 31.0 1.0
C3 A:PLM403 4.4 47.2 1.0
OH A:TYR175 4.5 41.8 1.0
HH A:TYR175 4.5 50.2 1.0
CG A:GLU69 4.5 41.0 1.0
H22 A:PLM403 4.6 45.5 1.0
CG A:GLU102 4.6 28.9 1.0
HB3 A:GLU69 4.6 43.9 1.0
HB3 A:GLU102 4.6 36.8 1.0
OE2 A:GLU202 4.7 39.7 1.0
CA A:GLU102 4.7 31.2 1.0
CG2 A:VAL72 4.7 37.0 1.0
CD A:GLU202 4.7 49.3 1.0
HD23 A:LEU198 4.7 44.3 1.0
HG23 A:VAL72 4.8 44.5 1.0
CE1 A:HIS205 4.8 37.8 1.0
H21 A:PLM403 4.8 45.5 1.0
HG22 A:VAL72 4.8 44.5 1.0
ND1 A:HIS205 4.8 32.0 1.0
CB A:GLU102 4.9 30.6 1.0
HG3 A:GLU69 4.9 49.3 1.0
CB A:GLU69 4.9 36.6 1.0
HE2 A:HIS105 4.9 39.7 1.0
CA A:GLU69 5.0 36.4 1.0

Reference:

J.J.Griese, R.Kositzki, P.Schrapers, R.M.Branca, A.Nordstrom, J.Lehtio, M.Haumann, M.Hogbom. Structural Basis For Oxygen Activation at A Heterodinuclear Manganese/Iron Cofactor. J.Biol.Chem. V. 290 25254 2015.
ISSN: ESSN 1083-351X
PubMed: 26324712
DOI: 10.1074/JBC.M115.675223
Page generated: Sat Oct 5 23:53:57 2024

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