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Sodium in PDB 4hr0: R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor

Enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor

All present enzymatic activity of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor:
1.17.4.1;

Protein crystallography data

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor, PDB code: 4hr0 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) 39.15 / 1.90
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.150, 97.738, 130.850, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.6

Other elements in 4hr0:

The structure of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor (pdb code 4hr0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor, PDB code: 4hr0:

Sodium binding site 1 out of 1 in 4hr0

Go back to Sodium Binding Sites List in 4hr0
Sodium binding site 1 out of 1 in the R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of R2-Like Ligand-Binding Oxidase with Aerobically Reconstituted Metal Cofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:20.9
occ:1.00
 O A:MET121 2.6 32.4 1.0
OE1 A:GLN113 2.6 31.2 1.0
O A:GLY119 2.7 32.9 1.0
HA2 A:GLY119 3.3 33.1 1.0
O A:ILE118 3.4 29.5 1.0
C A:GLY119 3.5 36.6 1.0
HG A:LEU123 3.6 40.3 1.0
C A:MET121 3.8 39.4 1.0
CD A:GLN113 3.9 38.0 1.0
CA A:GLY119 3.9 33.1 1.0
H A:MET121 4.1 34.9 1.0
HA A:ASP122 4.1 39.9 1.0
H A:LEU123 4.1 32.1 1.0
N A:MET121 4.3 34.9 1.0
HB3 A:GLN113 4.3 26.2 1.0
HD12 A:LEU123 4.4 43.6 1.0
HE22 A:GLN113 4.4 31.0 1.0
C A:ILE118 4.4 34.1 1.0
HD11 A:LEU123 4.5 43.6 1.0
HB3 A:MET121 4.5 38.5 1.0
CG A:LEU123 4.5 40.3 1.0
N A:GLN120 4.5 33.7 1.0
CA A:MET121 4.5 38.4 1.0
NE2 A:GLN113 4.6 31.0 1.0
HA3 A:GLY119 4.7 33.1 1.0
N A:GLY119 4.7 35.1 1.0
CD1 A:LEU123 4.7 43.6 1.0
C A:GLN120 4.7 39.2 1.0
N A:ASP122 4.7 34.6 1.0
N A:LEU123 4.8 32.1 1.0
HG13 A:ILE118 4.8 35.9 1.0
CA A:ASP122 4.9 39.9 1.0
CG A:GLN113 5.0 25.7 1.0

Reference:

J.J.Griese, K.Roos, N.Cox, H.S.Shafaat, R.M.M.Branca, J.Lehtio, A.Graslund, W.Lubitz, P.E.M.Siegbahn, M.Hogbom. Direct Observation of Structurally Encoded Metal Discrimination and Ether Bond Formation in A Heterodinuclear Metalloprotein Proc.Natl.Acad.Sci.Usa V. 110 17189 2013.
ISSN: ISSN 0027-8424
PubMed: 24101498
DOI: 10.1073/PNAS.1304368110
Page generated: Tue Dec 15 06:43:43 2020

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