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Sodium in PDB 5aog: Structure of Sorghum Peroxidase

Enzymatic activity of Structure of Sorghum Peroxidase

All present enzymatic activity of Structure of Sorghum Peroxidase:
1.11.1.7;

Protein crystallography data

The structure of Structure of Sorghum Peroxidase, PDB code: 5aog was solved by H.Kwon, C.I.Nnamchi, G.Parkin, I.Efimov, J.Agirre, J.Basran, E.L.Raven, P.C.E.Moody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.36 / 1.27
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.620, 58.620, 208.410, 90.00, 90.00, 120.00
R / Rfree (%) 13.612 / 15.931

Other elements in 5aog:

The structure of Structure of Sorghum Peroxidase also contains other interesting chemical elements:

Iron (Fe) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Sorghum Peroxidase (pdb code 5aog). 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 Structure of Sorghum Peroxidase, PDB code: 5aog:

Sodium binding site 1 out of 1 in 5aog

Go back to Sodium Binding Sites List in 5aog
Sodium binding site 1 out of 1 in the Structure of Sorghum Peroxidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Sorghum Peroxidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1343

b:19.2
occ:1.00
O A:VAL85 2.3 20.3 1.0
OD1 A:ASP82 2.4 19.3 1.0
O A:GLY87 2.4 18.1 1.0
OD1 A:ASP89 2.5 19.2 1.0
O A:ASP82 2.5 17.7 1.0
OG A:SER91 2.6 20.5 1.0
CG A:ASP82 3.2 18.5 1.0
C A:ASP82 3.4 16.3 1.0
C A:VAL85 3.5 20.0 1.0
CG A:ASP89 3.5 19.1 1.0
C A:GLY87 3.6 17.8 1.0
N A:GLY87 3.7 21.2 1.0
CB A:SER91 3.7 19.0 1.0
N A:SER91 3.7 18.4 1.0
OD2 A:ASP82 3.7 18.0 1.0
CA A:ASP82 3.9 16.9 1.0
OD2 A:ASP89 4.0 21.7 1.0
N A:ASP89 4.1 16.7 1.0
CB A:ASP82 4.2 18.0 1.0
CA A:SER91 4.2 19.3 1.0
CA A:GLY87 4.3 20.7 1.0
N A:ALA90 4.3 16.7 1.0
CB A:GLN86 4.3 23.1 1.0
N A:VAL92 4.4 18.2 1.0
N A:GLN86 4.4 20.6 1.0
CA A:VAL85 4.4 19.7 1.0
C A:GLN86 4.5 25.3 1.0
CG1 A:VAL92 4.5 22.7 1.0
N A:CYS83 4.5 17.0 1.0
CB A:VAL85 4.5 20.6 1.0
OE1 A:GLN86 4.6 27.1 1.0
CA A:GLN86 4.6 21.2 1.0
N A:CYS88 4.6 18.2 1.0
C A:ASP89 4.6 17.8 1.0
CB A:ASP89 4.7 18.0 1.0
N A:VAL85 4.7 19.6 1.0
CA A:ASP89 4.7 17.0 1.0
C A:ALA90 4.7 17.5 1.0
C A:SER91 4.8 19.0 1.0
CA A:CYS88 4.8 16.9 1.0
CA A:CYS83 4.9 17.7 1.0
CA A:ALA90 4.9 17.0 1.0
CG1 A:VAL85 4.9 24.2 1.0
C A:CYS88 5.0 16.8 1.0

Reference:

C.I.Nnamchi, G.Parkin, I.Efimov, J.Basran, H.Kwon, D.A.Svistunenko, J.Agirre, B.N.Okolo, A.Moneke, B.C.Nwanguma, P.C.E.Moody, E.L.Raven. Structural and Spectroscopic Characterisation of A Heme Peroxidase From Sorghum. J.Biol.Inorg.Chem. V. 21 63 2016.
ISSN: ISSN 0949-8257
PubMed: 26666777
DOI: 10.1007/S00775-015-1313-Z
Page generated: Tue Dec 15 10:23:29 2020

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