Sodium in PDB 3agb: F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana

All present enzymatic activity of F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana:
1.3.1.80;

The structure of F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3agb was solved by M.Sugishima, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.58 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.141, 84.431, 132.248, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 29.2

The binding sites of Sodium atom in the F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana (pdb code 3agb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3agb:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:34.0 occ:1.00 O A:LEU199 2.3 22.4 1.0 O A:VAL204 2.4 13.2 1.0 O A:LEU201 2.4 18.2 1.0 O A:HOH344 2.6 28.2 1.0 O A:HOH345 2.6 42.0 1.0 C A:LEU201 3.4 18.9 1.0 C A:LEU199 3.5 22.6 1.0 C A:VAL204 3.6 13.3 1.0 C A:LYS200 4.1 21.4 1.0 OD1 A:ASN205 4.1 15.0 1.0 N A:LEU201 4.1 20.5 1.0 N A:PRO202 4.1 18.1 1.0 CA A:PRO202 4.2 17.6 1.0 O A:LYS200 4.2 21.4 1.0 N A:VAL204 4.3 14.2 1.0 CA A:VAL204 4.3 13.6 1.0 CA A:LEU199 4.4 22.7 1.0 C A:PRO202 4.4 17.1 1.0 O A:PRO202 4.4 17.3 1.0 CA A:LEU201 4.4 19.6 1.0 N A:LYS200 4.5 22.2 1.0 CA A:LYS200 4.5 22.2 1.0 CD1 A:LEU199 4.6 22.6 1.0 N A:ASN205 4.6 12.7 1.0 CB A:VAL204 4.6 13.6 1.0 CA A:ASN205 4.8 12.9 1.0 CG A:ASN205 4.9 14.1 1.0 CG A:LEU199 5.0 23.6 1.0

Sodium binding site 2 out of 2 in the F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of F218V Mutant of the Substrate-Free Form of Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:41.5 occ:1.00 O B:HOH340 2.3 37.5 1.0 O B:HOH328 2.4 30.1 1.0 O B:LEU199 2.4 25.9 1.0 O B:VAL204 2.5 24.1 1.0 O B:HOH341 2.5 39.4 1.0 O B:LEU201 2.7 27.1 1.0 C B:LEU199 3.6 26.2 1.0 C B:LEU201 3.7 26.7 1.0 C B:VAL204 3.7 23.7 1.0 O B:LYS200 4.0 27.5 1.0 CA B:PRO202 4.1 26.0 1.0 O B:PRO202 4.2 25.5 1.0 C B:LYS200 4.2 27.3 1.0 C B:PRO202 4.2 25.5 1.0 N B:PRO202 4.3 26.3 1.0 N B:VAL204 4.4 24.3 1.0 OD1 B:ASN205 4.4 26.2 1.0 CA B:LEU199 4.4 26.1 1.0 N B:LEU201 4.5 27.1 1.0 CA B:VAL204 4.5 23.9 1.0 N B:LYS200 4.6 26.7 1.0 N B:ASN205 4.7 23.2 1.0 CD1 B:LEU199 4.7 25.5 1.0 CG B:ASN205 4.7 24.7 1.0 CA B:LEU201 4.8 27.1 1.0 CA B:LYS200 4.8 27.2 1.0 CA B:ASN205 4.8 22.8 1.0 ND2 B:ASN205 4.9 25.7 1.0 CB B:VAL204 4.9 23.8 1.0 N B:GLU203 5.0 25.4 1.0

M.Sugishima, Y.Okamoto, M.Noguchi, T.Kohchi, H.Tamiaki, K.Fukuyama. Crystal Structures of the Substrate-Bound Forms of Red Chlorophyll Catabolite Reductase: Implications For Site-Specific and Stereospecific Reaction J.Mol.Biol. V. 402 879 2010.
ISSN: ISSN 0022-2836
PubMed: 20727901
DOI: 10.1016/J.JMB.2010.08.021