Sodium in PDB 3agc: F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana

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

The structure of F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3agc 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)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.089, 84.321, 131.518, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 27

The binding sites of Sodium atom in the F218V Mutant of the Substrate-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana (pdb code 3agc). 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-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3agc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the F218V Mutant of the Substrate-Bound 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-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:29.0 occ:1.00 O A:VAL204 2.3 12.4 1.0 O A:HOH383 2.3 32.1 1.0 O A:HOH351 2.4 34.4 1.0 O A:LEU199 2.4 18.1 1.0 O A:LEU201 2.5 15.9 1.0 O A:HOH365 2.6 39.7 1.0 C A:VAL204 3.5 12.7 1.0 C A:LEU201 3.5 16.1 1.0 C A:LEU199 3.5 18.0 1.0 OD1 A:ASN205 4.1 14.2 1.0 C A:LYS200 4.2 17.9 1.0 O A:PRO202 4.2 14.9 1.0 N A:VAL204 4.2 12.9 1.0 CA A:PRO202 4.2 15.3 1.0 N A:LEU201 4.2 17.2 1.0 N A:PRO202 4.2 15.9 1.0 C A:PRO202 4.3 15.0 1.0 CA A:VAL204 4.3 12.7 1.0 O A:LYS200 4.3 18.1 1.0 CA A:LEU199 4.4 17.8 1.0 O A:HOH355 4.5 48.0 1.0 CA A:LEU201 4.5 16.6 1.0 N A:LYS200 4.5 18.1 1.0 N A:ASN205 4.5 12.6 1.0 CB A:VAL204 4.6 12.5 1.0 CA A:LYS200 4.6 18.3 1.0 CD1 A:LEU199 4.6 16.7 1.0 CA A:ASN205 4.7 12.7 1.0 CG A:ASN205 4.8 13.4 1.0

Sodium binding site 2 out of 2 in the F218V Mutant of the Substrate-Bound 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-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:35.6 occ:1.00 O B:HOH328 2.3 30.0 1.0 O B:LEU199 2.3 17.1 1.0 O B:HOH329 2.3 33.5 1.0 O B:VAL204 2.4 16.0 1.0 O B:HOH327 2.4 33.5 1.0 O B:LEU201 2.5 18.3 1.0 C B:LEU199 3.4 17.3 1.0 C B:LEU201 3.5 18.1 1.0 C B:VAL204 3.6 16.2 1.0 O B:PRO202 4.1 17.7 1.0 CA B:PRO202 4.1 17.7 1.0 C B:LYS200 4.2 18.4 1.0 ND2 B:ASN205 4.2 15.3 1.0 O B:HOH340 4.2 42.0 1.0 CA B:LEU199 4.2 17.0 1.0 N B:PRO202 4.2 17.8 1.0 C B:PRO202 4.2 17.4 1.0 N B:LEU201 4.2 18.4 1.0 N B:VAL204 4.3 16.8 1.0 O B:LYS200 4.3 18.7 1.0 CA B:VAL204 4.3 16.4 1.0 N B:LYS200 4.5 17.8 1.0 CA B:LEU201 4.5 18.3 1.0 CB B:VAL204 4.6 16.3 1.0 N B:ASN205 4.6 15.7 1.0 CA B:LYS200 4.7 18.4 1.0 CD2 B:LEU199 4.7 16.8 1.0 CA B:ASN205 4.8 15.5 1.0 CB B:LEU199 4.8 17.2 1.0 CG B:ASN205 4.9 16.3 1.0 N B:GLU203 4.9 17.5 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