Sodium in PDB 3aga: Crystal Structure of Rcc-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana

All present enzymatic activity of Crystal Structure of Rcc-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana:
1.3.1.80;

The structure of Crystal Structure of Rcc-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3aga 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)	19.96 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.500, 85.640, 133.300, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 29.9

The binding sites of Sodium atom in the Crystal Structure of Rcc-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana (pdb code 3aga). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rcc-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana, PDB code: 3aga:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Rcc-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 Crystal Structure of Rcc-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:64.9 occ:1.00 O A:LEU199 2.2 68.4 1.0 O A:VAL204 2.3 61.3 1.0 O A:LEU201 2.6 60.3 1.0 C A:LEU199 3.5 67.4 1.0 C A:VAL204 3.5 59.8 1.0 C A:LEU201 3.6 61.6 1.0 OD1 A:ASN205 3.7 63.2 1.0 O A:HOH23 3.8 55.2 1.0 O A:LYS200 3.8 70.2 1.0 C A:LYS200 4.0 68.9 1.0 O A:PRO202 4.0 62.7 1.0 CA A:PRO202 4.1 59.7 1.0 N A:PRO202 4.2 61.5 1.0 C A:PRO202 4.2 60.4 1.0 N A:VAL204 4.3 58.8 1.0 CA A:LEU199 4.3 65.3 1.0 CA A:VAL204 4.3 59.2 1.0 N A:LEU201 4.3 66.4 1.0 CG A:ASN205 4.4 62.4 1.0 N A:LYS200 4.4 68.4 1.0 CB A:VAL204 4.5 59.5 1.0 CA A:LYS200 4.5 69.3 1.0 N A:ASN205 4.5 59.2 1.0 CA A:LEU201 4.6 62.8 1.0 CD1 A:LEU199 4.6 62.5 1.0 CA A:ASN205 4.6 59.1 1.0 CG A:LEU199 4.9 62.6 1.0 CB A:LEU199 4.9 63.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Rcc-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 Crystal Structure of Rcc-Bound Red Chlorophyll Catabolite Reductase From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:82.0 occ:1.00 O B:HOH22 2.1 46.5 1.0 O B:LEU199 2.5 65.6 1.0 O B:LEU201 2.6 76.1 1.0 O B:VAL204 2.9 72.7 1.0 O B:LYS200 3.3 74.4 1.0 C B:LEU201 3.4 76.2 1.0 C B:LEU199 3.7 67.2 1.0 C B:LYS200 3.7 73.8 1.0 CA B:PRO202 3.9 78.4 1.0 O B:PRO202 3.9 76.7 1.0 N B:PRO202 3.9 78.4 1.0 C B:VAL204 4.1 73.3 1.0 C B:PRO202 4.1 77.8 1.0 N B:LEU201 4.3 74.5 1.0 CA B:LYS200 4.3 72.5 1.0 CA B:LEU201 4.5 74.4 1.0 N B:LYS200 4.5 69.7 1.0 OD1 B:ASN205 4.6 75.2 1.0 N B:VAL204 4.6 76.6 1.0 CA B:LEU199 4.7 66.7 1.0 CA B:VAL204 4.8 74.2 1.0 CG B:ASN205 5.0 75.0 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