Sodium in PDB 2zxk: Crystal Structure of Semet-Red Chlorophyll Catabolite Reductase

All present enzymatic activity of Crystal Structure of Semet-Red Chlorophyll Catabolite Reductase:
1.3.1.80;

The structure of Crystal Structure of Semet-Red Chlorophyll Catabolite Reductase, PDB code: 2zxk was solved by M.Sugishima, Y.Kitamori, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.48 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.978, 83.539, 120.404, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 29.1

The binding sites of Sodium atom in the Crystal Structure of Semet-Red Chlorophyll Catabolite Reductase (pdb code 2zxk). 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 Semet-Red Chlorophyll Catabolite Reductase, PDB code: 2zxk:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Semet-Red Chlorophyll Catabolite Reductase


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 Semet-Red Chlorophyll Catabolite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1 b:39.4 occ:1.00 O A:HOH320 2.2 43.1 1.0 O A:VAL204 2.4 14.1 1.0 O A:LEU199 2.5 23.0 1.0 O A:LEU201 2.6 19.1 1.0 C A:VAL204 3.6 14.8 1.0 C A:LEU199 3.7 24.0 1.0 C A:LEU201 3.7 19.6 1.0 N A:VAL204 4.2 15.9 1.0 OD1 A:ASN205 4.3 15.8 1.0 CA A:VAL204 4.3 14.5 1.0 CA A:PRO202 4.3 17.8 1.0 C A:LYS200 4.3 23.7 1.0 CD2 A:LEU199 4.4 21.7 1.0 O A:LYS200 4.4 24.0 1.0 CA A:LEU199 4.5 24.4 1.0 N A:PRO202 4.5 19.0 1.0 C A:PRO202 4.5 17.3 1.0 CB A:VAL204 4.5 14.6 1.0 N A:LEU201 4.5 22.1 1.0 O A:PRO202 4.5 15.7 1.0 N A:LYS200 4.7 24.2 1.0 CA A:LEU201 4.7 20.4 1.0 N A:ASN205 4.7 14.0 1.0 CA A:LYS200 4.8 24.4 1.0 CG A:ASN205 4.8 15.7 1.0 CA A:ASN205 4.9 15.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Semet-Red Chlorophyll Catabolite Reductase


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 Semet-Red Chlorophyll Catabolite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2 b:40.9 occ:1.00 O B:VAL204 2.1 26.7 1.0 O B:LEU201 2.6 29.5 1.0 O B:LEU199 2.6 27.5 1.0 O B:HOH320 2.9 43.2 1.0 C B:VAL204 3.2 27.1 1.0 C B:LEU201 3.6 30.0 1.0 C B:LEU199 3.7 28.1 1.0 N B:VAL204 3.8 28.4 1.0 CA B:VAL204 4.0 27.4 1.0 CB B:VAL204 4.2 27.6 1.0 CA B:PRO202 4.2 30.8 1.0 OD1 B:ASN205 4.2 26.3 1.0 C B:PRO202 4.2 30.7 1.0 N B:LEU201 4.3 28.7 1.0 N B:ASN205 4.3 26.7 1.0 N B:PRO202 4.3 30.4 1.0 CA B:LEU199 4.3 28.4 1.0 O B:PRO202 4.4 31.8 1.0 CD1 B:LEU199 4.5 26.5 1.0 CA B:LEU201 4.5 29.3 1.0 C B:LYS200 4.6 28.9 1.0 CA B:ASN205 4.6 25.9 1.0 N B:GLU203 4.7 30.5 1.0 N B:LYS200 4.7 28.2 1.0 CG B:LEU199 4.8 27.1 1.0 CG B:ASN205 4.8 26.8 1.0 C B:GLU203 4.9 29.4 1.0 CG1 B:VAL204 4.9 28.5 1.0 O B:LYS200 5.0 29.3 1.0

M.Sugishima, Y.Kitamori, M.Noguchi, T.Kohchi, K.Fukuyama. Crystal Structure of Red Chlorophyll Catabolite Reductase: Enlargement of the Ferredoxin-Dependent Bilin Reductase Family J.Mol.Biol. V. 389 376 2009.
ISSN: ISSN 0022-2836
PubMed: 19374909
DOI: 10.1016/J.JMB.2009.04.017