Sodium in PDB 2ddc: Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process

The structure of Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process, PDB code: 2ddc was solved by H.Shimizu, H.Tsutsui, N.Nukina, A.Miyawaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	97.629, 119.286, 49.068, 90.00, 120.18, 90.00
R / Rfree (%)	19 / 21.2

The structure of Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process (pdb code 2ddc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process, PDB code: 2ddc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1301 b:14.7 occ:1.00 O A:HOH1491 3.1 36.9 1.0 N A:ASP190 3.2 14.8 1.0 N A:VAL76 3.3 16.7 1.0 O A:HOH1472 3.4 35.2 1.0 CG2 A:VAL76 3.7 18.6 1.0 CA A:PRO189 3.8 13.7 1.0 CB A:VAL76 3.8 18.3 1.0 CA A:ILE75 3.9 18.0 1.0 C A:PRO189 4.0 14.4 1.0 CB A:ASP190 4.0 16.3 1.0 CB A:PRO189 4.0 13.3 1.0 CG A:ASP190 4.1 20.5 1.0 C A:ILE75 4.1 16.4 1.0 CG2 A:ILE75 4.1 17.0 1.0 CA A:VAL76 4.1 16.1 1.0 CA A:ASP190 4.2 15.4 1.0 O A:GLU74 4.2 23.4 1.0 OD2 A:ASP190 4.2 29.2 1.0 OD1 A:ASP190 4.6 23.2 1.0 CB A:ILE75 4.6 17.6 1.0 O A:HOH1499 4.6 37.9 1.0 O A:ASP190 4.6 13.6 1.0 C A:ASP190 4.8 14.5 1.0 O A:VAL76 5.0 14.9 1.0

Sodium binding site 2 out of 2 in the Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Unique Behavior of A Histidine Responsible For An Engineered Green-to- Red Photoconversion Process within 5.0Å range: probe atom residue distance (Å) B Occ B:Na2301 b:14.4 occ:1.00 O B:HOH2495 3.0 36.7 1.0 O B:HOH2510 3.2 38.4 1.0 N B:ASP190 3.2 14.1 1.0 N B:VAL76 3.2 15.9 1.0 O B:HOH2490 3.3 36.5 1.0 CG2 B:VAL76 3.7 18.2 1.0 CA B:PRO189 3.8 13.9 1.0 CB B:VAL76 3.8 17.6 1.0 CA B:ILE75 3.9 16.8 1.0 CB B:ASP190 4.0 17.2 1.0 C B:PRO189 4.0 13.6 1.0 CG B:ASP190 4.1 20.4 1.0 C B:ILE75 4.1 15.8 1.0 CB B:PRO189 4.1 14.3 1.0 CG2 B:ILE75 4.1 16.2 1.0 CA B:VAL76 4.1 16.1 1.0 CA B:ASP190 4.2 14.3 1.0 O B:GLU74 4.2 23.1 1.0 OD2 B:ASP190 4.4 27.6 1.0 OD1 B:ASP190 4.4 25.2 1.0 CB B:ILE75 4.5 18.0 1.0 O B:ASP190 4.6 14.2 1.0 O B:HOH2519 4.7 38.9 1.0 C B:ASP190 4.8 14.2 1.0 O B:VAL76 4.9 15.8 1.0 N B:ILE75 5.0 17.8 1.0

H.Tsutsui, H.Shimizu, H.Mizuno, N.Nukina, T.Furuta, A.Miyawaki. The E1 Mechanism in Photo-Induced Beta-Elimination Reactions For Green-to-Red Conversion of Fluorescent Proteins. Chem.Biol. V. 16 1140 2009.
ISSN: ISSN 1074-5521
PubMed: 19942137
DOI: 10.1016/J.CHEMBIOL.2009.10.010