Sodium in PDB 4dja: Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution

The structure of Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution, PDB code: 4dja was solved by P.Scheerer, F.Zhang, I.Oberpichler, T.Lamparter, N.Krauss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.95 / 1.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.388, 106.786, 55.913, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 18

The structure of Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution (pdb code 4dja). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution, PDB code: 4dja:

Sodium binding site 1 out of 1 in the Crystal Structure of A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution


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 A Prokaryotic (6-4) Photolyase Phrb From Agrobacterium Tumefaciens with An Fe-S Cluster and A 6,7-Dimethyl-8- Ribityllumazine Antenna Chromophore at 1.45A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:22.5 occ:1.00 OD2 A:ASP129 2.6 12.7 1.0 O A:HOH989 2.7 26.4 1.0 O A:HOH825 2.7 29.3 1.0 O A:GLU103 2.7 11.8 1.0 O A:HOH799 3.1 18.7 1.0 CG A:ASP129 3.5 12.4 1.0 CB A:ASP129 3.6 11.8 1.0 O A:PRO104 3.7 13.2 1.0 C A:PRO104 3.7 11.1 1.0 C A:GLU103 3.8 12.2 1.0 CE2 A:PHE132 4.0 14.1 1.0 CA A:PRO104 4.1 12.1 1.0 N A:GLY105 4.1 10.1 1.0 NH2 A:ARG131 4.2 12.0 1.0 CG A:GLU103 4.3 14.5 1.0 N A:PRO104 4.3 11.8 1.0 NH2 A:ARG315 4.5 20.1 1.0 NE2 A:GLN11 4.5 12.1 1.0 CA A:GLY105 4.5 11.4 1.0 O A:HOH707 4.7 15.7 1.0 OD1 A:ASP129 4.7 11.0 1.0 O A:HOH1043 4.7 26.0 1.0 CD2 A:PHE132 4.8 12.8 1.0 CA A:GLU103 4.9 11.7 1.0 CZ A:PHE132 5.0 13.0 1.0

F.Zhang, P.Scheerer, I.Oberpichler, T.Lamparter, N.Krauss. Crystal Structure of A Prokaryotic (6-4) Photolyase with An Fe-S Cluster and A 6,7-Dimethyl-8-Ribityllumazine Antenna Chromophore. Proc.Natl.Acad.Sci.Usa V. 110 7217 2013.
ISSN: ISSN 0027-8424
PubMed: 23589886
DOI: 10.1073/PNAS.1302377110