Sodium in PDB 6y45: Crystal Structure of the H33A Variant of Rsrr

The structure of Crystal Structure of the H33A Variant of Rsrr, PDB code: 6y45 was solved by R.Rohac, A.Volbeda, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.14 / 1.68
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.920, 117.000, 71.330, 90.00, 95.83, 90.00
R / Rfree (%)	15.9 / 20.5

The structure of Crystal Structure of the H33A Variant of Rsrr also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of the H33A Variant of Rsrr (pdb code 6y45). 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 the H33A Variant of Rsrr, PDB code: 6y45:

Sodium binding site 1 out of 1 in the Crystal Structure of the H33A Variant of Rsrr


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 the H33A Variant of Rsrr within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:53.0 occ:1.00 CG B:TRP123 3.7 38.6 1.0 CD2 B:TRP123 3.8 44.8 1.0 CD1 B:TRP123 3.8 40.1 1.0 CG D:TRP123 3.8 37.5 1.0 CD1 D:TRP123 3.8 37.6 1.0 SD D:MET1 3.8 78.5 1.0 CD2 D:TRP123 3.9 40.4 1.0 NE1 D:TRP123 3.9 36.7 1.0 CE2 B:TRP123 3.9 45.2 1.0 NE1 B:TRP123 3.9 38.0 1.0 CE2 D:TRP123 4.0 41.2 1.0 SD B:MET1 4.0 69.3 1.0 CB B:TRP123 4.3 32.9 1.0 CE D:MET1 4.3 76.8 1.0 CE B:MET1 4.3 66.7 1.0 CE3 B:TRP123 4.4 44.5 1.0 CB D:TRP123 4.4 35.2 1.0 CE3 D:TRP123 4.5 44.2 1.0 CZ2 D:TRP123 4.6 41.7 1.0 CB B:ALA87 4.6 39.1 1.0 CZ2 B:TRP123 4.6 43.7 1.0 OE1 B:GLU120 4.7 65.1 0.5 CZ3 B:TRP123 5.0 49.0 1.0

J.C.Crack, P.Amara, A.Volbeda, J.M.Mouesca, R.Rohac, M.T.Pellicer Martinez, C.Y.Huang, O.Gigarel, C.Rinaldi, N.E.Le Brun, J.C.Fontecilla-Camps. Electron and Proton Transfers Modulate Dna Binding By the Transcription Regulator Rsrr. J.Am.Chem.Soc. 2020.
ISSN: ESSN 1520-5126
PubMed: 32078310
DOI: 10.1021/JACS.9B12250