Sodium in PDB 4m1p: Crystal Structure of the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2

The structure of Crystal Structure of the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2, PDB code: 4m1p was solved by F.Chang, C.E.Dann Iii, D.P.Giedroc, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.38 / 2.56
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.204, 89.204, 57.985, 90.00, 90.00, 120.00
R / Rfree (%)	21.4 / 24.8

The structure of Crystal Structure of the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2 also contains other interesting chemical elements:

Copper

(Cu)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2 (pdb code 4m1p). 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 the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2, PDB code: 4m1p:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2


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 Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:67.0 occ:1.00 OE1 A:GLU90 2.5 80.1 1.0 O A:HOH303 2.6 44.2 1.0 OE2 A:GLU90 2.8 77.1 1.0 CD A:GLU90 2.9 75.8 1.0 CG A:GLU90 4.3 66.8 1.0 CB A:GLU90 4.8 59.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2


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 the Copper-Sensing Repressor Csor with Cu(I) From Geobacillus Thermodenitrificans NG80-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:68.6 occ:1.00 OG A:SER88 2.7 57.3 1.0 N A:THR14 2.8 67.6 1.0 OG A:SER92 2.9 64.9 1.0 OE1 A:GLN91 2.9 66.8 1.0 OG1 A:THR14 3.1 73.3 1.0 CA A:GLY13 3.2 67.7 1.0 CB A:SER88 3.3 54.4 1.0 O A:SER88 3.4 57.8 1.0 CB A:ALA83 3.4 40.9 1.0 C A:GLY13 3.5 66.2 1.0 CB A:THR14 3.8 67.9 1.0 CA A:THR14 3.8 66.0 1.0 CD A:GLN91 4.0 70.9 1.0 CB A:SER92 4.1 54.2 1.0 O A:HOH302 4.1 56.5 1.0 C A:SER88 4.1 56.0 1.0 CA A:SER88 4.3 53.4 1.0 N A:SER92 4.4 49.1 1.0 CB A:GLN91 4.5 58.9 1.0 CG A:GLN91 4.5 67.2 1.0 CA A:ALA83 4.5 49.0 1.0 N A:GLY13 4.6 70.4 1.0 CA A:SER92 4.7 50.8 1.0 O A:GLY13 4.7 63.7 1.0 C A:THR14 5.0 64.7 1.0

F.M.Chang, H.J.Coyne, C.Cubillas, P.Vinuesa, X.Fang, Z.Ma, D.Ma, J.D.Helmann, A.Garcia-De Los Santos, Y.X.Wang, C.E.Dann, D.P.Giedroc. Cu(I)-Mediated Allosteric Switching in A Copper-Sensing Operon Repressor (Csor). J.Biol.Chem. V. 289 19204 2014.
ISSN: ISSN 0021-9258
PubMed: 24831014
DOI: 10.1074/JBC.M114.556704