Sodium in PDB 2cfk: Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker)

All present enzymatic activity of Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker):
1.4.3.6;

The structure of Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker), PDB code: 2cfk was solved by D.B.Langley, A.P.Duff, H.C.Freeman, J.M.Guss, G.A.Juda, D.M.Dooley, S.M.Contakes, N.W.Halpern-Manners, A.R.Dunn, H.B.Gray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.02 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	157.885, 62.944, 92.013, 90.00, 112.20, 90.00
R / Rfree (%)	14.5 / 16.5

The structure of Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker) also contains other interesting chemical elements:

Ruthenium	(Ru)	2 atoms
Copper	(Cu)	1 atom

The binding sites of Sodium atom in the Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker) (pdb code 2cfk). 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 Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker), PDB code: 2cfk:

Sodium binding site 1 out of 1 in the Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Agao in Complex with WC5 (Ru-Wire Inhibitor, 5-Carbon Linker) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1630 b:26.5 occ:1.00 O A:MET441 2.3 14.1 1.0 OD1 A:ASP440 2.3 15.6 1.0 OD1 A:ASP581 2.4 16.2 1.0 O A:ILE582 2.4 12.2 1.0 O A:HOH2275 2.7 23.7 1.0 H A:ILE582 2.9 12.8 1.0 HD1 A:PHE446 3.1 19.2 1.0 H A:MET441 3.2 13.2 1.0 N A:ILE582 3.3 12.7 1.0 N A:MET441 3.4 13.1 1.0 C A:MET441 3.4 11.1 1.0 C A:ILE582 3.4 13.3 1.0 HH21 A:ARG49 3.5 23.7 1.0 HA A:ASP581 3.6 15.0 1.0 CG A:ASP440 3.6 16.5 1.0 CG A:ASP581 3.6 18.2 1.0 C A:ASP440 3.8 13.6 1.0 C A:ASP581 3.8 13.8 1.0 HB2 A:MET441 3.8 12.8 1.0 CA A:MET441 3.9 13.0 1.0 HA A:ASP440 3.9 12.9 1.0 CA A:ILE582 3.9 12.2 1.0 CD1 A:PHE446 3.9 18.4 1.0 HE1 A:PHE446 4.0 22.3 1.0 HH22 A:ARG49 4.0 23.7 1.0 NH2 A:ARG49 4.0 21.0 1.0 HG21 A:VAL583 4.1 14.3 1.0 HB2 A:TYR546 4.1 14.5 1.0 CA A:ASP581 4.1 15.7 1.0 CA A:ASP440 4.2 12.4 1.0 OD2 A:ASP440 4.3 16.3 1.0 CE1 A:PHE446 4.4 22.6 1.0 CB A:MET441 4.4 12.0 1.0 O A:ASP440 4.4 12.2 1.0 CB A:ASP581 4.5 16.8 1.0 OD2 A:ASP581 4.5 19.8 1.0 HA A:PHE446 4.5 16.9 1.0 HA A:ILE582 4.5 12.6 1.0 HG12 A:ILE582 4.5 16.7 1.0 CB A:ASP440 4.5 13.7 1.0 HA A:ALA442 4.5 13.5 1.0 N A:ALA442 4.6 12.9 1.0 HA A:VAL583 4.6 13.1 1.0 N A:VAL583 4.6 12.7 1.0 HB2 A:ALA442 4.6 13.3 1.0 O A:ASP581 4.7 13.5 1.0 HG13 A:ILE582 4.7 16.7 1.0 HB3 A:ASN273 4.7 14.2 1.0 HA A:MET441 4.7 12.5 1.0 HG22 A:VAL583 4.8 14.3 1.0 CG2 A:VAL583 4.8 14.9 1.0 O A:PHE446 4.9 17.6 1.0 HB3 A:PHE446 4.9 16.9 1.0 CB A:TYR546 4.9 14.0 1.0 CG1 A:ILE582 4.9 16.8 1.0 HB3 A:TYR546 5.0 14.5 1.0

D.B.Langley, D.E.Brown, L.E.Cheruzel, S.M.Contakes, A.P.Duff, K.M.Hilmer, D.M.Dooley, H.B.Gray, J.M.Guss, H.C.Freeman. Enantiomer-Specific Binding of Ruthenium(II) Molecular Wires By the Amine Oxidase of Arthrobacter Globiformis. J. Am. Chem. Soc. V. 130 8069 2008.
ISSN: ESSN 1520-5126
PubMed: 18507382
DOI: 10.1021/JA801289F