Sodium in PDB 2cfd: Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3)

All present enzymatic activity of Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3):
1.4.3.6;

The structure of Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3), PDB code: 2cfd 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)	29.99 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	192.287, 62.857, 158.171, 90.00, 117.47, 90.00
R / Rfree (%)	19.4 / 21.3

The structure of Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3) also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3) (pdb code 2cfd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3), PDB code: 2cfd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3)


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 WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:28.9 occ:1.00 OD1 A:ASP440 2.3 18.0 1.0 O A:ILE582 2.4 14.6 1.0 OD1 A:ASP581 2.4 18.4 1.0 O A:MET441 2.4 16.2 1.0 O A:HOH2156 2.7 27.1 1.0 H A:ILE582 2.8 16.2 1.0 H A:MET441 3.1 16.3 1.0 N A:ILE582 3.2 16.2 1.0 HD1 A:PHE446 3.2 20.9 1.0 N A:MET441 3.3 16.5 1.0 C A:ILE582 3.4 15.2 1.0 C A:MET441 3.5 17.0 1.0 HH21 A:ARG49 3.5 40.2 1.0 CG A:ASP440 3.6 16.7 1.0 HA A:ASP581 3.6 17.0 1.0 CG A:ASP581 3.7 18.3 1.0 C A:ASP440 3.8 15.7 1.0 C A:ASP581 3.8 16.5 1.0 HB2 A:MET441 3.8 16.6 1.0 CA A:ILE582 3.8 15.8 1.0 HA A:ASP440 3.9 15.8 1.0 CA A:MET441 3.9 16.7 1.0 HG21 A:VAL583 4.0 14.7 1.0 HB2 A:TYR546 4.0 19.0 1.0 CD1 A:PHE446 4.1 21.2 1.0 HH22 A:ARG49 4.1 40.2 1.0 NH2 A:ARG49 4.1 39.7 1.0 CA A:ASP581 4.1 16.9 1.0 HE1 A:PHE446 4.2 22.2 1.0 CA A:ASP440 4.2 15.9 1.0 OD2 A:ASP440 4.3 16.2 1.0 CB A:MET441 4.4 16.5 1.0 O A:ASP440 4.4 16.2 1.0 HA A:ILE582 4.4 15.7 1.0 HG13 A:ILE582 4.5 17.9 1.0 HA A:VAL583 4.5 15.2 1.0 CB A:ASP581 4.5 17.5 1.0 OD2 A:ASP581 4.5 20.3 1.0 CB A:ASP440 4.5 16.0 1.0 N A:VAL583 4.5 15.3 1.0 CE1 A:PHE446 4.5 22.2 1.0 HA A:PHE446 4.6 17.7 1.0 HG12 A:ILE582 4.6 17.9 1.0 HA A:ALA442 4.6 17.4 1.0 N A:ALA442 4.7 17.2 1.0 HB3 A:ALA442 4.7 17.4 1.0 O A:ASP581 4.7 16.9 1.0 HB3 A:ASN273 4.7 17.5 1.0 HG22 A:VAL583 4.8 14.7 1.0 HA A:MET441 4.8 16.7 1.0 CG2 A:VAL583 4.8 14.7 1.0 HB3 A:PHE446 4.8 18.0 1.0 CB A:TYR546 4.9 18.8 1.0 CG1 A:ILE582 4.9 18.3 1.0 O A:PHE446 4.9 16.9 1.0 HB2 A:ASN273 4.9 17.5 1.0 CA A:VAL583 5.0 15.2 1.0 HB3 A:TYR546 5.0 19.0 1.0 HD1 A:TYR546 5.0 19.5 1.0

Sodium binding site 2 out of 2 in the Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Agao in Complex with WC4L3 (Ru-Wire Inhibitor, 4-Carbon Linker, Lambda Enantiomer, Data Set 3) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na703 b:22.6 occ:1.00 O B:MET441 2.3 14.4 1.0 OD1 B:ASP581 2.4 14.9 1.0 OD1 B:ASP440 2.4 13.8 1.0 O B:ILE582 2.5 12.9 1.0 O B:HOH2248 2.6 24.9 1.0 H B:ILE582 2.9 14.7 1.0 HD1 B:PHE446 3.1 21.5 1.0 H B:MET441 3.2 13.3 1.0 N B:ILE582 3.3 14.8 1.0 N B:MET441 3.4 13.1 1.0 C B:MET441 3.4 13.5 1.0 C B:ILE582 3.5 14.0 1.0 HA B:ASP581 3.5 15.0 1.0 HH21 B:ARG49 3.6 25.6 1.0 CG B:ASP581 3.6 16.9 1.0 CG B:ASP440 3.7 14.6 1.0 C B:ASP581 3.8 15.1 1.0 C B:ASP440 3.9 13.4 1.0 CA B:MET441 3.9 13.6 1.0 CA B:ILE582 3.9 14.2 1.0 HB2 B:MET441 3.9 13.7 1.0 CD1 B:PHE446 4.0 21.9 1.0 HA B:ASP440 4.0 13.2 1.0 CA B:ASP581 4.0 15.1 1.0 HE1 B:PHE446 4.0 23.0 1.0 HB2 B:TYR546 4.0 15.8 1.0 HH22 B:ARG49 4.0 25.6 1.0 HG21 B:VAL583 4.1 12.2 1.0 NH2 B:ARG49 4.1 25.1 1.0 CA B:ASP440 4.3 13.2 1.0 OD2 B:ASP440 4.4 15.4 1.0 CB B:ASP581 4.4 15.3 1.0 CE1 B:PHE446 4.4 22.6 1.0 HA B:PHE446 4.5 16.1 1.0 HG12 B:ILE582 4.5 16.0 1.0 CB B:MET441 4.5 13.4 1.0 O B:ASP440 4.5 12.6 1.0 OD2 B:ASP581 4.5 19.4 1.0 HA B:ILE582 4.5 14.3 1.0 HA B:ALA442 4.5 12.8 1.0 HB1 B:ALA442 4.6 12.8 1.0 N B:ALA442 4.6 12.9 1.0 N B:VAL583 4.6 13.8 1.0 CB B:ASP440 4.6 13.4 1.0 HA B:VAL583 4.6 13.2 1.0 O B:ASP581 4.6 14.8 1.0 HG22 B:VAL583 4.7 12.2 1.0 HG13 B:ILE582 4.7 16.0 1.0 HA B:MET441 4.8 13.4 1.0 HB3 B:ASN273 4.8 14.4 1.0 O B:PHE446 4.8 16.1 1.0 CG2 B:VAL583 4.8 11.9 1.0 HB3 B:PHE446 4.9 16.6 1.0 CB B:TYR546 4.9 15.8 1.0 CG1 B:ILE582 4.9 16.4 1.0 OD1 B:ASN448 5.0 14.5 1.0 HB3 B:TYR546 5.0 15.8 1.0 HB2 B:ASN273 5.0 14.4 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: ISSN 0002-7863
PubMed: 18507382
DOI: 10.1021/JA801289F