Sodium in PDB 1w4n: Agao Covalent Complex with Tranylcypromine

All present enzymatic activity of Agao Covalent Complex with Tranylcypromine:
1.4.3.6;

The structure of Agao Covalent Complex with Tranylcypromine, PDB code: 1w4n was solved by A.P.Duff, D.M.Trambaiolo, D.B.Langley, G.A.Juda, E.M.Shepard, D.M.Dooley, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.28 / 1.65
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	158.113, 63.001, 184.490, 90.00, 112.04, 90.00
R / Rfree (%)	17.1 / 19.9

The structure of Agao Covalent Complex with Tranylcypromine also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

The binding sites of Sodium atom in the Agao Covalent Complex with Tranylcypromine (pdb code 1w4n). 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 Covalent Complex with Tranylcypromine, PDB code: 1w4n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Agao Covalent Complex with Tranylcypromine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Agao Covalent Complex with Tranylcypromine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:32.0 occ:1.00 OD1 A:ASP440 2.3 8.7 1.0 O A:MET441 2.4 10.3 1.0 OD1 A:ASP581 2.4 12.2 1.0 O A:ILE582 2.5 8.7 1.0 O A:HOH2337 2.6 24.9 1.0 H A:ILE582 2.8 9.7 1.0 HD1 A:PHE446 3.1 13.0 1.0 H A:MET441 3.2 9.4 1.0 N A:ILE582 3.2 9.8 1.0 N A:MET441 3.4 9.6 1.0 C A:MET441 3.4 12.1 1.0 C A:ILE582 3.4 9.2 1.0 HH21 A:ARG49 3.5 37.2 1.0 CG A:ASP440 3.6 11.3 1.0 HA A:ASP581 3.6 10.5 1.0 CG A:ASP581 3.6 15.7 1.0 C A:ASP581 3.8 10.7 1.0 C A:ASP440 3.8 7.6 1.0 HB2 A:MET441 3.8 10.4 1.0 HA A:ASP440 3.9 8.8 1.0 CA A:MET441 3.9 10.4 1.0 CA A:ILE582 3.9 8.7 1.0 HH22 A:ARG49 4.0 37.2 1.0 CD1 A:PHE446 4.0 13.7 1.0 HG21 A:VAL583 4.0 9.1 1.0 HB2 A:TYR546 4.0 11.5 1.0 NH2 A:ARG49 4.1 35.4 1.0 HE1 A:PHE446 4.1 13.9 1.0 CA A:ASP581 4.1 11.2 1.0 CA A:ASP440 4.3 9.0 1.0 OD2 A:ASP440 4.3 9.4 1.0 CB A:MET441 4.4 10.6 1.0 HG13 A:ILE582 4.4 12.5 1.0 OD2 A:ASP581 4.5 16.9 1.0 CE1 A:PHE446 4.5 11.9 1.0 CB A:ASP581 4.5 11.2 1.0 O A:ASP440 4.5 9.7 1.0 HA A:ILE582 4.5 9.6 1.0 HA A:PHE446 4.5 10.0 1.0 HB2 A:ALA442 4.5 10.7 1.0 HA A:VAL583 4.5 8.3 1.0 CB A:ASP440 4.5 9.5 1.0 HA A:ALA442 4.5 10.9 1.0 N A:VAL583 4.6 8.3 1.0 N A:ALA442 4.6 11.2 1.0 HG22 A:VAL583 4.6 9.1 1.0 O A:ASP581 4.7 10.4 1.0 HG12 A:ILE582 4.7 12.5 1.0 HB3 A:ASN273 4.7 11.2 1.0 CG2 A:VAL583 4.8 9.9 1.0 HA A:MET441 4.8 10.6 1.0 HB3 A:PHE446 4.8 10.3 1.0 O A:PHE446 4.9 9.8 1.0 CB A:TYR546 4.9 10.1 1.0 CG1 A:ILE582 4.9 12.2 1.0 HB2 A:ASN273 4.9 11.2 1.0 HB3 A:TYR546 5.0 11.5 1.0

Sodium binding site 2 out of 2 in the Agao Covalent Complex with Tranylcypromine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Agao Covalent Complex with Tranylcypromine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na703 b:26.4 occ:1.00 O B:MET441 2.4 6.4 1.0 OD1 B:ASP581 2.4 9.2 1.0 O B:ILE582 2.4 6.4 1.0 OD1 B:ASP440 2.5 6.6 1.0 O B:HOH2363 2.6 25.3 1.0 H B:ILE582 2.9 8.3 1.0 HD1 B:PHE446 3.1 11.6 1.0 N B:ILE582 3.2 7.8 1.0 H B:MET441 3.2 5.5 1.0 N B:MET441 3.4 4.6 1.0 C B:ILE582 3.4 5.1 1.0 C B:MET441 3.4 7.8 1.0 HA B:ASP581 3.5 9.1 1.0 HH21 B:ARG49 3.6 17.6 1.0 CG B:ASP581 3.6 15.7 1.0 CG B:ASP440 3.7 7.8 1.0 C B:ASP581 3.8 10.0 1.0 C B:ASP440 3.8 5.5 1.0 CA B:ILE582 3.9 7.8 1.0 CA B:MET441 3.9 7.8 1.0 HB2 B:MET441 3.9 7.6 1.0 HA B:ASP440 3.9 5.4 1.0 CD1 B:PHE446 4.0 10.5 1.0 HB2 B:TYR546 4.0 8.3 1.0 CA B:ASP581 4.0 8.2 1.0 HE1 B:PHE446 4.1 13.5 1.0 HH22 B:ARG49 4.1 17.6 1.0 HG21 B:VAL583 4.1 6.9 1.0 NH2 B:ARG49 4.2 15.2 1.0 CA B:ASP440 4.3 5.3 1.0 O B:ASP440 4.4 5.2 1.0 CB B:ASP581 4.4 10.3 1.0 CE1 B:PHE446 4.5 13.3 1.0 CB B:MET441 4.5 6.1 1.0 HA B:ILE582 4.5 7.0 1.0 OD2 B:ASP440 4.5 9.2 1.0 HA B:PHE446 4.5 7.7 1.0 OD2 B:ASP581 4.5 15.3 1.0 HG12 B:ILE582 4.5 8.6 1.0 HA B:ALA442 4.5 6.8 1.0 O B:ASP581 4.6 8.2 1.0 N B:VAL583 4.6 5.6 1.0 HA B:VAL583 4.6 6.7 1.0 HB1 B:ALA442 4.6 7.5 1.0 HG22 B:VAL583 4.6 6.9 1.0 HG13 B:ILE582 4.6 8.6 1.0 N B:ALA442 4.6 5.3 1.0 CB B:ASP440 4.6 4.4 1.0 HB3 B:PHE446 4.8 8.3 1.0 HA B:MET441 4.8 6.8 1.0 HB3 B:ASN273 4.8 6.6 1.0 CG2 B:VAL583 4.8 6.8 1.0 O B:PHE446 4.8 9.6 1.0 CB B:TYR546 4.9 7.6 1.0 HB3 B:TYR546 4.9 8.3 1.0 CG1 B:ILE582 4.9 8.8 1.0 OD1 B:ASN448 5.0 7.1 1.0 HB2 B:ASN273 5.0 6.6 1.0

D.B.Langley, D.M.Trambaiolo, A.P.Duff, D.M.Dooley, H.C.Freeman, J.M.Guss. Complexes of the Copper-Containing Amine Oxidase From Arthrobacter Globiformis with the Inhibitors Benzylhydrazine and Tranylcypromine. Acta Crystallogr.,Sect.F V. 64 577 2008.
ISSN: ESSN 1744-3091
PubMed: 18607080
DOI: 10.1107/S174430910801556X