Sodium in PDB 6sbq: The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One

All present enzymatic activity of The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One:
3.4.11.2;

The structure of The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One, PDB code: 6sbq was solved by E.Salomon, M.Schmitt, E.Mouray, A.G.Mcewen, M.Torchy, P.Poussin-Courmontagne, S.Alavi, C.Tarnus, J.Cavarelli, I.Florent, S.Albrecht, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.18 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.079, 109.241, 113.053, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 17.8

The structure of The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Sodium atom in the The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One (pdb code 6sbq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One, PDB code: 6sbq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1106 b:58.3 occ:1.00 O A:HOH1464 2.2 32.3 1.0 O A:HOH1726 2.4 25.9 1.0 O A:HOH2744 2.4 45.8 1.0 O A:HOH2222 2.6 34.0 1.0 O A:HOH2850 2.7 54.9 1.0 O A:HOH1495 2.8 30.7 1.0 NA A:NA1107 3.3 53.7 1.0 HD22 A:ASN992 3.4 24.1 1.0 O A:HOH1810 3.7 31.1 1.0 HD3 A:LYS311 3.9 27.8 0.5 OE2 A:GLU957 3.9 19.4 1.0 OD2 A:ASP995 4.1 19.2 1.0 HG3 A:GLU957 4.2 23.1 1.0 HE2 A:LYS311 4.2 26.1 0.5 ND2 A:ASN992 4.2 20.1 1.0 HB2 A:ASN992 4.2 21.6 1.0 O A:HOH2765 4.3 23.1 1.0 O A:HOH1387 4.4 20.6 0.5 O A:HOH2347 4.5 48.3 1.0 HD2 A:LYS311 4.6 27.8 0.5 HD21 A:ASN992 4.6 24.1 1.0 HG A:SER990 4.6 24.4 1.0 O A:HOH1639 4.6 26.0 1.0 CD A:LYS311 4.7 23.1 0.5 O A:HOH2805 4.7 64.8 1.0 CD A:GLU957 4.7 19.6 1.0 O A:HOH1882 4.8 18.6 1.0 HZ1 A:LYS311 4.8 26.0 0.5 HB3 A:ASN992 4.8 21.6 1.0 CB A:ASN992 4.9 18.0 1.0 CG A:GLU957 4.9 19.2 1.0 O A:HOH2868 5.0 57.6 1.0 HZ3 A:LYS311 5.0 28.2 0.5 OG A:SER990 5.0 20.3 1.0 O A:HOH2646 5.0 41.2 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Pfa-M1 in Complex with 7-Amino-4-Phenyl-5,7, 8,9-Tetrahydrobenzocyclohepten-6-One within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1107 b:53.7 occ:1.00 O A:HOH2222 2.3 34.0 1.0 O A:HOH2868 2.3 57.6 1.0 O A:HOH2832 2.5 57.5 1.0 O A:HOH2850 2.5 54.9 1.0 O A:HOH2744 2.6 45.8 1.0 O A:HOH2486 2.6 49.9 1.0 NA A:NA1106 3.3 58.3 1.0 O A:HOH2646 4.1 41.2 1.0 O A:HOH1810 4.1 31.1 1.0 O A:HOH2088 4.2 27.7 1.0 HA A:SER990 4.3 26.5 1.0 O A:HOH1583 4.3 57.8 1.0 HB2 A:SER990 4.4 24.9 1.0 O A:HOH1867 4.4 28.0 1.0 O A:HOH1639 4.5 26.0 1.0 OG A:SER990 4.7 20.3 1.0 O A:HOH2805 4.7 64.8 1.0 HG A:SER990 4.8 24.4 1.0 CB A:SER990 4.9 20.7 1.0 O A:HOH1464 5.0 32.3 1.0

E.Salomon, M.Schmitt, E.Mouray, A.G.Mcewen, L.Bounaadja, M.Torchy, P.Poussin-Courmontagne, S.Alavi, C.Tarnus, J.Cavarelli, I.Florent, S.Albrecht. Aminobenzosuberone Derivatives As Pfa-M1 Inhibitors: Molecular Recognition and Antiplasmodial Evaluation. Bioorg.Chem. V. 98 03750 2020.
ISSN: ISSN 0045-2068
PubMed: 32182520
DOI: 10.1016/J.BIOORG.2020.103750