Sodium in PDB 8rib: N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose

The structure of N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose, PDB code: 8rib was solved by V.Napolitano, J.Janna Olmos, G.M.Popowicz, G.Dubin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.08 / 1.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	56.009, 45.742, 52.616, 90, 118.87, 90
R / Rfree (%)	12.6 / 16.2

The structure of N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose (pdb code 8rib). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose, PDB code: 8rib:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na109 b:18.5 occ:1.00 H A:SER29 2.2 12.2 1.0 HH11 B:ARG63 2.3 31.3 1.0 HO1 B:EDO102 2.5 30.0 0.0 H12 B:EDO102 2.7 32.6 1.0 OE1 B:GLU60 3.0 19.2 1.0 O1 B:EDO102 3.0 38.1 1.0 HB3 A:PRO27 3.0 13.3 1.0 HB3 A:SER29 3.0 16.9 1.0 N A:SER29 3.0 11.8 1.0 HE B:ARG63 3.1 30.2 1.0 OG A:SER29 3.1 20.8 1.0 NH1 B:ARG63 3.1 30.6 1.0 HB A:THR28 3.2 12.8 1.0 HB2 B:GLU60 3.2 17.8 1.0 C1 B:EDO102 3.3 35.9 1.0 H A:THR28 3.3 11.8 1.0 HG A:SER29 3.3 30.0 0.0 CD B:GLU60 3.4 16.6 1.0 HG3 B:GLU60 3.4 16.9 1.0 CB A:SER29 3.4 17.1 1.0 N A:THR28 3.6 11.7 1.0 HB2 A:PRO27 3.6 12.8 1.0 H11 B:EDO102 3.7 38.0 1.0 HH12 B:ARG63 3.7 31.1 1.0 CB A:PRO27 3.7 12.7 1.0 CG B:GLU60 3.7 16.3 1.0 NE B:ARG63 3.8 31.0 1.0 CA A:SER29 3.8 13.2 1.0 CZ B:ARG63 3.9 29.0 1.0 CB B:GLU60 3.9 16.7 1.0 C A:THR28 4.0 10.4 1.0 CB A:THR28 4.0 12.1 1.0 CA A:THR28 4.0 11.4 1.0 HA B:GLU60 4.1 18.3 1.0 OE2 B:GLU60 4.1 16.1 1.0 C A:PRO27 4.1 10.2 1.0 HA A:PRO27 4.3 11.7 1.0 CA A:PRO27 4.3 11.8 1.0 HB2 A:SER29 4.4 16.9 1.0 HA A:SER29 4.4 12.7 1.0 H A:SER30 4.4 12.0 1.0 HO2 B:EDO102 4.5 21.8 1.0 C2 B:EDO102 4.6 37.3 1.0 CA B:GLU60 4.6 18.1 1.0 HG2 B:GLU60 4.7 15.4 1.0 O B:HOH205 4.7 42.2 1.0 HB3 B:GLU60 4.7 16.6 1.0 OG1 A:THR28 4.7 13.3 1.0 O2 B:EDO102 4.8 22.6 1.0 O B:HOH262 4.8 32.5 0.5 HD13 A:ILE64 4.9 14.6 1.0 HG21 A:THR28 4.9 12.5 1.0 O A:PRO27 4.9 11.2 1.0 HA A:THR28 5.0 10.8 1.0

Sodium binding site 2 out of 5 in the N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na105 b:27.7 occ:1.00 O B:LEU65 2.1 25.5 1.0 O B:HOH214 2.4 37.1 1.0 O B:LYS62 2.4 22.0 1.0 O B:ARG63 2.7 21.6 1.0 O9 B:MLI104 3.0 44.7 1.0 HA B:ARG63 3.0 22.7 1.0 C B:ARG63 3.2 20.2 1.0 C B:LEU65 3.3 26.0 1.0 O7 B:MLI104 3.4 36.7 1.0 O B:HOH210 3.4 39.3 1.0 C B:LYS62 3.5 20.1 1.0 CA B:ARG63 3.5 20.9 1.0 N B:LEU65 3.8 19.6 1.0 H B:LEU65 3.9 19.1 1.0 N B:ARG63 3.9 19.9 1.0 C3 B:MLI104 4.0 42.3 1.0 C2 B:MLI104 4.0 37.3 1.0 HB2 B:LEU65 4.0 21.4 1.0 CA B:LEU65 4.0 21.0 1.0 C B:ILE64 4.1 19.1 1.0 HA B:SER66 4.2 38.4 1.0 H11 B:MLI104 4.2 46.0 1.0 C1 B:MLI104 4.2 45.2 1.0 N B:ILE64 4.2 18.1 1.0 N B:SER66 4.3 30.9 1.0 O B:ILE64 4.4 20.1 1.0 CB B:LEU65 4.5 21.2 1.0 CA B:SER66 4.6 38.6 1.0 C B:SER66 4.7 46.1 1.0 HA B:LYS62 4.7 19.4 1.0 CA B:LYS62 4.7 19.8 1.0 CA B:ILE64 4.8 17.7 1.0 HB3 B:LEU65 4.8 22.8 1.0 H B:ILE64 4.8 17.6 1.0 H B:ARG63 4.9 19.5 1.0 O B:SER66 4.9 52.5 1.0 HG3 B:ARG63 4.9 27.9 1.0 O6 B:MLI104 4.9 44.7 1.0 CB B:ARG63 4.9 22.9 1.0 HA B:LEU65 4.9 20.9 1.0 HB3 B:LYS62 5.0 22.1 1.0

Sodium binding site 3 out of 5 in the N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na106 b:48.0 occ:1.00 H B:ARG7 2.4 32.0 1.0 H B:GLU6 3.0 42.5 1.0 HB2 B:SER5 3.1 45.3 1.0 N B:ARG7 3.2 30.7 1.0 HB2 B:ARG7 3.3 34.0 1.0 HB3 B:GLU6 3.5 40.9 1.0 N B:GLU6 3.5 41.3 1.0 HB2 B:GLU6 3.7 43.6 1.0 HB3 B:ARG7 3.7 33.0 1.0 CB B:ARG7 3.9 32.8 1.0 HG B:SER5 3.9 30.0 0.0 CB B:SER5 3.9 44.6 1.0 OG B:SER5 3.9 38.9 1.0 CB B:GLU6 3.9 41.5 1.0 CA B:GLU6 4.0 38.8 1.0 C B:GLU6 4.0 31.9 1.0 CA B:ARG7 4.1 28.6 1.0 HH22 B:ARG10 4.2 30.9 1.0 C B:SER5 4.3 39.3 1.0 CA B:SER5 4.5 45.9 1.0 HA B:SER5 4.6 47.4 1.0 HA B:ARG7 4.6 28.2 1.0 HB3 B:SER5 4.6 45.3 1.0 HH12 B:ARG10 4.7 31.7 1.0 H B:GLU8 4.8 30.1 1.0 NH2 B:ARG10 4.9 29.8 1.0 HA B:GLU6 5.0 38.1 1.0

Sodium binding site 4 out of 5 in the N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na107 b:43.4 occ:1.00 HG3 B:GLU16 2.2 24.4 1.0 OE1 B:GLU16 2.8 32.4 1.0 OG B:SER12 2.9 26.4 0.5 O B:SER12 2.9 17.4 0.5 O B:SER12 3.0 16.4 0.5 CG B:GLU16 3.0 25.3 1.0 HA B:SER12 3.2 17.0 0.5 HA B:SER12 3.2 18.4 0.5 HB B:VAL15 3.2 14.5 1.0 HG11 B:VAL15 3.3 15.5 1.0 HB3 B:SER12 3.3 19.2 0.5 HG2 B:GLU16 3.3 24.4 1.0 CD B:GLU16 3.3 31.6 1.0 HG B:SER12 3.5 30.0 0.0 H B:GLU16 3.6 15.3 1.0 C B:SER12 3.6 17.0 0.5 C B:SER12 3.7 16.5 0.5 CA B:SER12 3.7 17.2 0.5 CA B:SER12 3.7 18.6 0.5 CB B:SER12 3.9 21.8 0.5 CB B:SER12 3.9 18.9 0.5 CG1 B:VAL15 3.9 15.1 1.0 HG12 B:VAL15 3.9 15.4 1.0 CB B:VAL15 4.0 13.3 1.0 N B:GLU16 4.1 14.6 1.0 CB B:GLU16 4.3 19.3 1.0 HB2 B:SER12 4.3 22.6 0.5 OG B:SER12 4.3 19.7 0.5 HB2 B:GLU16 4.4 19.8 1.0 O B:HOH246 4.4 37.3 1.0 OE2 B:GLU16 4.6 40.5 1.0 HB3 B:SER12 4.6 22.6 0.5 HA B:GLU16 4.7 16.5 1.0 CA B:GLU16 4.7 16.3 1.0 HG B:SER12 4.7 30.0 0.0 HG22 B:VAL15 4.8 15.0 1.0 HB2 B:SER12 4.8 19.6 0.5 O B:HOH211 4.8 47.5 1.0 HG13 B:VAL15 4.8 14.3 1.0 C B:VAL15 4.8 13.4 1.0 N B:ASN13 4.9 17.0 1.0 CA B:VAL15 4.9 12.8 1.0 H B:VAL15 4.9 13.1 1.0

Sodium binding site 5 out of 5 in the N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of N-Terminal Domain of Trypanosoma Brucei PEX14 in Complex with A Pyrazolo-Pyrazolo[4,3-C]Pyridin-3-Yl Compound Showing A Novel Binding Pose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na108 b:16.3 occ:1.00 O B:HOH248 2.0 13.6 0.5 HZ2 B:LYS56 2.8 16.1 1.0 HZ3 B:LYS56 2.9 15.6 1.0 HG1 B:THR28 3.0 30.0 0.0 OG1 B:THR28 3.1 13.1 1.0 HE1 B:PHE49 3.1 12.6 1.0 O B:HOH248 3.1 10.6 0.5 NZ B:LYS56 3.2 16.0 1.0 HZ2 A:LYS56 3.2 14.7 1.0 HZ1 A:LYS56 3.2 15.3 1.0 HA A:GLN54 3.2 14.4 1.0 HB3 A:GLN54 3.3 14.6 1.0 HE2 B:LYS56 3.3 14.7 1.0 CE B:LYS56 3.6 15.7 1.0 HE3 B:LYS56 3.6 15.9 1.0 HB3 B:GLN54 3.6 17.8 1.0 NZ A:LYS56 3.6 14.8 1.0 HG2 A:GLN54 3.7 18.3 1.0 O A:HOH242 3.8 16.0 1.0 CE1 B:PHE49 3.9 12.7 1.0 CA A:GLN54 3.9 13.7 1.0 CB A:GLN54 3.9 14.7 1.0 HZ3 A:LYS56 3.9 14.4 1.0 HD1 B:PHE49 4.0 13.0 1.0 HZ1 B:LYS56 4.0 16.3 1.0 HZ2 B:LYS31 4.1 12.5 1.0 HG22 B:THR28 4.2 14.1 1.0 HG23 B:THR28 4.2 13.2 1.0 CB B:THR28 4.3 12.5 1.0 HG3 B:GLN54 4.3 22.2 1.0 CD1 B:PHE49 4.3 13.1 1.0 CG A:GLN54 4.3 17.6 1.0 C A:GLN54 4.3 12.3 1.0 O B:HOH270 4.4 24.1 0.5 HE22 B:GLN54 4.4 25.3 1.0 CB B:GLN54 4.4 18.3 1.0 CG2 B:THR28 4.4 13.9 1.0 HB2 B:GLN54 4.5 17.8 1.0 HE22 A:GLN54 4.5 17.5 1.0 HA B:THR28 4.5 11.1 1.0 O A:GLN54 4.6 12.4 1.0 HD2 A:PRO55 4.6 14.9 1.0 HE3 B:LYS31 4.7 11.8 1.0 CG B:GLN54 4.8 23.1 1.0 HB2 A:GLN54 4.8 14.3 1.0 HE3 A:LYS56 4.8 14.3 1.0 CE A:LYS56 4.8 14.1 1.0 NZ B:LYS31 4.9 12.3 1.0 CA B:THR28 4.9 11.6 1.0 CZ B:PHE49 4.9 12.8 1.0 O A:GLY53 5.0 17.7 1.0 HB B:THR28 5.0 13.2 1.0 HG3 A:GLN54 5.0 17.9 1.0

F.Menezes, V.Napolitano, T.Frohlich, S.Rioton, J.D.Janna Olmos, G.Dubin, G.M.Popowicz. Quantum Chemistry in A Pocket To Be Published.