Iodine in PDB 7nqx: Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818

The structure of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818, PDB code: 7nqx was solved by N.Mohamad, A.O'donoghue, A.L.Kantsadi, I.Vakonakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.97 / 2.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.979, 102.575, 103.829, 90, 90, 90
R / Rfree (%)	21.9 / 23.9

The structure of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iodine atom in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 (pdb code 7nqx). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818, PDB code: 7nqx:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1006 b:111.2 occ:0.50 I4 A:PYZ1006 0.0 111.2 0.5 N1 A:PYZ1006 1.2 254.3 0.5 N2 A:PYZ1006 1.5 254.3 0.5 C4 A:PYZ1006 2.1 111.1 0.5 C5 A:PYZ1006 2.5 254.3 0.5 C3 A:PYZ1006 2.7 254.3 0.5 C5 A:PYZ1006 3.1 111.1 0.5 C3 A:PYZ1006 3.1 111.0 0.5 OD1 A:ASP190 3.1 76.2 1.0 C4 A:PYZ1006 3.2 254.2 0.5 NE2 A:GLN186 3.8 70.3 1.0 CG A:LYS189 3.9 67.0 1.0 N A:ASP190 4.1 62.8 1.0 CD A:LYS189 4.1 71.0 1.0 C A:LYS189 4.1 61.3 1.0 CA A:ASP190 4.1 64.8 1.0 O A:LYS189 4.1 61.5 1.0 N1 A:PYZ1006 4.2 111.0 0.5 N2 A:PYZ1006 4.2 110.9 0.5 CB A:ALA193 4.3 63.7 1.0 CG A:ASP190 4.3 75.2 1.0 CB A:LYS189 4.3 62.0 1.0 CE A:LYS189 4.4 75.8 1.0 CB A:ASP190 4.8 67.3 1.0 CA A:LYS189 4.9 59.5 1.0

Iodine binding site 2 out of 7 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1006 b:254.1 occ:0.50 I4 A:PYZ1006 0.0 254.1 0.5 N1 A:PYZ1006 1.1 111.0 0.5 C4 A:PYZ1006 2.1 254.2 0.5 N2 A:PYZ1006 2.2 110.9 0.5 C5 A:PYZ1006 2.2 111.1 0.5 OD1 A:ASN198 3.0 71.6 1.0 C5 A:PYZ1006 3.1 254.3 0.5 C3 A:PYZ1006 3.1 254.3 0.5 C3 A:PYZ1006 3.2 111.0 0.5 C4 A:PYZ1006 3.2 111.1 0.5 N A:VAL199 3.6 59.9 1.0 CA A:ASN198 3.9 64.0 1.0 CG A:ASN198 4.1 70.6 1.0 C A:ASN198 4.2 62.1 1.0 N1 A:PYZ1006 4.2 254.3 0.5 N2 A:PYZ1006 4.2 254.3 0.5 O A:VAL199 4.3 58.5 1.0 O A:LEU197 4.5 64.6 1.0 CB A:ASN198 4.5 66.3 1.0 CA A:VAL199 4.6 57.7 1.0 C A:VAL199 4.8 58.1 1.0 CB A:VAL199 4.8 54.7 1.0 CE A:LYS189 5.0 75.8 1.0

Iodine binding site 3 out of 7 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1007 b:67.1 occ:0.25 I4 A:PYZ1007 0.0 67.1 0.2 C4 A:PYZ1007 0.7 61.9 0.2 C3 A:PYZ1007 1.0 61.8 0.2 C5 A:PYZ1007 1.4 61.6 0.2 N2 A:PYZ1007 1.8 61.6 0.2 N1 A:PYZ1007 1.9 61.4 0.2 C4 A:PYZ1007 2.1 66.6 0.2 I4 A:PYZ1007 2.6 62.2 0.2 C5 A:PYZ1007 3.1 66.4 0.2 C3 A:PYZ1007 3.1 66.2 0.2 OH A:TYR179 3.5 54.0 1.0 NH2 A:ARG105 3.7 60.0 1.0 O A:HOH1118 3.8 57.2 1.0 CE1 A:TYR179 4.1 50.1 1.0 N1 A:PYZ1007 4.2 66.1 0.2 N2 A:PYZ1007 4.2 65.9 0.2 CZ A:TYR179 4.2 51.5 1.0 CA A:ARG101 4.3 48.9 1.0 O A:LYS100 4.4 50.7 1.0 CE1 A:PHE180 4.5 46.6 1.0 CG A:ARG101 4.5 50.0 1.0 O A:HOH1130 4.7 43.0 1.0 CZ A:ARG105 4.8 59.3 1.0 NH1 A:ARG101 4.8 47.0 1.0 CB A:ARG101 4.8 49.0 1.0 CG2 A:THR256 4.8 59.0 1.0 NE A:ARG105 4.9 58.9 1.0 N A:ARG101 5.0 48.8 1.0 C A:LYS100 5.0 49.1 1.0 NE2 A:GLN184 5.0 51.0 1.0

Iodine binding site 4 out of 7 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 within 5.0Å range: probe atom residue distance (Å) B Occ A:I1007 b:62.2 occ:0.25 I4 A:PYZ1007 0.0 62.2 0.2 C4 A:PYZ1007 0.6 66.6 0.2 C3 A:PYZ1007 1.0 66.2 0.2 C5 A:PYZ1007 1.3 66.4 0.2 N2 A:PYZ1007 1.7 65.9 0.2 N1 A:PYZ1007 1.7 66.1 0.2 C4 A:PYZ1007 2.1 61.9 0.2 I4 A:PYZ1007 2.6 67.1 0.2 C5 A:PYZ1007 3.1 61.6 0.2 C3 A:PYZ1007 3.1 61.8 0.2 OG1 A:THR42 3.6 51.0 1.0 OH A:TYR179 3.7 54.0 1.0 CG A:LYS100 4.0 43.9 1.0 CG2 A:THR234 4.0 52.0 1.0 CG A:ARG101 4.1 50.0 1.0 O A:LYS100 4.1 50.7 1.0 N1 A:PYZ1007 4.2 61.4 0.2 N2 A:PYZ1007 4.2 61.6 0.2 C A:LYS100 4.2 49.1 1.0 CG2 A:THR42 4.3 49.3 1.0 CD A:LYS100 4.3 45.7 1.0 N A:ARG101 4.4 48.8 1.0 CB A:LYS100 4.4 46.0 1.0 CA A:ARG101 4.5 48.9 1.0 O3 A:PO41008 4.5 80.1 1.0 CE A:LYS100 4.5 45.7 1.0 CB A:THR42 4.6 49.3 1.0 NH1 A:ARG101 4.8 47.0 1.0 CE1 A:PHE180 4.8 46.6 1.0 CB A:ARG101 4.9 49.0 1.0 CZ A:TYR179 5.0 51.5 1.0 CZ A:ARG101 5.0 50.1 1.0 CA A:LYS100 5.0 48.0 1.0

Iodine binding site 5 out of 7 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 within 5.0Å range: probe atom residue distance (Å) B Occ B:I504 b:89.8 occ:0.50 I4 B:PYZ504 0.0 89.8 0.5 N1 B:PYZ504 0.8 185.0 0.2 N2 B:PYZ504 0.9 185.0 0.2 C5 B:PYZ504 1.4 185.0 0.2 C3 B:PYZ504 1.4 185.0 0.2 C4 B:PYZ504 1.7 185.0 0.2 C4 B:PYZ504 2.1 89.8 0.5 OG1 B:THR42 2.9 69.2 1.0 C5 B:PYZ504 3.1 89.9 0.5 C3 B:PYZ504 3.1 89.9 0.5 I4 B:PYZ504 3.7 185.0 0.2 CG2 B:THR234 3.8 93.5 1.0 CG2 B:THR42 3.9 68.2 1.0 CG B:LYS100 3.9 66.0 1.0 CB B:THR42 4.0 67.3 1.0 OH B:TYR179 4.0 96.0 1.0 CG B:ARG101 4.1 76.8 1.0 CD B:LYS100 4.1 65.5 1.0 N1 B:PYZ504 4.2 90.1 0.5 N2 B:PYZ504 4.2 90.1 0.5 CB B:LYS100 4.2 66.6 1.0 O1 B:PO4507 4.3 114.8 1.0 CE B:LYS100 4.4 65.7 1.0 C B:LYS100 4.4 70.2 1.0 O B:LYS100 4.4 71.0 1.0 N B:ARG101 4.5 71.5 1.0 NH1 B:ARG101 4.6 83.3 1.0 CA B:ARG101 4.7 73.0 1.0 O3 B:PO4507 4.8 114.9 1.0 CZ B:ARG101 4.8 82.3 1.0 NE B:ARG101 5.0 80.6 1.0 CA B:THR42 5.0 64.8 1.0 CA B:LYS100 5.0 67.0 1.0

Iodine binding site 6 out of 7 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 within 5.0Å range: probe atom residue distance (Å) B Occ B:I504 b:185.0 occ:0.25 I4 B:PYZ504 0.0 185.0 0.2 N2 B:PYZ504 0.8 90.1 0.5 C3 B:PYZ504 1.0 89.9 0.5 N1 B:PYZ504 1.5 90.1 0.5 C4 B:PYZ504 1.8 89.8 0.5 C5 B:PYZ504 2.0 89.9 0.5 C4 B:PYZ504 2.1 185.0 0.2 C5 B:PYZ504 3.1 185.0 0.2 C3 B:PYZ504 3.1 185.0 0.2 NH2 B:ARG105 3.4 105.0 1.0 I4 B:PYZ504 3.7 89.8 0.5 OH B:TYR179 4.1 96.0 1.0 CA B:ARG101 4.2 73.0 1.0 N1 B:PYZ504 4.2 185.0 0.2 N2 B:PYZ504 4.2 185.0 0.2 CG B:ARG101 4.4 76.8 1.0 CZ B:ARG105 4.4 105.6 1.0 NH1 B:ARG101 4.4 83.3 1.0 CE1 B:TYR179 4.5 92.3 1.0 NE B:ARG105 4.5 104.1 1.0 CB B:ARG101 4.5 74.6 1.0 CG2 B:THR256 4.7 109.9 1.0 O B:ARG101 4.7 75.5 1.0 O B:LYS100 4.7 71.0 1.0 CZ B:TYR179 4.7 93.6 1.0 CB B:THR256 4.8 109.5 1.0 C B:ARG101 4.9 74.5 1.0

Iodine binding site 7 out of 7 in the Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 within 5.0Å range: probe atom residue distance (Å) B Occ B:I505 b:136.7 occ:0.75 I4 B:PYZ505 0.0 136.7 0.8 C4 B:PYZ505 2.1 136.6 0.8 C5 B:PYZ505 3.1 136.5 0.8 C3 B:PYZ505 3.1 136.5 0.8 OD1 B:ASP115 3.8 114.4 1.0 NE B:ARG101 3.9 80.6 1.0 CD2 B:HIS257 3.9 111.7 1.0 OD2 B:ASP98 4.0 78.1 1.0 NE2 B:HIS257 4.0 112.6 1.0 CD B:ARG101 4.1 78.5 1.0 O B:ASP115 4.1 103.4 1.0 CG B:ASP115 4.1 113.6 1.0 CB B:HIS118 4.1 96.6 1.0 N1 B:PYZ505 4.2 136.4 0.8 CB B:ASP115 4.2 107.7 1.0 N2 B:PYZ505 4.2 136.4 0.8 NE1 B:TRP119 4.2 80.6 1.0 CZ B:ARG101 4.3 82.3 1.0 CA B:ASP115 4.3 105.3 1.0 CG B:HIS118 4.4 102.7 1.0 C B:ASP115 4.7 103.5 1.0 NH1 B:ARG101 4.7 83.3 1.0 NH2 B:ARG101 4.7 81.1 1.0 CE2 B:TRP119 4.8 80.3 1.0 ND1 B:HIS118 4.8 105.5 1.0 OD2 B:ASP115 4.8 116.6 1.0 CZ2 B:TRP119 4.9 80.7 1.0

N.Mohamad, A.O'donoghue, A.L.Kantsadi, I.Vakonakis. Structures of P. Falciparum HSP70-X Nucleotide Binding Domain with Small Molecule Ligands To Be Published.