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

Protein crystallography data

The structure of Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818, PDB code: 7ooh 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 (%) 22.1 / 23.6

Other elements in 7ooh:

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

Iodine Binding Sites:

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

Iodine binding site 1 out of 5 in 7ooh

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Iodine binding site 1 out of 5 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:I504

b:155.9
occ:0.82
 I4 A:PYZ504 0.0 155.9 0.8
C4 A:PYZ504 0.9 47.4 0.2
C3 A:PYZ504 1.1 47.4 0.2
C5 A:PYZ504 1.2 47.4 0.2
N1 A:PYZ504 1.5 47.5 0.2
N2 A:PYZ504 1.5 47.6 0.2
C4 A:PYZ504 2.1 156.1 0.8
I4 A:PYZ504 2.9 47.4 0.2
C5 A:PYZ504 3.1 156.2 0.8
C3 A:PYZ504 3.1 156.1 0.8
O A:HOH1122 3.6 55.7 1.0
NH2 A:ARG105 3.6 57.0 1.0
OH A:TYR179 3.7 53.3 1.0
N1 A:PYZ504 4.2 156.2 0.8
CE1 A:TYR179 4.2 50.1 1.0
N2 A:PYZ504 4.2 156.1 0.8
CA A:ARG101 4.2 49.0 1.0
CZ A:TYR179 4.4 51.4 1.0
O A:LYS100 4.4 50.1 1.0
CG A:ARG101 4.4 50.6 1.0
CE1 A:PHE180 4.6 46.5 1.0
NH1 A:ARG101 4.7 48.8 1.0
CB A:ARG101 4.7 49.3 1.0
CZ A:ARG105 4.7 57.6 1.0
O A:HOH1126 4.7 43.8 1.0
CG2 A:THR256 4.8 58.7 1.0
NE A:ARG105 4.8 57.7 1.0
N A:ARG101 4.9 48.7 1.0
O A:ARG101 5.0 51.4 1.0
C A:LYS100 5.0 48.9 1.0
CB A:THR256 5.0 58.7 1.0

Iodine binding site 2 out of 5 in 7ooh

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Iodine binding site 2 out of 5 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:I504

b:47.4
occ:0.17
 I4 A:PYZ504 0.0 47.4 0.2
C4 A:PYZ504 0.9 156.1 0.8
C3 A:PYZ504 0.9 156.1 0.8
C5 A:PYZ504 1.3 156.2 0.8
N2 A:PYZ504 1.4 156.1 0.8
N1 A:PYZ504 1.5 156.2 0.8
C4 A:PYZ504 2.1 47.4 0.2
I4 A:PYZ504 2.9 155.9 0.8
C5 A:PYZ504 3.1 47.4 0.2
C3 A:PYZ504 3.1 47.4 0.2
OG1 A:THR42 3.4 52.7 1.0
CG A:LYS100 3.9 43.8 1.0
OH A:TYR179 3.9 53.3 1.0
CG2 A:THR234 4.0 52.5 1.0
CG A:ARG101 4.1 50.6 1.0
CG2 A:THR42 4.1 50.6 1.0
CD A:LYS100 4.2 45.9 1.0
O A:LYS100 4.2 50.1 1.0
N1 A:PYZ504 4.2 47.5 0.2
N2 A:PYZ504 4.2 47.6 0.2
C A:LYS100 4.2 48.9 1.0
CB A:LYS100 4.3 45.6 1.0
CB A:THR42 4.3 50.6 1.0
O3 A:PO4507 4.3 81.1 1.0
N A:ARG101 4.4 48.7 1.0
CE A:LYS100 4.4 46.2 1.0
CA A:ARG101 4.5 49.0 1.0
NH1 A:ARG101 4.8 48.8 1.0
CB A:ARG101 4.9 49.3 1.0
CZ A:ARG101 4.9 51.1 1.0
CA A:LYS100 4.9 47.7 1.0
CE1 A:PHE180 4.9 46.5 1.0

Iodine binding site 3 out of 5 in 7ooh

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Iodine binding site 3 out of 5 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
B:I504

b:90.9
occ:0.51
 I4 B:PYZ504 0.0 90.9 0.5
N1 B:PYZ504 0.7 246.1 0.5
N2 B:PYZ504 0.9 246.1 0.5
C5 B:PYZ504 1.4 246.1 0.5
C3 B:PYZ504 1.5 246.1 0.5
C4 B:PYZ504 1.8 246.1 0.5
C4 B:PYZ504 2.1 90.9 0.5
OG1 B:THR42 2.9 69.1 1.0
C5 B:PYZ504 3.1 91.0 0.5
C3 B:PYZ504 3.1 91.0 0.5
CG2 B:THR234 3.8 93.4 1.0
I4 B:PYZ504 3.8 246.2 0.5
CG2 B:THR42 3.9 68.2 1.0
CG B:LYS100 4.0 66.0 1.0
CB B:THR42 4.0 67.3 1.0
OH B:TYR179 4.1 96.4 1.0
CD B:LYS100 4.1 65.4 1.0
CG B:ARG101 4.1 76.8 1.0
N1 B:PYZ504 4.2 91.1 0.5
N2 B:PYZ504 4.2 91.1 0.5
CB B:LYS100 4.3 66.8 1.0
O1 B:PO4506 4.3 115.4 1.0
CE B:LYS100 4.4 65.2 1.0
C B:LYS100 4.4 70.4 1.0
O B:LYS100 4.4 71.1 1.0
N B:ARG101 4.5 71.6 1.0
NH1 B:ARG101 4.7 82.7 1.0
CA B:ARG101 4.7 73.0 1.0
O3 B:PO4506 4.8 115.6 1.0
CZ B:ARG101 4.8 81.9 1.0
NE B:ARG101 5.0 80.3 1.0
CA B:THR42 5.0 64.8 1.0
CB B:THR234 5.0 92.9 1.0

Iodine binding site 4 out of 5 in 7ooh

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Iodine binding site 4 out of 5 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
B:I504

b:246.2
occ:0.49
 I4 B:PYZ504 0.0 246.2 0.5
N2 B:PYZ504 0.9 91.1 0.5
C3 B:PYZ504 1.1 91.0 0.5
N1 B:PYZ504 1.7 91.1 0.5
C4 B:PYZ504 2.0 90.9 0.5
C4 B:PYZ504 2.1 246.1 0.5
C5 B:PYZ504 2.2 91.0 0.5
C5 B:PYZ504 3.1 246.1 0.5
C3 B:PYZ504 3.1 246.1 0.5
NH2 B:ARG105 3.4 105.1 1.0
I4 B:PYZ504 3.8 90.9 0.5
CA B:ARG101 4.1 73.0 1.0
N1 B:PYZ504 4.2 246.1 0.5
N2 B:PYZ504 4.2 246.1 0.5
OH B:TYR179 4.2 96.4 1.0
CG B:ARG101 4.3 76.8 1.0
NH1 B:ARG101 4.3 82.7 1.0
CZ B:ARG105 4.4 105.9 1.0
CB B:ARG101 4.4 74.7 1.0
NE B:ARG105 4.5 104.7 1.0
CE1 B:TYR179 4.6 92.7 1.0
O B:ARG101 4.6 75.3 1.0
CG2 B:THR256 4.6 110.5 1.0
CB B:THR256 4.7 110.1 1.0
O B:LYS100 4.8 71.1 1.0
CZ B:TYR179 4.9 94.0 1.0
C B:ARG101 4.9 74.3 1.0

Iodine binding site 5 out of 5 in 7ooh

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Iodine binding site 5 out of 5 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:I507

b:169.3
occ:1.00
 OD1 B:ASP115 3.7 114.2 1.0
CD2 B:HIS257 3.8 112.1 1.0
NE2 B:HIS257 3.9 113.0 1.0
NE B:ARG101 3.9 80.3 1.0
CG B:ASP115 4.0 113.4 1.0
CD B:ARG101 4.0 78.4 1.0
OD2 B:ASP98 4.1 77.0 1.0
O B:ASP115 4.1 103.0 1.0
CB B:ASP115 4.1 107.4 1.0
CA B:ASP115 4.2 105.1 1.0
CB B:HIS118 4.2 96.8 1.0
CZ B:ARG101 4.3 81.9 1.0
NE1 B:TRP119 4.3 80.2 1.0
CG B:HIS118 4.5 103.2 1.0
C B:ASP115 4.6 103.2 1.0
NH1 B:ARG101 4.7 82.7 1.0
OD2 B:ASP115 4.7 116.6 1.0
NH2 B:ARG101 4.7 80.7 1.0
ND1 B:HIS118 4.7 106.2 1.0
CE2 B:TRP119 4.8 80.0 1.0
CZ2 B:TRP119 4.9 80.3 1.0

Reference:

N.Mohamad, A.O'donoghue, A.L.Kantsadi, I.Vakonakis. Plasmodium Falciparum HSP70-X Chaperone Nucleotide Binding Domain in Complex with Ncl-00023818 To Be Published.
Page generated: Mon Aug 12 01:52:18 2024

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