Iodine in PDB 6aya: Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide

The structure of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide, PDB code: 6aya was solved by A.T.Gres, K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.24 / 2.40
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	92.544, 92.544, 58.288, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 27.4

The structure of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iodine atom in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide (pdb code 6aya). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide, PDB code: 6aya:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:62.6 occ:0.78 N A:LYS158 3.6 94.9 1.0 N A:GLU159 3.8 89.7 1.0 CB A:LYS158 3.9 0.3 1.0 CA A:GLY156 3.9 70.8 1.0 C A:LYS158 4.0 0.4 1.0 CD A:PRO157 4.0 75.7 1.0 CA A:LYS158 4.0 0.5 1.0 N A:PRO157 4.1 76.0 1.0 C A:GLY156 4.1 73.7 1.0 CB A:GLU159 4.2 67.0 1.0 CA A:GLU159 4.3 81.6 1.0 CG A:PRO157 4.6 77.8 1.0 CG A:LYS158 4.7 0.8 1.0 O A:LYS158 4.7 0.1 1.0 C A:PRO157 4.7 94.9 1.0 O A:GLY156 4.8 64.5 1.0 N A:GLY156 4.9 56.1 1.0 CA A:PRO157 5.0 78.7 1.0

Iodine binding site 2 out of 7 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:51.0 occ:0.77 NH1 A:ARG173 3.8 45.1 1.0 CD A:ARG173 3.9 48.5 1.0 OE1 A:GLU35 4.0 83.6 1.0 CG A:LYS170 4.1 66.6 1.0 CG A:PRO34 4.2 54.5 1.0 CD A:PRO34 4.4 61.4 1.0 CB A:PRO34 4.4 55.2 1.0 OG A:SER33 4.6 63.4 1.0 NZ A:LYS170 4.6 92.7 1.0 CZ A:ARG173 4.7 51.8 1.0 CA A:LYS170 4.7 56.5 1.0 NE A:ARG173 4.8 47.5 1.0 CB A:LYS170 4.8 61.0 1.0 CB A:ARG173 4.9 45.6 1.0 CE A:LYS170 4.9 90.3 1.0 CG A:ARG173 4.9 48.7 1.0 O A:LYS170 4.9 55.7 1.0

Iodine binding site 3 out of 7 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:73.9 occ:0.61 CG A:MET144 3.8 67.5 1.0 SD A:MET144 4.0 81.4 1.0 CE1 A:TYR145 4.4 89.2 1.0 CD1 A:TYR145 4.6 82.5 1.0 O A:MET144 4.7 68.7 1.0

Iodine binding site 4 out of 7 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:86.1 occ:0.54 NH2 A:ARG18 3.3 97.1 1.0 NE A:ARG18 3.7 93.7 1.0 CZ A:ARG18 4.0 97.8 1.0 O A:ARG18 4.6 69.9 1.0 CB A:ALA22 4.7 41.2 1.0 CB A:ARG18 4.7 66.4 1.0 CD A:ARG18 4.9 79.3 1.0

Iodine binding site 5 out of 7 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:80.2 occ:0.48 NZ A:LYS182 3.5 52.1 1.0 CA A:ARG173 3.7 44.0 1.0 N A:ARG173 3.8 51.9 1.0 CB A:ARG173 4.0 45.6 1.0 CE A:LYS182 4.0 44.4 1.0 CG A:LEU172 4.1 49.9 1.0 CD A:LYS182 4.2 47.9 1.0 C A:LEU172 4.2 47.0 1.0 CD2 A:LEU172 4.4 57.3 1.0 O A:LEU172 4.4 42.0 1.0 CG A:ARG173 4.4 48.7 1.0 O A:HOH404 4.4 43.5 1.0 CB A:LEU172 4.6 46.0 1.0 O A:TYR169 4.6 49.2 1.0 CD1 A:TYR169 4.8 49.0 1.0

Iodine binding site 6 out of 7 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:0.5 occ:0.39 CD A:PRO17 3.6 67.0 1.0 CB A:SER16 3.8 44.4 1.0 CG A:ARG18 3.9 65.6 1.0 CD A:ARG18 4.1 79.3 1.0 N A:PRO17 4.2 59.4 1.0 N A:ARG18 4.3 54.8 1.0 CG A:PRO17 4.3 63.9 1.0 OG A:SER16 4.3 52.6 1.0 CB A:PRO17 4.7 59.2 1.0 CA A:SER16 4.7 55.8 1.0 CB A:ARG18 4.7 66.4 1.0 C A:SER16 4.8 62.3 1.0 CA A:PRO17 4.9 64.6 1.0

Iodine binding site 7 out of 7 in the Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Structure of the Native Full-Length Hiv-1 Capsid Protein in Complex with NUP153 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:I307 b:0.8 occ:0.52 O A:HOH451 3.5 75.5 1.0 CG2 A:ILE124 4.1 73.5 1.0 CD A:PRO125 4.4 83.5 1.0 CH2 A:TRP80 4.5 52.2 1.0 O A:HOH403 4.7 75.3 1.0 CA A:ILE124 4.7 91.6 1.0 CD1 A:ILE129 4.8 57.1 1.0 CB A:ILE124 4.8 81.1 1.0

A.T.Gres, K.A.Kirby, S.G.Sarafianos. Characterization of Hiv-1 Capsid Interactions with Host Cell Factors To Be Published.