Iodine in PDB 7mkc: N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)

The structure of N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74), PDB code: 7mkc was solved by 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)	45.38 / 2.65
Space group	P 6
Cell size a, b, c (Å), α, β, γ (°)	90.358, 90.358, 55.695, 90, 90, 120
R / Rfree (%)	18.3 / 24.2

The binding sites of Iodine atom in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) (pdb code 7mkc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74), PDB code: 7mkc:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I301 b:56.3 occ:0.65 NH1 A:ARG173 3.5 49.2 1.0 CD A:ARG173 3.7 50.3 1.0 NZ A:LYS170 3.7 75.1 1.0 OE1 A:GLU35 3.8 58.4 1.0 CG A:LYS170 4.1 65.0 1.0 CG A:PRO34 4.4 49.8 1.0 CD A:PRO34 4.4 51.3 1.0 CZ A:ARG173 4.5 53.7 1.0 NE A:ARG173 4.5 53.6 1.0 CB A:PRO34 4.6 48.6 1.0 CA A:LYS170 4.6 54.4 1.0 OG A:SER33 4.6 85.8 1.0 CB A:LYS170 4.7 59.5 1.0 CD A:GLU35 4.7 61.8 1.0 CG A:ARG173 4.7 49.2 1.0 CD A:LYS170 4.8 74.3 1.0 CE A:LYS170 4.9 76.8 1.0 O A:LYS170 4.9 52.0 1.0 CB A:ARG173 4.9 51.5 1.0

Iodine binding site 2 out of 6 in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I302 b:162.4 occ:0.56 CA A:GLY156 3.5 59.2 1.0 N A:LYS158 3.7 77.7 1.0 CD A:PRO157 3.7 68.0 1.0 C A:GLY156 3.8 67.2 1.0 N A:PRO157 3.8 69.0 1.0 C A:LYS158 3.9 75.9 1.0 N A:GLU159 4.0 70.3 1.0 CG A:PRO157 4.1 70.7 1.0 CA A:LYS158 4.2 81.5 1.0 CB A:GLU159 4.3 64.7 1.0 O A:LYS158 4.4 79.9 1.0 CB A:LYS158 4.4 95.6 1.0 O A:GLY156 4.4 64.1 1.0 CA A:GLU159 4.5 61.6 1.0 C A:PRO157 4.6 74.1 1.0 CA A:PRO157 4.7 72.7 1.0 N A:GLY156 4.7 55.9 1.0 CB A:PRO157 4.9 69.9 1.0

Iodine binding site 3 out of 6 in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I303 b:114.3 occ:0.67 NH2 A:ARG162 3.6 87.6 1.0 N A:ARG162 3.7 55.0 1.0 CZ A:ARG162 3.9 86.2 1.0 CB A:PHE161 3.9 49.0 1.0 O A:MET215 3.9 54.8 1.0 NE A:ARG162 3.9 91.5 1.0 CB A:ARG162 4.0 67.6 1.0 N A:PHE161 4.0 52.6 1.0 CA A:GLN219 4.2 83.6 1.0 CA A:PHE161 4.3 51.8 1.0 N A:GLN219 4.3 79.2 1.0 O A:CYS218 4.4 77.7 1.0 CA A:ARG162 4.4 56.3 1.0 C A:PHE161 4.4 51.3 1.0 C A:CYS218 4.5 74.1 1.0 CG A:MET215 4.5 76.3 1.0 OE1 A:GLN219 4.6 102.5 1.0 NH1 A:ARG162 4.6 81.4 1.0 CA A:MET215 4.6 66.3 1.0 C A:MET215 4.6 59.5 1.0 CB A:MET215 4.6 68.5 1.0 CG A:ARG162 4.8 83.8 1.0 CB A:PRO160 4.8 59.3 1.0 C A:PRO160 4.8 56.6 1.0 CD A:ARG162 4.9 92.3 1.0 CG A:PHE161 4.9 46.9 1.0 CD2 A:PHE161 4.9 48.7 1.0

Iodine binding site 4 out of 6 in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I304 b:160.4 occ:0.68 CD A:PRO17 3.8 63.8 1.0 CG A:PRO17 3.8 63.0 1.0 N A:ARG18 3.9 58.1 1.0 CB A:ARG18 4.1 77.9 1.0 CB A:SER16 4.1 62.4 1.0 N A:PRO17 4.3 61.8 1.0 CB A:PRO17 4.3 62.4 1.0 OG A:SER16 4.6 59.2 1.0 CA A:ARG18 4.6 65.1 1.0 CA A:PRO17 4.7 60.0 1.0 C A:PRO17 4.8 57.8 1.0 CG A:ARG18 4.8 85.4 1.0 CA A:SER16 4.9 60.2 1.0 C A:SER16 4.9 57.4 1.0

Iodine binding site 5 out of 6 in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I305 b:115.6 occ:0.63 O A:HOH408 3.1 43.3 1.0 O A:HOH412 4.5 41.1 1.0

Iodine binding site 6 out of 6 in the N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of N74D Mutant of the Hiv-1 Capsid Protein in Complex with Pf-3450074 (PF74) within 5.0Å range: probe atom residue distance (Å) B Occ A:I306 b:101.0 occ:0.52 CA A:PRO125 3.4 65.7 1.0 C A:PRO125 3.5 61.1 1.0 N A:GLU128 3.5 54.9 1.0 N A:GLY127 3.6 56.8 1.0 CB A:PRO125 3.7 65.3 1.0 CE A:MET118 3.8 60.4 1.0 CG A:GLU128 3.8 73.8 1.0 N A:VAL126 3.8 57.9 1.0 CA A:GLY127 3.8 51.1 1.0 O A:PRO125 3.9 65.5 1.0 CG A:MET118 3.9 60.3 1.0 C A:GLY127 4.1 51.0 1.0 CB A:GLU128 4.2 64.3 1.0 SD A:MET118 4.4 65.1 1.0 CA A:GLU128 4.5 57.6 1.0 CB A:MET118 4.6 63.4 1.0 C A:VAL126 4.6 57.0 1.0 N A:PRO125 4.8 67.1 1.0 CA A:VAL126 4.8 57.9 1.0 O A:ALA47 4.9 57.5 1.0 O A:ILE124 4.9 72.6 1.0

A.Selyutina, L.M.Simons, K.A.Kirby, A.Bulnes-Ramos, P.Hu, S.G.Sarafianos, J.F.Hultquist, F.Diaz-Griffero. TRIM5ALPHA Restriction of Hiv-1-N74D Viruses in Lymphocytes Is Caused By A Loss of Cyclophilin A Protection. Viruses V. 14 363 2022.
ISSN: ESSN 1999-4915
PubMed: 35215956
DOI: 10.3390/V14020363