Iodine in PDB 4ph3: N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)

The structure of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin), PDB code: 4ph3 was solved by F.Trajtenberg, G.Obal, O.Pritsch, A.Buschiazzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.37 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.613, 66.242, 81.355, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 55;

Binding sites:

The binding sites of Iodine atom in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) (pdb code 4ph3). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 55 binding sites of Iodine where determined in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin), PDB code: 4ph3:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:34.7 occ:0.33 I A:IOD201 0.0 34.7 0.3 I A:IOD201 1.3 36.7 0.5 N A:GLN93 4.0 38.9 1.0 CG A:PRO92 4.1 44.7 1.0 CA A:GLN93 4.1 37.7 1.0 CB A:GLN93 4.2 38.2 1.0 C A:PRO92 4.4 42.4 1.0 CB A:PRO92 4.4 40.2 1.0 CG A:GLN93 4.5 41.1 1.0 O A:PRO92 4.8 41.9 1.0 CA A:PRO92 4.9 38.5 1.0

Iodine binding site 2 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I201 b:36.7 occ:0.46 I A:IOD201 0.0 36.7 0.5 I A:IOD201 1.3 34.7 0.3 CA A:GLN93 4.1 37.7 1.0 N A:GLN93 4.2 38.9 1.0 C A:PRO92 4.3 42.4 1.0 O A:PRO92 4.4 41.9 1.0 CB A:GLN93 4.4 38.2 1.0 CG A:GLN93 4.5 41.1 1.0 CB A:PRO92 4.6 40.2 1.0 CG A:PRO92 4.7 44.7 1.0

Iodine binding site 3 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I202 b:48.3 occ:0.64 ND2 A:ASN85 3.7 82.7 1.0 CA A:ASN85 3.8 54.4 1.0 CB A:LEU87 3.9 52.3 1.0 O A:GLU82 3.9 47.8 1.0 O A:LEU87 3.9 57.5 1.0 N A:LEU87 4.0 53.3 1.0 CA A:GLU82 4.1 43.1 1.0 C A:ASN85 4.1 59.0 1.0 CD2 A:PHE90 4.2 39.4 1.0 CG A:ASN85 4.3 88.8 1.0 CA A:LEU87 4.3 52.5 1.0 O A:ALA81 4.4 47.7 1.0 C A:GLU82 4.4 48.4 1.0 CG A:GLU82 4.5 46.4 1.0 CG A:LEU87 4.5 56.7 1.0 N A:THR86 4.5 54.3 1.0 O A:ASN85 4.5 60.1 1.0 I A:IOD214 4.5 67.8 0.3 CB A:PHE90 4.6 39.6 1.0 C A:LEU87 4.6 56.5 1.0 N A:ASN85 4.6 54.0 1.0 CD1 A:LEU87 4.6 56.9 1.0 CB A:ASN85 4.6 58.0 1.0 O A:PHE90 4.7 44.8 1.0 CB A:GLU82 4.8 43.7 1.0 CG A:PHE90 4.9 39.2 1.0 N A:GLU82 4.9 44.1 1.0 OD1 A:ASN85 5.0 83.5 1.0

Iodine binding site 4 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I203 b:54.4 occ:0.59 CE A:LYS122 3.7 51.5 1.0 NE2 A:GLN38 3.7 66.1 1.0 CG A:GLN34 3.9 56.5 1.0 CA A:GLN34 4.1 35.2 1.0 CG2 A:ILE37 4.4 33.4 1.0 CB A:GLN34 4.4 37.6 1.0 NZ A:LYS122 4.5 47.9 1.0 CB A:ILE37 4.5 32.5 1.0 O A:GLN34 4.7 34.8 1.0 I A:IOD219 4.8 3.0 0.1 N A:GLN34 4.8 34.7 1.0 CD A:LYS122 4.8 46.4 1.0 OE1 A:GLN34 4.8 78.3 1.0 CG1 A:ILE37 4.8 33.7 1.0 CD A:GLN34 4.8 78.6 1.0 CD A:GLN38 4.9 78.4 1.0 C A:GLN34 5.0 35.8 1.0

Iodine binding site 5 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:52.6 occ:0.40 I A:IOD204 0.0 52.6 0.4 I A:IOD204 1.8 47.1 0.2 NZ A:LYS23 3.5 64.3 1.0 CG A:GLN20 3.7 49.0 1.0 CD A:LYS23 3.8 44.8 1.0 CE A:LYS23 4.0 56.7 1.0 CB A:GLN20 4.1 35.2 1.0 CE A:LYS24 4.2 89.8 1.0 CA A:GLN20 4.3 33.9 1.0 CD A:GLN20 4.4 70.6 1.0 NE2 A:GLN20 4.4 64.0 1.0 NZ A:LYS24 4.6 98.6 1.0 CD2 A:TYR60 4.7 25.9 1.0 CE2 A:TYR60 4.8 26.0 1.0 CG A:LYS23 4.8 32.5 1.0 O A:GLN20 4.9 41.3 1.0

Iodine binding site 6 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I204 b:47.1 occ:0.18 I A:IOD204 0.0 47.1 0.2 I A:IOD204 1.8 52.6 0.4 NE2 A:GLN20 3.4 64.0 1.0 O A:HOH324 3.4 47.2 1.0 CG A:GLN20 3.4 49.0 1.0 CD A:GLN20 3.8 70.6 1.0 CE2 A:TYR60 4.1 26.0 1.0 CB A:GLN20 4.5 35.2 1.0 CD2 A:TYR60 4.5 25.9 1.0 CA A:GLN20 4.9 33.9 1.0 CD A:LYS23 5.0 44.8 1.0 OE1 A:GLN20 5.0 67.7 1.0

Iodine binding site 7 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I205 b:50.4 occ:0.47 O A:HOH337 3.3 54.5 1.0 NE1 A:TRP14 3.5 29.4 1.0 OE1 A:GLN46 3.8 67.5 1.0 O A:HOH338 3.8 51.1 1.0 CD1 A:TRP14 3.9 29.6 1.0 CA A:ALA43 4.0 28.6 1.0 CB A:ALA43 4.2 29.1 1.0 O A:ALA43 4.2 33.2 1.0 CB A:GLN46 4.3 36.1 1.0 OE1 A:GLU18 4.4 44.7 1.0 CD A:GLN46 4.6 74.3 1.0 C A:ALA43 4.6 32.7 1.0 CD1 A:ILE22 4.7 30.0 1.0 CE2 A:TRP14 4.8 30.0 1.0 CB A:ALA47 4.8 34.3 1.0 O B:HOH342 4.9 53.3 1.0

Iodine binding site 8 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:51.7 occ:0.39 I A:IOD206 0.0 51.7 0.4 I A:IOD206 1.7 41.1 0.2 NZ B:LYS29 3.6 73.2 1.0 CA A:GLN46 4.1 35.0 1.0 CE B:LYS29 4.1 54.6 1.0 CG2 B:VAL35 4.1 38.0 1.0 CG A:GLN46 4.2 51.7 1.0 O A:GLN46 4.2 40.2 1.0 CB A:GLN46 4.3 36.1 1.0 CG1 B:VAL35 4.5 38.8 1.0 NE2 A:GLN46 4.7 70.0 1.0 C A:GLN46 4.7 39.5 1.0 CB B:VAL35 4.8 38.3 1.0 CD B:LYS29 4.8 40.0 1.0 CD A:GLN46 5.0 74.3 1.0

Iodine binding site 9 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I206 b:41.1 occ:0.20 I A:IOD206 0.0 41.1 0.2 I A:IOD206 1.7 51.7 0.4 NE2 A:GLN46 3.5 70.0 1.0 CG A:GLN46 3.8 51.7 1.0 NZ B:LYS29 3.9 73.2 1.0 CB A:GLN46 4.0 36.1 1.0 CD A:GLN46 4.1 74.3 1.0 CG1 B:VAL35 4.4 38.8 1.0 CA A:GLN46 4.4 35.0 1.0 CE B:LYS29 4.5 54.6 1.0 CD B:LYS29 4.8 40.0 1.0 O A:GLN46 4.8 40.2 1.0 CG2 B:VAL35 4.9 38.0 1.0

Iodine binding site 10 out of 55 in the N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of N-Terminal Domain of the Capsid Protein From Bovine Leukaemia Virus (with No Beta-Hairpin) within 5.0Å range: probe atom residue distance (Å) B Occ A:I207 b:47.7 occ:0.60 OG1 A:THR98 3.2 41.9 1.0 O A:HOH310 3.6 33.1 1.0 CB A:THR96 3.9 37.4 1.0 CB A:THR98 4.0 40.2 1.0 CG2 A:ILE78 4.1 33.6 1.0 N A:THR98 4.1 33.4 1.0 OG1 A:THR96 4.1 35.9 1.0 N A:LEU97 4.3 31.9 1.0 CG2 A:THR96 4.5 32.3 1.0 I A:IOD220 4.6 54.5 0.3 CG1 A:ILE78 4.6 35.5 1.0 CB A:ILE78 4.7 34.7 1.0 CA A:THR98 4.7 33.5 1.0 CB A:LEU97 4.8 32.9 1.0 CA A:THR96 4.9 31.4 1.0 CA A:LEU97 4.9 32.6 1.0 C A:THR96 4.9 34.8 1.0 C A:LEU97 5.0 36.6 1.0

G.Obal, F.Trajtenberg, F.Carrion, L.Tome, N.Larrieux, X.Zhang, O.Pritsch, A.Buschiazzo. Structural Virology. Conformational Plasticity of A Native Retroviral Capsid Revealed By X-Ray Crystallography. Science V. 349 95 2015.
ISSN: ESSN 1095-9203
PubMed: 26044299
DOI: 10.1126/SCIENCE.AAA5182