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Iodine in PDB 6axs: Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein

Protein crystallography data

The structure of Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axs 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) 36.08 / 2.40
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 92.475, 92.475, 57.675, 90.00, 90.00, 120.00
R / Rfree (%) 22.8 / 26.6

Other elements in 6axs:

The structure of Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein (pdb code 6axs). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axs:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 6axs

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Iodine binding site 1 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


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 V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:48.2
occ:0.84
 N A:LYS158 3.7 63.3 1.0
N A:GLU159 3.7 53.1 1.0
CA A:GLY156 3.8 59.6 1.0
CD A:PRO157 3.9 71.0 1.0
CB A:LYS158 4.0 68.4 1.0
C A:LYS158 4.0 57.5 1.0
CA A:LYS158 4.1 63.5 1.0
C A:GLY156 4.1 61.9 1.0
N A:PRO157 4.1 70.0 1.0
CB A:GLU159 4.1 44.7 1.0
CA A:GLU159 4.3 44.3 1.0
CG A:PRO157 4.5 65.1 1.0
O A:LYS158 4.7 57.7 1.0
C A:PRO157 4.8 64.1 1.0
O A:GLY156 4.8 49.4 1.0
N A:GLY156 4.9 52.0 1.0
CA A:PRO157 5.0 65.2 1.0

Iodine binding site 2 out of 10 in 6axs

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Iodine binding site 2 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


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 V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:56.1
occ:0.82
 NH1 A:ARG173 3.7 44.8 1.0
CG A:LYS170 3.8 61.4 1.0
OE1 A:GLU35 4.0 56.6 1.0
CD A:ARG173 4.0 45.3 1.0
CG A:PRO34 4.2 43.5 1.0
NZ A:LYS170 4.3 72.1 1.0
CD A:PRO34 4.4 43.7 1.0
CB A:LYS170 4.5 56.2 1.0
CB A:PRO34 4.5 42.6 1.0
OG A:SER33 4.5 57.6 1.0
CA A:LYS170 4.5 46.8 1.0
CZ A:ARG173 4.7 45.0 1.0
CE A:LYS170 4.7 68.7 1.0
NE A:ARG173 4.8 46.6 1.0
CD A:LYS170 4.9 60.6 1.0

Iodine binding site 3 out of 10 in 6axs

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Iodine binding site 3 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


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 V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:61.9
occ:0.64
 CG A:MET144 3.7 71.7 1.0
SD A:MET144 4.0 73.8 1.0
CE1 A:TYR145 4.2 68.5 1.0
CD1 A:TYR145 4.4 71.5 1.0
O A:MET144 4.6 64.8 1.0

Iodine binding site 4 out of 10 in 6axs

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Iodine binding site 4 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


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 V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:68.7
occ:0.60
 CG2 A:ILE37 3.8 49.4 1.0
CA A:PRO38 3.9 59.5 1.0
O A:ILE37 4.0 40.9 1.0
N A:PRO38 4.0 55.3 1.0
C A:ILE37 4.1 50.6 1.0
CB A:SER41 4.3 59.8 1.0
CD1 A:ILE135 4.5 55.3 1.0
CG A:PRO38 4.6 60.4 1.0
CB A:PRO38 4.6 59.1 1.0
OG A:SER41 4.7 67.8 1.0
CD A:PRO38 4.7 60.0 1.0
CB A:ILE37 4.8 60.8 1.0
CG2 A:ILE135 4.9 36.5 1.0

Iodine binding site 5 out of 10 in 6axs

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Iodine binding site 5 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


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 V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:81.2
occ:0.52
 OG1 A:THR148 3.1 80.7 1.0
OG A:SER146 3.2 67.9 1.0
CB A:ALA174 4.1 37.9 1.0
CB A:SER146 4.2 54.6 1.0
CA A:THR171 4.2 39.1 1.0
CD A:PRO147 4.4 68.6 1.0
CB A:THR148 4.5 70.5 1.0
OG1 A:THR171 4.5 44.2 1.0
NZ A:LYS170 4.6 72.1 1.0
N A:THR171 4.6 47.5 1.0
CA A:SER146 4.6 57.8 1.0
CD A:LYS170 4.7 60.6 1.0
N A:THR148 4.7 70.3 1.0
O A:LYS170 4.7 42.0 1.0
CG A:LYS170 4.7 61.4 1.0
CB A:THR171 4.8 40.5 1.0
CG2 A:THR171 4.8 30.9 1.0
C A:LYS170 4.8 43.1 1.0
N A:PRO147 4.9 70.5 1.0
CG A:PRO147 5.0 63.6 1.0
O A:HOH444 5.0 52.5 1.0

Iodine binding site 6 out of 10 in 6axs

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Iodine binding site 6 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


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 V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:71.0
occ:0.58
 CA A:ARG173 3.8 44.3 1.0
CG A:LEU172 3.8 36.1 1.0
N A:ARG173 3.9 47.8 1.0
CD2 A:LEU172 4.0 37.1 1.0
C A:LEU172 4.0 49.5 1.0
O A:LEU172 4.1 46.7 1.0
NZ A:LYS182 4.1 60.0 1.0
CD A:LYS182 4.1 52.8 1.0
CB A:ARG173 4.2 48.0 1.0
CB A:LEU172 4.4 38.9 1.0
O A:HOH417 4.4 52.8 1.0
CE A:LYS182 4.5 54.6 1.0
O A:TYR169 4.6 44.2 1.0
CG A:ARG173 4.7 47.2 1.0
CA A:LEU172 4.9 45.4 1.0
CD1 A:TYR169 4.9 43.4 1.0

Iodine binding site 7 out of 10 in 6axs

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Iodine binding site 7 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


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 V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:99.0
occ:0.63
 CB A:ASN21 3.6 68.1 1.0
CA A:ASN21 3.8 56.3 1.0
N A:ASN21 4.0 55.6 1.0
ND2 A:ASN21 4.0 74.3 1.0
CG A:ASN21 4.3 78.7 1.0
O A:PRO17 4.4 63.7 1.0
CG A:LEU20 4.7 48.2 1.0
C A:LEU20 4.7 55.0 1.0
CD2 A:LEU20 4.7 44.6 1.0

Iodine binding site 8 out of 10 in 6axs

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Iodine binding site 8 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:0.0
occ:0.55
 CL A:CL314 3.7 73.0 1.0
CG2 A:ILE124 3.9 69.9 1.0
CD A:PRO125 4.1 50.3 1.0
CG1 A:ILE124 4.3 77.7 1.0
CA A:ILE124 4.3 73.3 1.0
CB A:ILE124 4.4 70.7 1.0
CD1 A:ILE129 4.5 42.0 1.0
CH2 A:TRP80 4.6 44.4 1.0
O A:PRO123 4.8 83.1 1.0
O A:HOH401 4.9 35.5 1.0
N A:PRO125 5.0 54.0 1.0

Iodine binding site 9 out of 10 in 6axs

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Iodine binding site 9 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:0.9
occ:0.48
 NH2 A:ARG18 3.3 0.1 1.0
NE A:ARG18 3.5 0.8 1.0
CZ A:ARG18 3.8 0.1 1.0
CB A:ALA22 4.2 64.8 1.0
O A:ARG18 4.5 96.4 1.0
CD A:ARG18 4.7 0.5 1.0

Iodine binding site 10 out of 10 in 6axs

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Iodine binding site 10 out of 10 in the Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Structure of the V11I/T58A/P122A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I310

b:77.6
occ:0.40
 O A:HOH440 3.7 47.2 1.0
CD1 A:ILE153 3.8 52.8 1.0
NH2 A:ARG167 3.9 52.7 1.0
CG2 A:THR148 3.9 71.2 1.0
CB A:THR148 4.7 70.5 1.0
O A:ASP152 4.9 63.6 1.0
CB A:ASP152 4.9 58.1 1.0
CZ A:ARG167 5.0 46.0 1.0

Reference:

M.Novikova, A.T.Gres, K.A.Kirby, S.G.Sarafianos, E.O.Freed. Identification of A Novel Element in Hiv-1 Capsid Critical For Assembly and Maturation To Be Published.
Page generated: Sun Aug 11 22:31:13 2024

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