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Iodine in PDB 6axw: Structure of the I124A Mutant of the Hiv-1 Capsid Protein

Protein crystallography data

The structure of Structure of the I124A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axw 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) 57.95 / 2.40
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 92.611, 92.611, 57.954, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 23.6

Other elements in 6axw:

The structure of Structure of the I124A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein (pdb code 6axw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the Structure of the I124A Mutant of the Hiv-1 Capsid Protein, PDB code: 6axw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 6axw

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Iodine binding site 1 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:44.8
occ:0.93
 N A:LYS158 3.7 51.0 1.0
CD A:PRO157 3.9 49.1 1.0
N A:GLU159 3.9 46.6 1.0
CA A:GLY156 3.9 43.0 1.0
N A:PRO157 4.0 46.3 1.0
C A:GLY156 4.1 43.5 1.0
C A:LYS158 4.1 50.0 1.0
CA A:LYS158 4.2 52.7 1.0
CB A:LYS158 4.2 56.8 1.0
CB A:GLU159 4.3 43.2 1.0
CA A:GLU159 4.5 44.8 1.0
CG A:PRO157 4.5 51.4 1.0
O A:LYS158 4.7 50.5 1.0
O A:GLY156 4.7 40.5 1.0
C A:PRO157 4.8 50.0 1.0
CA A:PRO157 4.9 48.8 1.0
CG A:LYS158 5.0 61.3 1.0

Iodine binding site 2 out of 9 in 6axw

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Iodine binding site 2 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:39.2
occ:0.78
 O A:HOH468 3.6 45.3 1.0
NH1 A:ARG173 3.8 37.4 1.0
CD A:ARG173 4.0 35.9 1.0
OE1 A:GLU35 4.0 46.1 1.0
CG A:LYS170 4.1 43.6 1.0
CG A:PRO34 4.4 41.8 1.0
CD A:PRO34 4.5 41.4 1.0
CB A:PRO34 4.5 40.9 1.0
CA A:LYS170 4.6 37.2 1.0
CB A:LYS170 4.6 40.5 1.0
CZ A:ARG173 4.6 38.4 1.0
NE A:ARG173 4.7 37.6 1.0
NZ A:LYS170 4.7 53.0 1.0
CD A:LYS170 4.8 46.4 1.0
OG A:SER33 4.9 48.1 1.0
O A:LYS170 4.9 38.5 1.0
CD A:GLU35 4.9 44.8 1.0

Iodine binding site 3 out of 9 in 6axw

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Iodine binding site 3 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:49.5
occ:0.63
 O A:HOH525 3.3 59.2 1.0
CG2 A:ILE37 3.9 41.0 1.0
CA A:PRO38 4.0 37.1 1.0
N A:PRO38 4.1 36.9 1.0
CB A:SER41 4.2 36.7 1.0
O A:ILE37 4.2 36.1 1.0
C A:ILE37 4.3 36.6 1.0
CB A:PRO38 4.4 38.2 1.0
OG A:SER41 4.5 39.1 1.0
O A:HOH437 4.5 58.1 1.0
CD1 A:ILE135 4.5 40.0 1.0
CD A:PRO38 4.6 37.2 1.0
CG2 A:ILE135 4.7 35.4 1.0
CB A:ILE37 4.9 39.4 1.0

Iodine binding site 4 out of 9 in 6axw

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Iodine binding site 4 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:46.7
occ:0.64
 CE A:MET144 3.9 66.2 1.0
CG A:MET144 4.2 57.8 1.0
CE1 A:TYR145 4.3 58.4 1.0
CD1 A:TYR145 4.5 57.0 1.0
SD A:MET144 4.5 62.4 1.0
O A:MET144 4.7 55.3 1.0

Iodine binding site 5 out of 9 in 6axw

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Iodine binding site 5 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:55.2
occ:0.47
 CE A:LYS182 3.6 66.5 1.0
CA A:ARG173 3.7 36.6 1.0
N A:ARG173 3.7 36.8 1.0
CG A:LEU172 4.0 39.3 1.0
C A:LEU172 4.0 37.9 1.0
CD2 A:LEU172 4.1 39.9 1.0
CB A:ARG173 4.1 35.3 1.0
CD A:LYS182 4.2 62.5 1.0
O A:LEU172 4.2 39.5 1.0
CB A:LEU172 4.3 36.4 1.0
O A:TYR169 4.5 37.1 1.0
O A:HOH440 4.7 50.0 1.0
CG A:ARG173 4.7 36.1 1.0
CA A:LEU172 4.8 36.8 1.0
CD1 A:TYR169 4.8 35.1 1.0
NZ A:LYS182 4.9 66.8 1.0
C A:ARG173 5.0 37.6 1.0

Iodine binding site 6 out of 9 in 6axw

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Iodine binding site 6 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:52.6
occ:0.41
 C A:GLY206 3.8 58.7 1.0
N A:PRO207 3.9 61.4 1.0
O A:GLY206 4.0 56.1 1.0
O A:LEU202 4.0 46.8 1.0
CA A:LYS203 4.1 49.2 1.0
CA A:PRO207 4.2 60.0 1.0
CG1 A:VAL191 4.3 41.8 1.0
CA A:GLY206 4.3 57.8 1.0
CG2 A:VAL191 4.4 40.6 1.0
CG A:LYS203 4.5 55.3 1.0
CB A:PRO207 4.6 63.7 1.0
C A:LEU202 4.6 45.6 1.0
N A:LYS203 4.6 48.1 1.0
CD A:PRO207 4.7 63.7 1.0
CB A:VAL191 4.7 41.2 1.0
N A:GLY206 4.7 53.4 1.0
O A:LYS203 4.7 47.9 1.0
CG A:PRO207 4.8 66.2 1.0
C A:LYS203 4.9 47.8 1.0
CB A:LYS203 4.9 52.3 1.0

Iodine binding site 7 out of 9 in 6axw

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Iodine binding site 7 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:85.5
occ:0.64
 CD A:PRO17 4.0 53.5 1.0
CB A:ARG18 4.0 55.3 1.0
N A:ARG18 4.0 50.4 1.0
CB A:SER16 4.1 51.6 1.0
N A:PRO17 4.4 51.1 1.0
CG A:PRO17 4.4 55.2 1.0
O A:HOH481 4.5 46.4 1.0
OG A:SER16 4.5 50.7 1.0
CB A:PRO17 4.5 53.2 1.0
CA A:ARG18 4.7 50.9 1.0
CA A:SER16 4.9 52.0 1.0
C A:SER16 4.9 49.9 1.0
CA A:PRO17 4.9 51.2 1.0
C A:PRO17 5.0 49.5 1.0

Iodine binding site 8 out of 9 in 6axw

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Iodine binding site 8 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:87.3
occ:0.69
 O A:HOH552 3.1 52.5 1.0
CB A:ALA124 3.7 51.2 1.0
CA A:ALA124 3.9 51.7 1.0
CH2 A:TRP80 3.9 45.6 1.0
CZ2 A:TRP80 4.1 45.5 1.0
CD A:PRO125 4.1 49.8 1.0
CD1 A:ILE129 4.2 46.6 1.0
C A:ALA124 4.4 50.6 1.0
N A:PRO125 4.6 49.6 1.0
CG A:PRO99 4.8 57.3 1.0
O A:HOH505 5.0 57.1 1.0

Iodine binding site 9 out of 9 in 6axw

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Iodine binding site 9 out of 9 in the Structure of the I124A 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 I124A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:82.6
occ:0.66
 O A:HOH431 3.3 46.0 1.0
NE A:ARG18 3.4 67.5 1.0
CD A:ARG18 3.6 63.8 1.0
CG A:ARG18 3.8 58.8 1.0
CZ A:ARG18 4.3 72.4 1.0
NH1 A:ARG18 4.7 75.1 1.0
CB A:ALA22 4.7 40.3 1.0
O A:ARG18 4.9 44.8 1.0

Reference:

M.Novikova, L.J.Adams, J.Fontana, A.T.Gres, M.Balasubramaniam, D.C.Winkler, S.B.Kudchodkar, F.Soheilian, S.G.Sarafianos, A.C.Steven, E.O.Freed. Identification of A Structural Element in Hiv-1 Gag Required For Virus Particle Assembly and Maturation. Mbio V. 9 2018.
ISSN: ESSN 2150-7511
PubMed: 30327442
DOI: 10.1128/MBIO.01567-18
Page generated: Sun Aug 11 22:33:46 2024

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