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Iodine in PDB 3p05: X-Ray Structure of Pentameric Hiv-1 Ca

Protein crystallography data

The structure of X-Ray Structure of Pentameric Hiv-1 Ca, PDB code: 3p05 was solved by O.Pornillos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.58 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.723, 130.308, 81.831, 90.00, 97.37, 90.00
R / Rfree (%) 23 / 26.6

Iodine Binding Sites:

The binding sites of Iodine atom in the X-Ray Structure of Pentameric Hiv-1 Ca (pdb code 3p05). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the X-Ray Structure of Pentameric Hiv-1 Ca, PDB code: 3p05:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 3p05

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Iodine binding site 1 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I232

b:80.5
occ:1.00
 CD E:LYS170 3.5 65.4 1.0
NH1 E:ARG173 3.6 47.6 1.0
N A:GLY61 3.7 40.8 1.0
OE1 E:GLU35 3.7 51.4 1.0
CD E:PRO34 4.0 43.9 1.0
CD E:ARG173 4.0 56.1 1.0
CG E:PRO34 4.1 46.5 1.0
OG E:SER33 4.1 70.0 1.0
CG A:GLN63 4.1 42.4 1.0
NE2 A:GLN63 4.1 47.4 1.0
CD A:GLN63 4.2 55.3 1.0
CE E:LYS170 4.3 76.3 1.0
CA A:GLY60 4.3 46.1 1.0
CB E:PRO34 4.5 42.2 1.0
C A:GLY60 4.5 52.8 1.0
CZ E:ARG173 4.6 46.7 1.0
CG E:LYS170 4.6 57.9 1.0
CA A:GLY61 4.6 52.3 1.0
CA E:LYS170 4.7 49.4 1.0
CB E:LYS170 4.7 52.2 1.0
CD E:GLU35 4.7 59.5 1.0
NE E:ARG173 4.7 55.5 1.0
N E:GLU35 4.7 45.4 1.0
N E:PRO34 4.8 48.1 1.0
O A:VAL59 4.8 43.2 1.0
OE1 A:GLN63 4.8 53.8 1.0
CB E:ARG173 4.9 52.8 1.0
CB E:GLU35 5.0 38.4 1.0

Iodine binding site 2 out of 10 in 3p05

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Iodine binding site 2 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I232

b:0.6
occ:1.00
 O A:TYR169 4.0 48.4 1.0
N A:ARG173 4.1 51.1 1.0
CB A:LEU172 4.1 48.9 1.0
CA A:ARG173 4.1 53.9 1.0
CB A:ARG173 4.1 59.0 1.0
CD1 A:TYR169 4.3 52.2 1.0
C A:LEU172 4.4 54.4 1.0
OE1 B:GLN67 4.4 63.0 1.0
CG A:ARG173 4.4 51.2 1.0
O A:LEU172 4.8 59.4 1.0
CD1 A:LEU172 4.9 56.4 1.0
CA A:LEU172 4.9 50.0 1.0
C A:TYR169 4.9 45.7 1.0

Iodine binding site 3 out of 10 in 3p05

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Iodine binding site 3 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I233

b:0.3
occ:1.00
 CE B:MET144 3.2 74.5 1.0
OE1 A:GLN219 3.3 98.9 1.0
NH2 A:ARG162 3.6 77.9 1.0
NE A:ARG162 3.9 80.4 1.0
CE A:MET215 4.2 71.9 1.0
CZ A:ARG162 4.2 82.5 1.0
CB A:GLN219 4.2 85.6 1.0
O A:MET215 4.4 68.6 1.0
CD A:GLN219 4.4 0.9 1.0
O B:MET144 4.6 73.7 1.0
CB A:ARG162 4.6 65.7 1.0
CB A:MET215 4.7 57.4 1.0
C A:MET215 4.9 64.0 1.0
CG A:GLN219 4.9 96.1 1.0

Iodine binding site 4 out of 10 in 3p05

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Iodine binding site 4 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I234

b:76.5
occ:1.00
 CD A:LYS170 3.5 64.8 1.0
OE1 A:GLU35 3.6 51.0 1.0
NH1 A:ARG173 3.6 42.9 1.0
NE2 B:GLN63 3.7 46.1 1.0
CG B:GLN63 3.7 43.7 1.0
CD B:GLN63 3.7 53.4 1.0
CD A:PRO34 3.9 42.0 1.0
N B:GLY61 3.9 37.0 1.0
OG A:SER33 3.9 76.6 1.0
CG A:PRO34 4.1 45.1 1.0
CD A:ARG173 4.2 49.3 1.0
CE A:LYS170 4.4 73.4 1.0
OE1 B:GLN63 4.5 48.3 1.0
CD A:GLU35 4.6 57.0 1.0
CB A:PRO34 4.6 43.1 1.0
CZ A:ARG173 4.6 48.8 1.0
N A:GLU35 4.6 45.1 1.0
CA B:GLY60 4.7 47.3 1.0
N A:PRO34 4.7 48.4 1.0
CA B:GLY61 4.7 51.9 1.0
CG A:LYS170 4.7 57.0 1.0
C B:GLY60 4.8 51.1 1.0
O B:VAL59 4.8 41.1 1.0
CB A:LYS170 4.8 49.0 1.0
CA A:LYS170 4.8 51.1 1.0
NE A:ARG173 4.9 55.4 1.0
CB A:GLU35 5.0 35.9 1.0
O B:GLY61 5.0 40.4 1.0

Iodine binding site 5 out of 10 in 3p05

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Iodine binding site 5 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I232

b:58.9
occ:1.00
 CD B:LYS170 3.4 64.1 1.0
NH1 B:ARG173 3.6 43.8 1.0
CG C:GLN63 3.6 43.2 1.0
CG B:PRO34 3.8 47.6 1.0
N C:GLY61 3.8 39.4 1.0
CD B:PRO34 3.9 40.2 1.0
CD C:GLN63 3.9 52.6 1.0
NE2 C:GLN63 4.0 46.6 1.0
CD B:ARG173 4.0 50.4 1.0
OG B:SER33 4.3 72.5 1.0
CE B:LYS170 4.3 74.1 1.0
OE1 B:GLU35 4.4 56.7 1.0
CA C:GLY61 4.4 48.9 1.0
CB B:PRO34 4.5 42.3 1.0
CG B:LYS170 4.5 57.7 1.0
CB B:LYS170 4.5 48.6 1.0
CA B:LYS170 4.5 51.1 1.0
CZ B:ARG173 4.6 46.5 1.0
OE1 C:GLN63 4.7 45.2 1.0
NE B:ARG173 4.7 51.3 1.0
C C:GLY60 4.8 51.8 1.0
CB B:ARG173 4.9 53.2 1.0
O C:GLY61 4.9 46.4 1.0
CA C:GLY60 4.9 47.3 1.0
N B:PRO34 4.9 47.4 1.0
CG B:ARG173 5.0 49.2 1.0

Iodine binding site 6 out of 10 in 3p05

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Iodine binding site 6 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I232

b:0.6
occ:1.00
 OE1 C:GLU35 3.4 51.6 1.0
CD C:LYS170 3.4 64.6 1.0
NH1 C:ARG173 3.7 45.3 1.0
NE2 D:GLN63 3.8 45.4 1.0
CD D:GLN63 3.8 52.4 1.0
CG D:GLN63 3.9 39.5 1.0
OG C:SER33 4.0 68.8 1.0
N D:GLY61 4.1 44.5 1.0
CD C:ARG173 4.1 53.2 1.0
CD C:PRO34 4.1 39.8 1.0
CE C:LYS170 4.3 76.4 1.0
CD C:GLU35 4.4 62.3 1.0
OE1 D:GLN63 4.5 51.6 1.0
CG C:PRO34 4.5 49.2 1.0
CG C:LYS170 4.6 57.2 1.0
CA D:GLY60 4.6 47.7 1.0
CZ C:ARG173 4.7 51.3 1.0
CB C:LYS170 4.7 49.8 1.0
CA C:LYS170 4.7 48.8 1.0
O D:VAL59 4.7 44.4 1.0
C D:GLY60 4.8 54.4 1.0
NE C:ARG173 4.9 53.6 1.0
N C:GLU35 4.9 42.3 1.0
CB C:GLU35 4.9 45.2 1.0
CB C:PRO34 5.0 45.8 1.0
CA D:GLY61 5.0 49.9 1.0

Iodine binding site 7 out of 10 in 3p05

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Iodine binding site 7 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I232

b:0.3
occ:1.00
 CD2 D:LEU151 3.6 79.6 1.0
CD1 D:LEU189 4.0 75.5 1.0
CG D:LEU151 4.4 80.8 1.0
CG2 D:ILE150 4.6 56.4 1.0
CD1 D:LEU151 4.6 78.7 1.0
CG D:LEU189 4.9 77.0 1.0

Iodine binding site 8 out of 10 in 3p05

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Iodine binding site 8 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I233

b:67.1
occ:1.00
 CD D:LYS170 3.4 67.6 1.0
OE1 D:GLU35 3.6 57.0 1.0
NE2 E:GLN63 3.8 52.2 1.0
NH1 D:ARG173 3.8 44.1 1.0
N E:GLY61 3.8 45.0 1.0
CG E:GLN63 3.8 40.5 1.0
CD D:PRO34 3.9 42.3 1.0
OG D:SER33 3.9 69.1 1.0
CD E:GLN63 3.9 58.4 1.0
CG D:PRO34 4.1 48.9 1.0
CE D:LYS170 4.2 78.1 1.0
CD D:ARG173 4.3 53.0 1.0
CB D:PRO34 4.5 44.1 1.0
CA E:GLY60 4.6 49.4 1.0
CG D:LYS170 4.6 53.0 1.0
CA E:GLY61 4.6 51.4 1.0
CB D:LYS170 4.6 50.2 1.0
CD D:GLU35 4.6 57.7 1.0
N D:PRO34 4.6 47.6 1.0
OE1 E:GLN63 4.7 50.9 1.0
C E:GLY60 4.7 52.9 1.0
N D:GLU35 4.7 43.0 1.0
CA D:LYS170 4.7 51.2 1.0
CZ D:ARG173 4.8 46.9 1.0
O E:VAL59 4.9 49.9 1.0
O E:GLY61 4.9 46.5 1.0
CB D:GLU35 5.0 39.0 1.0

Iodine binding site 9 out of 10 in 3p05

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Iodine binding site 9 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I235

b:0.9
occ:1.00
 OE1 A:GLU71 3.3 72.8 1.0
CB A:GLU71 3.4 49.1 1.0
CB E:GLU212 3.6 46.8 1.0
O A:MET68 3.7 45.2 1.0
OE2 A:GLU75 3.8 79.3 1.0
OE1 E:GLU212 4.1 67.9 1.0
N E:GLU212 4.1 45.1 1.0
CB E:THR210 4.1 55.4 1.0
CD A:GLU71 4.1 82.6 1.0
OG1 A:THR72 4.2 43.7 1.0
OG1 E:THR210 4.3 53.3 1.0
CG A:GLU71 4.3 64.3 1.0
CA A:MET68 4.3 45.0 1.0
N A:THR72 4.3 40.2 1.0
C A:MET68 4.4 41.4 1.0
CB A:MET68 4.4 38.0 1.0
CA E:GLU212 4.5 54.9 1.0
CA A:GLU71 4.5 49.5 1.0
C A:GLU71 4.6 52.3 1.0
NZ A:LYS140 4.6 66.7 1.0
CG A:MET68 4.6 57.4 1.0
CG2 E:THR210 4.7 48.5 1.0
CG E:GLU212 4.8 57.8 1.0
CD A:GLU75 4.8 81.9 1.0
CD E:GLU212 4.8 78.3 1.0
N E:LEU211 4.9 54.1 1.0
CE A:LYS140 4.9 67.0 1.0

Iodine binding site 10 out of 10 in 3p05

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Iodine binding site 10 out of 10 in the X-Ray Structure of Pentameric Hiv-1 Ca


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of X-Ray Structure of Pentameric Hiv-1 Ca within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I233

b:0.8
occ:1.00
 N E:LYS158 3.2 86.2 1.0
CB E:LYS158 3.3 91.9 1.0
CA E:LYS158 3.6 90.0 1.0
CD E:PRO157 3.6 91.8 1.0
N E:GLU159 3.7 82.7 1.0
C E:LYS158 3.8 86.3 1.0
CG E:PRO157 3.8 96.6 1.0
N E:PRO157 4.1 93.3 1.0
C E:PRO157 4.4 88.2 1.0
C E:GLY156 4.4 85.2 1.0
CG E:LYS158 4.4 93.0 1.0
CA E:GLY156 4.5 75.5 1.0
CA E:GLU159 4.6 71.0 1.0
O E:LYS158 4.6 80.6 1.0
CA E:PRO157 4.7 87.4 1.0
CB E:GLU159 4.7 65.8 1.0
CB E:PRO157 4.9 89.1 1.0

Reference:

O.Pornillos, B.K.Ganser-Pornillos, M.Yeager. Atomic-Level Modelling of the Hiv Capsid. Nature V. 469 424 2011.
ISSN: ISSN 0028-0836
PubMed: 21248851
DOI: 10.1038/NATURE09640
Page generated: Sun Dec 13 19:29:00 2020

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