Atomistry » Iodine » PDB 5w4i-6axx » 5w4o
Atomistry »
  Iodine »
    PDB 5w4i-6axx »
      5w4o »

Iodine in PDB 5w4o: Structure of the R18A Mutant of the Hiv-1 Capsid Protein

Protein crystallography data

The structure of Structure of the R18A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4o 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) 46.46 / 2.09
Space group P 6
Cell size a, b, c (Å), α, β, γ (°) 92.921, 92.921, 58.053, 90.00, 90.00, 120.00
R / Rfree (%) 21.7 / 24.6

Other elements in 5w4o:

The structure of Structure of the R18A Mutant of the Hiv-1 Capsid Protein also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of the R18A Mutant of the Hiv-1 Capsid Protein (pdb code 5w4o). 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 R18A Mutant of the Hiv-1 Capsid Protein, PDB code: 5w4o:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Iodine binding site 1 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 1 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:48.7
occ:0.94
 CG A:LYS158 3.5 74.7 1.0
N A:LYS158 3.6 54.9 1.0
CD A:PRO157 3.7 50.7 1.0
N A:GLU159 3.8 53.4 1.0
CA A:GLY156 3.8 43.1 1.0
N A:PRO157 3.8 49.4 1.0
C A:GLY156 3.9 45.6 1.0
CE A:LYS158 4.1 90.6 1.0
CG A:PRO157 4.1 58.1 1.0
CB A:LYS158 4.2 67.1 1.0
CA A:LYS158 4.2 58.0 1.0
C A:LYS158 4.2 55.4 1.0
CD A:LYS158 4.3 83.5 1.0
CB A:GLU159 4.3 49.5 1.0
CA A:GLU159 4.4 51.1 1.0
C A:PRO157 4.6 53.0 1.0
O A:GLY156 4.7 44.1 1.0
CA A:PRO157 4.7 52.7 1.0
N A:GLY156 4.9 40.3 1.0

Iodine binding site 2 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 2 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:45.5
occ:0.78
 NH1 A:ARG173 3.7 48.3 1.0
CG A:LYS170 3.9 58.9 1.0
CD A:ARG173 4.1 45.0 1.0
OE1 A:GLU35 4.1 50.4 1.0
CG A:PRO34 4.4 47.4 1.0
CB A:LYS170 4.5 50.8 1.0
CD A:LYS170 4.5 65.3 1.0
CB A:PRO34 4.6 45.8 1.0
CD A:PRO34 4.6 45.7 1.0
OG A:SER33 4.7 56.8 1.0
CA A:LYS170 4.7 41.6 1.0
CZ A:ARG173 4.7 45.3 1.0
CE A:LYS170 4.7 70.9 1.0
NE A:ARG173 4.8 44.9 1.0
CD A:GLU35 5.0 50.9 1.0

Iodine binding site 3 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 3 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:52.8
occ:0.52
 CG2 A:ILE37 3.9 45.0 1.0
CA A:PRO38 4.0 44.5 1.0
N A:PRO38 4.1 44.1 1.0
CB A:SER41 4.2 49.3 1.0
O A:ILE37 4.2 41.6 1.0
C A:ILE37 4.3 42.2 1.0
CD1 A:ILE135 4.3 45.0 1.0
CB A:PRO38 4.4 44.6 1.0
OG A:SER41 4.5 52.8 1.0
CD A:PRO38 4.6 43.9 1.0
CG2 A:ILE135 4.7 39.5 1.0
CB A:ILE37 4.8 45.4 1.0

Iodine binding site 4 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 4 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:57.1
occ:0.55
 CE1 A:TYR145 4.0 65.7 1.0
CG A:MET144 4.2 66.8 1.0
CD1 A:TYR145 4.3 64.5 1.0
CE A:MET144 4.3 72.9 1.0
O A:MET144 4.3 60.3 1.0
SD A:MET144 4.8 67.5 1.0

Iodine binding site 5 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 5 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I305

b:94.0
occ:0.42
 CA A:ASN21 3.8 48.2 1.0
CB A:ASN21 3.8 52.2 1.0
OD1 A:ASN21 3.8 61.1 1.0
O A:HOH502 4.0 52.8 1.0
N A:ASN21 4.0 44.8 1.0
CG A:ASN21 4.3 57.7 1.0
C A:LEU20 4.5 41.0 1.0
CB A:LEU20 4.7 44.6 1.0
O A:HOH500 4.7 60.9 1.0
O A:LEU20 4.9 41.6 1.0
O A:PRO17 4.9 49.2 1.0

Iodine binding site 6 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 6 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I306

b:78.9
occ:0.41
 OG A:SER146 3.3 47.5 1.0
OG1 A:THR148 3.3 61.6 1.0
CD A:PRO147 3.8 55.3 1.0
CB A:ALA174 4.0 46.0 1.0
CA A:THR171 4.2 34.0 1.0
OG1 A:THR171 4.3 39.3 1.0
CB A:SER146 4.3 46.9 1.0
CG A:PRO147 4.4 57.4 1.0
N A:PRO147 4.6 55.3 1.0
N A:THR148 4.6 59.9 1.0
N A:THR171 4.6 35.0 1.0
CB A:THR148 4.7 60.3 1.0
CB A:THR171 4.7 39.4 1.0
CG A:LYS170 4.7 58.9 1.0
CE A:LYS170 4.7 70.9 1.0
O A:LYS170 4.7 39.7 1.0
CA A:SER146 4.7 49.3 1.0
O A:HOH468 4.8 62.6 1.0
CG2 A:THR171 4.8 40.6 1.0
C A:LYS170 4.9 38.6 1.0
C A:SER146 5.0 49.3 1.0
O A:THR148 5.0 52.0 1.0

Iodine binding site 7 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 7 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I307

b:71.7
occ:0.32
 O A:HOH468 3.3 62.6 1.0
NH1 A:ARG167 3.5 41.4 1.0
CL A:CL312 3.6 72.6 1.0
CD A:ARG167 3.8 37.2 1.0
CD1 A:ILE153 4.0 39.5 1.0
CG2 A:THR148 4.3 61.7 1.0
CB A:ARG167 4.4 34.4 1.0
CG A:ARG167 4.4 36.8 1.0
CZ A:ARG167 4.5 41.0 1.0
O A:HOH486 4.5 57.3 1.0
NE A:ARG167 4.6 36.6 1.0

Iodine binding site 8 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 8 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I308

b:64.1
occ:0.43
 CA A:ARG173 3.7 43.5 1.0
O A:HOH484 3.8 57.9 1.0
N A:ARG173 3.9 42.5 1.0
NZ A:LYS182 3.9 62.2 1.0
CG A:LEU172 4.0 42.5 1.0
O A:LEU172 4.0 42.4 1.0
C A:LEU172 4.0 40.0 1.0
CD2 A:LEU172 4.1 42.5 1.0
CB A:ARG173 4.2 43.9 1.0
CD A:LYS182 4.2 62.7 1.0
O A:HOH422 4.4 54.4 1.0
CE A:LYS182 4.5 62.6 1.0
CB A:LEU172 4.5 41.5 1.0
CG A:ARG173 4.5 45.5 1.0
O A:TYR169 4.6 32.0 1.0
CA A:LEU172 5.0 38.4 1.0
C A:ARG173 5.0 42.9 1.0

Iodine binding site 9 out of 9 in 5w4o

Go back to Iodine Binding Sites List in 5w4o
Iodine binding site 9 out of 9 in the Structure of the R18A 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 R18A Mutant of the Hiv-1 Capsid Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I309

b:77.7
occ:0.42
 O A:HOH444 3.3 44.8 1.0
ND2 A:ASN57 3.3 35.9 1.0
CG A:ASN57 4.3 38.5 1.0
CB A:ASN57 4.3 37.3 1.0
OG1 A:THR54 4.4 44.1 1.0
CA A:THR54 4.4 40.1 1.0
O A:ASN53 4.5 34.0 1.0
N A:THR54 4.6 40.4 1.0
C A:ASN53 4.7 38.4 1.0
CB A:THR54 5.0 43.8 1.0

Reference:

P.Craveur, A.T.Gres, K.A.Kirby, D.Liu, J.A.Hammond, Y.Deng, S.Forli, D.S.Goodsell, J.R.Williamson, S.G.Sarafianos, A.J.Olson. Novel Intersubunit Interaction Critical For Hiv-1 Core Assembly Defines A Potentially Targetable Inhibitor Binding Pocket. Mbio V. 10 2019.
ISSN: ESSN 2150-7511
PubMed: 30862755
DOI: 10.1128/MBIO.02858-18
Page generated: Sun Aug 11 22:17:13 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy