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Iodine in PDB 4e91: Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3, PDB code: 4e91 was solved by C.T.Lemke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.61 / 1.70
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.783, 65.783, 143.323, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.3

Other elements in 4e91:

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Chlorine (Cl) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 (pdb code 4e91). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3, PDB code: 4e91:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 4e91

Go back to Iodine Binding Sites List in 4e91
Iodine binding site 1 out of 4 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I203

b:18.8
occ:0.94
N A:ARG18 3.8 14.1 1.0
CD A:PRO17 3.9 15.9 1.0
CB A:ARG18 3.9 17.2 1.0
CB A:PRO17 4.3 14.0 1.0
CG A:PRO17 4.3 15.1 1.0
N A:PRO17 4.3 15.4 1.0
CA A:ARG18 4.5 13.8 1.0
CB A:SER16 4.5 19.7 1.0
OG A:SER16 4.6 18.5 1.0
CA A:PRO17 4.7 15.1 1.0
C A:PRO17 4.7 14.7 1.0
C A:SER16 5.0 16.2 1.0

Iodine binding site 2 out of 4 in 4e91

Go back to Iodine Binding Sites List in 4e91
Iodine binding site 2 out of 4 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I204

b:18.3
occ:0.75
O A:HOH312 3.6 17.5 0.8
CB A:SER44 3.9 14.4 1.0
CA A:SER44 4.0 16.0 1.0
CB A:MET55 4.0 15.0 1.0
O A:ASP51 4.1 13.7 1.0
CD2 A:LEU52 4.2 12.7 1.0
CB A:ALA47 4.2 14.6 1.0
CG A:MET55 4.2 16.3 1.0
CG1 A:ILE15 4.3 23.7 1.0
C A:ASP51 4.3 14.3 1.0
CB A:ASP51 4.4 16.7 1.0
CA A:LEU52 4.4 12.8 1.0
CG A:LEU43 4.5 17.6 1.0
N A:LEU52 4.5 12.4 1.0
CD2 A:LEU43 4.5 18.5 1.0
CE A:MET55 4.6 18.7 1.0
O A:HOH354 4.6 21.2 0.6
N A:SER44 4.6 15.2 1.0
O A:LEU43 4.6 18.0 1.0
CD1 A:ILE15 4.7 24.0 1.0
CG A:LEU52 4.7 12.4 1.0
C A:LEU43 4.8 15.2 1.0

Iodine binding site 3 out of 4 in 4e91

Go back to Iodine Binding Sites List in 4e91
Iodine binding site 3 out of 4 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I205

b:21.8
occ:0.36
C3 B:0OE201 3.5 25.7 1.0
O A:HOH459 3.7 35.8 0.9
CG A:GLU35 3.7 19.4 1.0
CB A:GLU35 3.8 19.2 1.0
N A:GLU35 3.9 13.3 1.0
CD A:PRO34 3.9 15.0 1.0
CG A:PRO34 3.9 15.2 1.0
CB A:SER33 4.0 18.0 1.0
CD A:GLU35 4.1 27.6 1.0
C38 B:0OE201 4.1 33.5 1.0
C32 B:0OE201 4.1 25.8 1.0
OG A:SER33 4.2 21.9 1.0
C4 B:0OE201 4.3 23.8 1.0
C12 B:0OE201 4.3 21.0 1.0
N A:PRO34 4.3 15.2 1.0
OE1 A:GLU35 4.3 30.9 1.0
CA A:GLU35 4.5 15.3 1.0
OE2 A:GLU35 4.6 35.0 1.0
N2 B:0OE201 4.6 28.3 1.0
N13 B:0OE201 4.6 20.6 1.0
N16 B:0OE201 4.7 18.4 1.0
C A:SER33 4.8 14.2 1.0
CA A:SER33 4.8 15.1 1.0
C A:PRO34 4.8 14.0 1.0
N34 B:0OE201 4.8 34.6 1.0
C33 B:0OE201 4.8 32.0 1.0
O A:HOH335 4.9 18.9 0.6
C31 B:0OE201 5.0 23.7 1.0
CA A:PRO34 5.0 13.9 1.0

Iodine binding site 4 out of 4 in 4e91

Go back to Iodine Binding Sites List in 4e91
Iodine binding site 4 out of 4 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Inhibitor BD3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I206

b:25.4
occ:0.36
O A:HOH329 3.6 20.9 1.0
N A:ALA64 3.7 19.2 1.0
CB A:GLN63 3.8 22.5 1.0
CE1 A:HIS62 4.1 18.5 1.0
N A:GLN63 4.2 17.1 1.0
CB A:ALA64 4.2 23.8 1.0
CA A:GLN63 4.3 21.8 1.0
NE2 A:HIS62 4.4 17.5 1.0
C A:GLN63 4.4 20.6 1.0
CA A:ALA64 4.5 20.6 1.0
ND1 A:HIS62 4.5 15.7 1.0

Reference:

C.T.Lemke, S.Titolo, U.Von Schwedler, N.Goudreau, J.F.Mercier, E.Wardrop, A.M.Faucher, R.Coulombe, S.S.Banik, L.Fader, A.Gagnon, S.H.Kawai, J.Rancourt, M.Tremblay, C.Yoakim, B.Simoneau, J.Archambault, W.I.Sundquist, S.W.Mason. Distinct Effects of Two Hiv-1 Capsid Assembly Inhibitor Families That Bind the Same Site Within the N-Terminal Domain of the Viral Ca Protein. J.Virol. V. 86 6643 2012.
ISSN: ISSN 0022-538X
PubMed: 22496222
DOI: 10.1128/JVI.00493-12
Page generated: Sun Dec 13 19:32:25 2020

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