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Chlorine in PDB 4i54: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121

Protein crystallography data

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121, PDB code: 4i54 was solved by M.Le-Khac, W.A.Hendrickson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.63 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.324, 68.775, 94.443, 90.00, 90.89, 90.00
R / Rfree (%) 19.6 / 26.1

Other elements in 4i54:

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121 (pdb code 4i54). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121, PDB code: 4i54:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4i54

Go back to Chlorine Binding Sites List in 4i54
Chlorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:34.9
occ:1.00
CL1 A:1C1501 0.0 34.9 1.0
C24 A:1C1501 1.7 29.0 1.0
C22 A:1C1501 2.7 28.6 1.0
C26 A:1C1501 2.8 29.6 1.0
F23 A:1C1501 2.9 28.1 1.0
CA A:PHE376 3.5 28.3 1.0
C A:PHE376 3.5 36.5 1.0
CD1 A:PHE382 3.7 30.3 1.0
N A:PHE376 3.8 33.1 1.0
O A:PHE376 3.8 34.3 1.0
N A:ASN377 3.9 41.2 1.0
CE1 A:PHE382 3.9 41.1 1.0
C21 A:1C1501 3.9 29.0 1.0
O A:VAL255 4.0 47.2 1.0
C27 A:1C1501 4.0 36.0 1.0
C A:SER375 4.2 32.4 1.0
CG1 A:VAL255 4.3 27.8 1.0
O A:SER375 4.4 28.6 1.0
CB A:ASN377 4.4 40.8 1.0
C20 A:1C1501 4.4 41.0 1.0
CH2 A:TRP112 4.5 41.3 1.0
CA A:ASN377 4.6 40.5 1.0
C A:VAL255 4.6 35.9 1.0
OG A:SER375 4.7 53.8 1.0
CB A:VAL255 4.8 31.3 1.0
CB A:SER375 4.9 29.5 1.0
CB A:PHE376 4.9 41.5 1.0
CG A:PHE382 5.0 42.0 1.0

Chlorine binding site 2 out of 2 in 4i54

Go back to Chlorine Binding Sites List in 4i54
Chlorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 H375S Core in Complex with Dmj-II-121 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:55.6
occ:1.00
CL1 B:1C1501 0.0 55.6 1.0
C24 B:1C1501 1.8 51.7 1.0
C26 B:1C1501 2.8 49.6 1.0
C22 B:1C1501 2.8 49.0 1.0
F23 B:1C1501 3.1 48.2 1.0
C B:PHE376 3.4 55.2 1.0
CA B:PHE376 3.5 45.8 1.0
CD1 B:PHE382 3.6 59.7 1.0
N B:ASN377 3.7 44.3 1.0
N B:PHE376 3.8 47.2 1.0
O B:PHE376 3.8 48.5 1.0
CE1 B:PHE382 3.8 59.8 1.0
O B:VAL255 3.9 49.1 1.0
C27 B:1C1501 4.0 66.3 1.0
C21 B:1C1501 4.0 50.2 1.0
CG1 B:VAL255 4.2 46.3 1.0
CB B:ASN377 4.3 48.5 1.0
C B:SER375 4.3 53.6 1.0
CA B:ASN377 4.4 51.5 1.0
CH2 B:TRP112 4.5 55.8 1.0
C20 B:1C1501 4.5 62.8 1.0
O B:SER375 4.6 49.4 1.0
C B:VAL255 4.7 44.9 1.0
OG B:SER375 4.8 65.5 1.0
CB B:VAL255 4.8 44.9 1.0
CB B:SER375 4.9 64.5 1.0
CG B:PHE382 4.9 52.2 1.0
CB B:PHE376 5.0 45.0 1.0

Reference:

J.M.Lalonde, M.Le-Khac, D.M.Jones, J.R.Courter, J.Park, A.Schon, A.M.Princiotto, X.Wu, J.R.Mascola, E.Freire, J.Sodroski, N.Madani, W.A.Hendrickson, A.B.Smith. Structure-Based Design and Synthesis of An Hiv-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. Acs Med Chem Lett V. 4 338 2013.
PubMed: 23667716
DOI: 10.1021/ML300407Y
Page generated: Sat Dec 12 10:44:46 2020

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