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Fluorine in PDB 4dvv: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261

Protein crystallography data

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261, PDB code: 4dvv was solved by Y.D.Kwon, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.39 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.779, 68.079, 94.350, 90.00, 91.42, 90.00
R / Rfree (%) 18.1 / 21.5

Other elements in 4dvv:

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261 (pdb code 4dvv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261, PDB code: 4dvv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4dvv

Go back to Fluorine Binding Sites List in 4dvv
Fluorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F513

b:38.0
occ:1.00
F08 A:0M1513 0.0 38.0 1.0
C02 A:0M1513 1.3 37.0 1.0
C03 A:0M1513 2.3 30.9 1.0
C01 A:0M1513 2.4 49.0 1.0
CL1 A:0M1513 2.9 46.0 1.0
CA A:SER256 3.1 24.1 1.0
OG A:SER375 3.1 39.7 1.0
C A:SER256 3.3 34.2 1.0
O A:SER375 3.3 27.2 1.0
N A:SER256 3.4 23.2 1.0
N A:THR257 3.5 26.1 1.0
C06 A:0M1513 3.6 48.9 1.0
C04 A:0M1513 3.6 44.3 1.0
CG2 A:THR257 3.7 23.7 1.0
CG1 A:VAL255 3.7 24.6 1.0
C A:VAL255 3.8 31.0 1.0
O A:VAL255 3.8 29.9 1.0
O A:SER256 3.8 23.9 1.0
C A:SER375 3.9 31.2 1.0
C05 A:0M1513 4.1 41.5 1.0
CB A:SER375 4.2 29.9 1.0
N A:PHE376 4.4 23.0 1.0
CD1 A:ILE475 4.5 28.6 1.0
CB A:SER256 4.5 27.6 1.0
CB A:THR257 4.5 31.5 1.0
CA A:PHE376 4.5 22.6 1.0
CA A:THR257 4.6 24.6 1.0
CA A:SER375 4.6 27.2 1.0
CB A:VAL255 4.7 27.9 1.0
OG1 A:THR257 4.7 30.0 1.0
O14 A:0M1513 4.7 46.7 1.0
N09 A:0M1513 4.8 44.1 1.0
CA A:VAL255 4.8 23.0 1.0

Fluorine binding site 2 out of 2 in 4dvv

Go back to Fluorine Binding Sites List in 4dvv
Fluorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with As-I-261 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F513

b:57.6
occ:1.00
F08 B:0M1513 0.0 57.6 1.0
C02 B:0M1513 1.3 53.1 1.0
C03 B:0M1513 2.3 50.6 1.0
C01 B:0M1513 2.4 57.4 1.0
CL1 B:0M1513 2.9 55.2 1.0
OG B:SER375 3.1 51.3 1.0
O B:SER375 3.4 37.3 1.0
CA B:SER256 3.4 35.0 1.0
C06 B:0M1513 3.6 59.8 1.0
C B:SER256 3.6 37.6 1.0
C04 B:0M1513 3.6 61.0 1.0
N B:SER256 3.7 39.5 1.0
O B:VAL255 3.7 39.4 1.0
CG1 B:VAL255 3.8 35.2 1.0
C B:VAL255 3.8 33.8 1.0
CG2 B:THR257 3.8 38.1 1.0
N B:THR257 3.8 37.4 1.0
C B:SER375 3.8 38.3 1.0
CB B:SER375 4.0 38.6 1.0
C05 B:0M1513 4.1 63.0 1.0
O B:SER256 4.2 39.8 1.0
N B:PHE376 4.4 37.6 1.0
CA B:PHE376 4.5 40.4 1.0
CA B:SER375 4.5 35.0 1.0
CD1 B:ILE475 4.6 63.7 1.0
CB B:VAL255 4.7 29.6 1.0
O14 B:0M1513 4.7 58.4 1.0
CB B:THR257 4.7 47.0 1.0
OG1 B:THR257 4.7 41.0 1.0
CB B:SER256 4.8 32.9 1.0
N09 B:0M1513 4.8 62.7 1.0
CA B:THR257 4.8 40.9 1.0
CA B:VAL255 4.8 29.1 1.0

Reference:

Y.D.Kwon, J.M.Lalonde, Y.Yang, M.A.Elban, A.Sugawara, J.R.Courter, D.M.Jones, A.B.Smith, A.K.Debnath, P.D.Kwong. Crystal Structures of Hiv-1 GP120 Envelope Glycoprotein in Complex with Nbd Analogues That Target the CD4-Binding Site. Plos One V. 9 85940 2014.
ISSN: ESSN 1932-6203
PubMed: 24489681
DOI: 10.1371/JOURNAL.PONE.0085940
Page generated: Sun Dec 13 12:01:41 2020

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