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Fluorine in PDB 4dvw: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-167

Protein crystallography data

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-167, PDB code: 4dvw 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) 27.74 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.591, 68.533, 94.155, 90.00, 91.27, 90.00
R / Rfree (%) 18.5 / 23.3

Other elements in 4dvw:

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-167 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 Mae-II-167 (pdb code 4dvw). 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 Mae-II-167, PDB code: 4dvw:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4dvw

Go back to Fluorine Binding Sites List in 4dvw
Fluorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-167


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 Mae-II-167 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F512

b:36.8
occ:1.00
F08 A:0M4512 0.0 36.8 1.0
C02 A:0M4512 1.3 33.1 1.0
C03 A:0M4512 2.3 34.8 1.0
C01 A:0M4512 2.4 33.6 1.0
H1 A:0M4512 2.6 41.8 1.0
CL1 A:0M4512 2.9 40.2 1.0
OG A:SER375 3.1 42.4 1.0
CA A:SER256 3.1 23.6 1.0
C A:SER256 3.3 29.9 1.0
O A:SER375 3.4 28.6 1.0
N A:SER256 3.4 19.6 1.0
CG1 A:VAL255 3.5 27.6 1.0
N A:THR257 3.6 28.2 1.0
C06 A:0M4512 3.6 31.7 1.0
C04 A:0M4512 3.6 38.5 1.0
CG2 A:THR257 3.6 24.7 1.0
C A:VAL255 3.8 31.0 1.0
O A:SER256 3.8 25.9 1.0
O A:VAL255 3.9 27.1 1.0
C A:SER375 3.9 32.5 1.0
C05 A:0M4512 4.1 34.7 1.0
CB A:SER375 4.2 25.7 1.0
N A:PHE376 4.5 26.9 1.0
H3 A:0M4512 4.5 38.0 1.0
CD1 A:ILE475 4.5 21.0 1.0
CB A:SER256 4.5 25.0 1.0
CB A:THR257 4.5 31.9 1.0
CA A:PHE376 4.6 25.1 1.0
CA A:THR257 4.6 24.8 1.0
CB A:VAL255 4.6 27.2 1.0
CA A:SER375 4.7 33.2 1.0
O14 A:0M4512 4.7 32.3 1.0
OG1 A:THR257 4.7 31.1 1.0
CA A:VAL255 4.8 21.0 1.0
N09 A:0M4512 4.8 35.0 1.0

Fluorine binding site 2 out of 2 in 4dvw

Go back to Fluorine Binding Sites List in 4dvw
Fluorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Mae-II-167


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 Mae-II-167 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F512

b:50.2
occ:1.00
F08 B:0M4512 0.0 50.2 1.0
C02 B:0M4512 1.3 46.0 1.0
C03 B:0M4512 2.3 49.8 1.0
C01 B:0M4512 2.4 45.1 1.0
H1 B:0M4512 2.6 59.8 1.0
CL1 B:0M4512 2.9 45.5 1.0
OG B:SER375 3.0 41.9 1.0
CA B:SER256 3.4 34.1 1.0
O B:SER375 3.5 35.3 1.0
C B:SER256 3.6 38.5 1.0
C06 B:0M4512 3.6 55.1 1.0
C04 B:0M4512 3.6 56.4 1.0
CG1 B:VAL255 3.6 34.5 1.0
N B:SER256 3.7 33.4 1.0
CG2 B:THR257 3.7 39.9 1.0
O B:VAL255 3.7 49.9 1.0
C B:VAL255 3.8 32.7 1.0
N B:THR257 3.9 36.6 1.0
C B:SER375 3.9 42.4 1.0
CB B:SER375 4.0 41.4 1.0
O B:SER256 4.0 38.3 1.0
C05 B:0M4512 4.1 58.3 1.0
N B:PHE376 4.4 34.8 1.0
H3 B:0M4512 4.5 66.1 1.0
CA B:PHE376 4.5 35.7 1.0
CA B:SER375 4.6 37.5 1.0
CB B:VAL255 4.7 33.1 1.0
CB B:THR257 4.7 40.6 1.0
O14 B:0M4512 4.7 49.9 1.0
CD1 B:ILE475 4.7 42.7 1.0
CB B:SER256 4.7 38.2 1.0
OG1 B:THR257 4.8 40.0 1.0
CA B:THR257 4.8 38.5 1.0
CA B:VAL255 4.8 37.2 1.0
N09 B:0M4512 4.8 53.1 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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