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Chlorine in PDB 2qsc: Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide

Protein crystallography data

The structure of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide, PDB code: 2qsc was solved by C.H.Bell, A.Schiefner, R.L.Stanfield, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.80
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.912, 39.858, 97.960, 90.00, 108.50, 90.00
R / Rfree (%) 21.9 / 26.4

Other elements in 2qsc:

The structure of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide (pdb code 2qsc). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide, PDB code: 2qsc:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2qsc

Go back to Chlorine Binding Sites List in 2qsc
Chlorine binding site 1 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl217

b:63.0
occ:1.00
ZN L:ZN215 2.3 60.7 1.0
OD1 L:ASN138 3.0 51.8 1.0
ND2 L:ASN138 3.2 51.8 1.0
CG L:ASN138 3.3 51.5 1.0
OG1 H:THR192 3.8 55.3 1.0
NE2 H:HIS172 3.8 47.7 1.0
ND2 L:ASN137 3.9 51.8 1.0
OD1 L:ASN137 4.0 51.8 1.0
CG L:ASN137 4.4 51.3 1.0
CA H:GLY169 4.4 49.3 1.0
CE1 H:HIS172 4.4 47.9 1.0
CB L:ASN138 4.5 51.2 1.0
O H:GLY169 4.8 49.3 1.0
CD2 H:HIS172 4.8 48.0 1.0
C H:GLY169 5.0 49.3 1.0

Chlorine binding site 2 out of 4 in 2qsc

Go back to Chlorine Binding Sites List in 2qsc
Chlorine binding site 2 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl232

b:50.4
occ:1.00
ZN H:ZN231 2.6 49.5 1.0
OE1 H:GLU85 3.8 48.3 1.0
CL H:CL233 4.1 55.7 1.0
OE2 H:GLU85 4.2 47.7 1.0
CD H:GLU85 4.3 48.2 1.0
CD H:ARG83 4.8 49.8 1.0

Chlorine binding site 3 out of 4 in 2qsc

Go back to Chlorine Binding Sites List in 2qsc
Chlorine binding site 3 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl233

b:55.7
occ:1.00
ZN H:ZN231 2.7 49.5 1.0
OG1 H:THR84 3.0 48.4 1.0
N H:THR84 3.4 48.6 1.0
CB H:ARG83 3.9 48.6 1.0
CB H:THR84 4.0 48.5 1.0
CA H:ARG83 4.0 48.6 1.0
CL H:CL232 4.1 50.4 1.0
CD H:ARG83 4.1 49.8 1.0
C H:ARG83 4.2 48.5 1.0
OE1 H:GLU85 4.3 48.3 1.0
CA H:THR84 4.3 48.5 1.0
CG H:ARG83 4.6 48.9 1.0

Chlorine binding site 4 out of 4 in 2qsc

Go back to Chlorine Binding Sites List in 2qsc
Chlorine binding site 4 out of 4 in the Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure Analysis of Anti-Hiv-1 V3-Fab F425-B4E8 in Complex with A V3-Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl234

b:52.9
occ:1.00
ZN H:ZN230 2.7 42.6 1.0
OG1 H:THR56 3.1 48.9 1.0
CB H:SER52 3.6 48.2 1.0
OD2 H:ASP53 3.7 49.3 1.0
CB H:THR56 3.7 48.4 1.0
OG H:SER52 3.8 48.2 1.0
OD1 H:ASP53 4.2 49.1 1.0
O P:ILE309 4.3 50.1 1.0
CG H:ASP53 4.3 49.0 1.0
O P:HIS308 4.4 50.9 1.0
CG2 H:THR56 4.5 48.4 1.0
OE2 H:GLU55 4.7 50.3 1.0
CA H:THR56 5.0 48.4 1.0
N H:THR56 5.0 48.4 1.0

Reference:

C.H.Bell, R.Pantophlet, A.Schiefner, L.A.Cavacini, R.L.Stanfield, D.R.Burton, I.A.Wilson. Structure of Antibody F425-B4E8 in Complex with A V3 Peptide Reveals A New Binding Mode For Hiv-1 Neutralization. J.Mol.Biol. V. 375 969 2008.
ISSN: ISSN 0022-2836
PubMed: 18068724
DOI: 10.1016/J.JMB.2007.11.013
Page generated: Sat Dec 12 09:17:37 2020

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