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Zinc in PDB 3ley: 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41

Protein crystallography data

The structure of 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41, PDB code: 3ley was solved by G.Ofek, F.J.Guenaga, W.R.Schief, J.Skinner, D.Baker, R.Wyatt, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.10 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.249, 80.160, 72.139, 90.00, 97.07, 90.00
R / Rfree (%) 17.7 / 21.5

Zinc Binding Sites:

The binding sites of Zinc atom in the 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41 (pdb code 3ley). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41, PDB code: 3ley:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3ley

Go back to Zinc Binding Sites List in 3ley
Zinc binding site 1 out of 3 in the 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn222

b:59.9
occ:1.00
NE2 H:HIS163 2.2 36.9 1.0
ND2 L:ASN143 2.3 40.5 1.0
O L:HOH268 2.5 42.6 1.0
O H:HOH244 2.5 51.5 1.0
CD2 H:HIS163 3.0 31.1 1.0
OD1 L:ASN143 3.0 47.9 1.0
CG L:ASN143 3.0 41.3 1.0
CE1 H:HIS163 3.3 39.9 1.0
O L:HOH269 3.3 50.4 1.0
O L:HOH238 4.0 32.2 1.0
CG H:HIS163 4.2 32.3 1.0
ND1 H:HIS163 4.3 32.9 1.0
OD2 L:ASP175 4.4 38.4 1.0
CB L:ASN143 4.5 35.2 1.0
OG L:SER179 4.5 24.1 1.0
OD2 L:ASP172 4.7 48.8 1.0
O H:HOH235 4.8 30.5 1.0
N L:ASN143 4.9 25.7 1.0

Zinc binding site 2 out of 3 in 3ley

Go back to Zinc Binding Sites List in 3ley
Zinc binding site 2 out of 3 in the 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn223

b:46.4
occ:1.00
O H:HOH288 2.4 43.3 1.0
OD2 H:ASP1 2.6 70.3 1.0
O H:HOH275 2.7 47.1 1.0
CG H:ASP1 3.4 67.0 1.0
CB H:ASP1 3.4 60.2 1.0
O H:HOH296 4.5 38.7 1.0
OD1 H:ASP1 4.6 68.0 1.0
OE1 H:GLN3 4.9 60.3 1.0
CA H:ASP1 4.9 53.1 1.0
CB H:GLN3 5.0 45.6 1.0

Zinc binding site 3 out of 3 in 3ley

Go back to Zinc Binding Sites List in 3ley
Zinc binding site 3 out of 3 in the 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2F5 Epitope Scaffold Elicited Anti-Hiv-1 Monoclonal Antibody 6A7 in Complex with Hiv-1 GP41 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn233

b:71.7
occ:1.00
NE2 L:HIS194 2.5 62.6 1.0
OE1 L:GLU190 2.8 70.3 1.0
O L:HOH290 2.8 46.9 1.0
OE2 L:GLU190 3.0 67.2 1.0
CD L:GLU190 3.0 66.6 1.0
CD2 L:HIS194 3.2 58.3 1.0
CE1 L:HIS194 3.5 63.3 1.0
O L:GLU190 3.9 47.8 1.0
CB L:ARG193 4.0 55.8 1.0
CG L:GLU190 4.1 63.4 1.0
CA L:GLU190 4.2 53.5 1.0
CD L:ARG193 4.3 64.9 1.0
CG L:HIS194 4.4 56.4 1.0
CB L:GLU190 4.4 57.1 1.0
ND1 L:HIS194 4.5 62.4 1.0
C L:GLU190 4.5 49.2 1.0
CG L:ARG193 4.8 59.6 1.0

Reference:

G.Ofek, F.J.Guenaga, W.R.Schief, J.Skinner, D.Baker, R.Wyatt, P.D.Kwong. Elicitation of Structure-Specific Antibodies By Epitope Scaffolds. Proc.Natl.Acad.Sci.Usa V. 107 17880 2010.
ISSN: ISSN 0027-8424
PubMed: 20876137
DOI: 10.1073/PNAS.1004728107
Page generated: Wed Dec 16 04:32:12 2020

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