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Sodium in PDB 3s3z: Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10

Protein crystallography data

The structure of Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10, PDB code: 3s3z was solved by J.R.Keeffe, P.J.Bjorkman, S.L.Mayo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.81 / 1.75
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 47.990, 47.990, 79.318, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 21.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10 (pdb code 3s3z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10, PDB code: 3s3z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3s3z

Go back to Sodium Binding Sites List in 3s3z
Sodium binding site 1 out of 2 in the Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na213

b:11.1
occ:0.50
O A:HOH229 2.8 17.0 1.0
N A:THR31 3.3 14.8 1.0
OD1 A:ASN30 3.6 16.5 1.0
O A:THR31 3.7 16.2 1.0
CB A:THR31 3.8 15.8 1.0
O A:HOH235 3.8 21.3 1.0
O A:HOH248 3.8 22.7 1.0
O A:HOH282 3.9 26.2 1.0
CA A:THR31 4.0 15.2 1.0
OG1 A:THR31 4.1 16.5 1.0
C A:THR31 4.3 15.7 1.0
C A:ASN30 4.4 14.9 1.0
CA A:ASN30 4.4 16.0 1.0
CG A:ASN30 4.4 17.5 1.0

Sodium binding site 2 out of 2 in 3s3z

Go back to Sodium Binding Sites List in 3s3z
Sodium binding site 2 out of 2 in the Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure An Tandem Cyanovirin-N Dimer, CVN2L10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na214

b:35.0
occ:1.00
CG2 A:ILE94 3.4 16.1 0.5
CG2 A:ILE94 3.7 17.1 0.5
O A:HOH225 4.6 22.6 1.0
CB A:ASP95 4.7 18.9 1.0
CB A:ILE94 4.9 16.1 0.5

Reference:

J.R.Keeffe, P.N.Gnanapragasam, S.K.Gillespie, J.Yong, P.J.Bjorkman, S.L.Mayo. Designed Oligomers of Cyanovirin-N Show Enhanced Hiv Neutralization. Proc.Natl.Acad.Sci.Usa V. 108 14079 2011.
ISSN: ISSN 0027-8424
PubMed: 21799112
DOI: 10.1073/PNAS.1108777108
Page generated: Mon Oct 7 12:53:40 2024

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