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Sodium in PDB 3zfe: Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711

Protein crystallography data

The structure of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711, PDB code: 3zfe was solved by P.Plevka, R.Perera, M.L.Yap, J.Cardosa, R.J.Kuhn, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.4 / 2.70
Space group I 2 3 14
Cell size a, b, c (Å), α, β, γ (°) 594.500, 594.500, 594.500, 90.00, 90.00, 90.00
R / Rfree (%) 24.02 / n/a

Other elements in 3zfe:

The structure of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 (pdb code 3zfe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711, PDB code: 3zfe:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3zfe

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Sodium binding site 1 out of 6 in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1298

b:7.5
occ:1.00
 ND2 A:ASN31 2.5 22.1 1.0
O A:ASN71 2.5 27.0 1.0
OG1 A:THR28 2.6 24.8 1.0
O A:GLY29 2.7 21.7 1.0
CG A:ASN31 3.5 22.1 1.0
C A:ASN71 3.7 27.0 1.0
CB A:THR28 3.7 24.8 1.0
C A:GLY29 3.8 21.7 1.0
OD1 A:ASN31 3.9 22.1 1.0
N A:ASN31 4.2 27.7 1.0
CB A:ASN71 4.3 30.4 1.0
C A:THR28 4.4 19.8 1.0
C A:GLN30 4.4 20.8 1.0
CA A:ASN71 4.4 27.0 1.0
CA A:GLN30 4.4 20.8 1.0
N A:GLY29 4.5 21.7 1.0
N A:ASN71 4.5 27.0 1.0
O A:THR28 4.6 19.8 1.0
N A:GLN30 4.6 20.8 1.0
CB A:ASN31 4.7 22.1 1.0
CA A:THR28 4.7 19.8 1.0
N A:SER72 4.8 27.0 1.0
CG2 A:THR28 4.8 24.8 1.0
CA A:ASN31 4.8 27.7 1.0
CA A:GLY29 4.8 21.7 1.0
CA A:SER72 5.0 27.0 1.0

Sodium binding site 2 out of 6 in 3zfe

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Sodium binding site 2 out of 6 in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1299

b:27.0
occ:1.00
 O A:SER56 2.7 26.0 1.0
OE1 C:GLN221 2.7 32.4 1.0
OE2 C:GLU116 3.3 62.3 1.0
O A:THR58 3.8 32.0 1.0
C A:SER56 3.8 26.0 1.0
CD C:GLN221 4.0 32.4 1.0
CG C:GLU116 4.0 62.3 1.0
CD C:GLU116 4.0 62.3 1.0
O C:ALA220 4.2 22.9 1.0
CA A:ASN57 4.4 36.4 1.0
N A:ASN57 4.5 36.4 1.0
C A:ASN57 4.6 36.4 1.0
N A:THR58 4.6 32.0 1.0
CA C:GLN221 4.6 20.9 1.0
NE2 C:GLN221 4.7 32.4 1.0
CA A:SER56 4.8 26.0 1.0
CB A:SER56 4.8 38.6 1.0
C A:THR58 4.8 32.0 1.0
CB C:GLU116 4.9 62.3 1.0
OG A:SER56 4.9 38.6 1.0

Sodium binding site 3 out of 6 in 3zfe

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Sodium binding site 3 out of 6 in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1300

b:7.5
occ:1.00
 O D:GLU63 2.6 48.1 1.0
O A:LEU47 2.6 25.2 1.0
O D:ALA65 2.7 53.8 1.0
O A:VAL44 2.8 28.3 1.0
NE2 A:GLN48 3.1 39.3 1.0
O A:PRO45 3.3 26.9 1.0
C D:GLU63 3.6 48.1 1.0
C A:PRO45 3.7 26.9 1.0
CA A:PRO45 3.8 26.9 1.0
C A:LEU47 3.8 25.2 1.0
C A:VAL44 3.8 28.3 1.0
CD D:PRO67 3.8 46.5 1.0
C D:ALA65 3.9 53.8 1.0
CD A:GLN48 4.0 39.3 1.0
CA D:GLU63 4.2 48.1 1.0
N A:PRO45 4.2 26.9 1.0
CG D:PRO67 4.3 46.5 1.0
N A:LEU47 4.4 25.2 1.0
N D:ALA65 4.5 53.8 1.0
OE1 A:GLN48 4.5 39.3 1.0
O D:THR62 4.5 53.9 1.0
N D:MET64 4.6 39.0 1.0
C D:MET64 4.6 39.0 1.0
CA A:LEU47 4.6 25.2 1.0
OD1 A:ASN57 4.6 42.8 1.0
N A:ALA46 4.7 20.9 1.0
N A:GLN48 4.8 24.2 1.0
CA D:ALA65 4.8 53.8 1.0
N D:ALA66 4.8 50.8 1.0
CA D:ALA66 4.9 50.8 1.0
N D:PRO67 4.9 42.2 1.0
CA D:MET64 4.9 39.0 1.0
CG2 A:VAL44 4.9 30.3 1.0
CA A:GLN48 4.9 24.2 1.0
O D:MET64 4.9 39.0 1.0
CG A:GLN48 5.0 39.3 1.0
CB A:LEU47 5.0 20.9 1.0

Sodium binding site 4 out of 6 in 3zfe

Go back to Sodium Binding Sites List in 3zfe
Sodium binding site 4 out of 6 in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1301

b:26.4
occ:1.00
 CB A:GLU164 3.0 0.1 1.0
OG A:SER168 3.1 21.1 1.0
N A:GLU164 3.4 35.7 1.0
CB A:SER168 3.4 21.1 1.0
CA A:GLU164 3.6 35.7 1.0
CG A:GLU164 3.6 0.1 1.0
CA A:SER168 3.8 24.6 1.0
OG A:SER165 3.8 35.1 1.0
N A:SER165 3.8 24.9 1.0
C A:GLU164 3.9 35.7 1.0
CB A:SER165 4.5 35.1 1.0
C A:PRO163 4.6 30.3 1.0
O A:GLU164 4.7 35.7 1.0
N A:SER168 4.7 24.6 1.0
CA A:SER165 4.8 24.9 1.0
N A:LEU169 4.8 24.9 1.0
C A:SER168 4.9 24.6 1.0
CA A:PRO163 5.0 30.3 1.0

Sodium binding site 5 out of 6 in 3zfe

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Sodium binding site 5 out of 6 in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1255

b:14.5
occ:1.00
 O B:TYR41 2.8 22.2 1.0
OG B:SER40 2.8 28.0 1.0
O A:SER15 2.8 41.7 1.0
OG A:SER17 3.6 0.3 1.0
C A:SER15 3.8 41.7 1.0
NH2 B:ARG103 3.9 19.9 1.0
C B:TYR41 3.9 22.2 1.0
CB B:SER40 3.9 28.0 1.0
OG B:SER43 4.0 45.8 1.0
N B:SER43 4.3 22.8 1.0
CA A:SER15 4.4 41.7 1.0
CA B:CYS42 4.4 27.4 1.0
C B:SER40 4.5 33.0 1.0
N B:CYS42 4.6 27.4 1.0
O B:SER40 4.6 33.0 1.0
N B:TYR41 4.6 22.2 1.0
N A:SER17 4.7 0.4 1.0
C B:CYS42 4.8 27.4 1.0
CA B:SER40 4.8 33.0 1.0
N A:VAL16 4.9 58.7 1.0
CB A:SER17 4.9 0.3 1.0
CB A:SER15 4.9 48.5 1.0
CA B:TYR41 4.9 22.2 1.0
CZ B:ARG103 5.0 19.9 1.0

Sodium binding site 6 out of 6 in 3zfe

Go back to Sodium Binding Sites List in 3zfe
Sodium binding site 6 out of 6 in the Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Human Enterovirus 71 in Complex with Capsid Binding Inhibitor WIN51711 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1243

b:7.5
occ:1.00
 NE2 A:GLN189 2.7 24.7 1.0
O C:VAL20 2.7 27.6 1.0
OG C:SER21 3.5 36.0 1.0
CD A:GLN189 3.7 24.7 1.0
C C:VAL20 3.9 27.6 1.0
CA C:SER21 3.9 23.3 1.0
CG A:GLN189 4.0 24.7 1.0
CB C:SER21 4.2 36.0 1.0
CB A:GLN189 4.2 24.7 1.0
N C:SER21 4.4 23.3 1.0
OE1 A:GLN189 4.7 24.7 1.0

Reference:

P.Plevka, R.Perera, M.L.Yap, J.Cardosa, R.J.Kuhn, M.G.Rossmann. Structure of Human Enterovirus 71 in Complex with A Capsid- Binding Inhibitor. Proc.Natl.Acad.Sci.Usa V. 110 5463 2013.
ISSN: ISSN 0027-8424
PubMed: 23509286
DOI: 10.1073/PNAS.1222379110
Page generated: Mon Oct 7 14:05:22 2024

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