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Sodium in PDB 4c10: Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19

Other elements in 4c10:

The structure of Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 (pdb code 4c10). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19, PDB code: 4c10:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4c10

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Sodium binding site 1 out of 6 in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 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 4c10

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Sodium binding site 2 out of 6 in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 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 4c10

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Sodium binding site 3 out of 6 in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 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 3.5 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 4c10

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Sodium binding site 4 out of 6 in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 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 4c10

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Sodium binding site 5 out of 6 in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 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
CB A:SER17 4.9 0.3 1.0
N A:VAL16 4.9 58.7 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 4c10

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Sodium binding site 6 out of 6 in the Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Cryo-Em Reconstruction of Empty Enterovirus 71 in Complex with A Neutralizing Antibody E19 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, P.Lim, R.Perera, J.Cardosa, A.Suksatu, R.J.Kuhn, M.G.Rossmann. Neutralizing Antibodies Can Initiate Genome Release From Human Enterovirus 71. Proc.Natl.Acad.Sci.Usa V. 111 2134 2014.
ISSN: ISSN 0027-8424
PubMed: 24469789
DOI: 10.1073/PNAS.1320624111
Page generated: Mon Oct 7 14:36:28 2024

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