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Chlorine in PDB 5c9a: Crystal Structure of Empty Coxsackievirus A16 Particle

Protein crystallography data

The structure of Crystal Structure of Empty Coxsackievirus A16 Particle, PDB code: 5c9a was solved by J.Ren, X.Wang, L.Zhu, Z.Hu, Q.Gao, P.Yang, X.Li, J.Wang, X.Shen, E.E.Fry, Z.Rao, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.98 / 2.70
Space group P 41 21 2 14
Cell size a, b, c (Å), α, β, γ (°) 491.400, 491.400, 708.900, 90.00, 90.00, 90.00
R / Rfree (%) 29.1 / 29.1

Other elements in 5c9a:

The structure of Crystal Structure of Empty Coxsackievirus A16 Particle also contains other interesting chemical elements:

Potassium (K) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Empty Coxsackievirus A16 Particle (pdb code 5c9a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Empty Coxsackievirus A16 Particle, PDB code: 5c9a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 5c9a

Go back to Chlorine Binding Sites List in 5c9a
Chlorine binding site 1 out of 7 in the Crystal Structure of Empty Coxsackievirus A16 Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Empty Coxsackievirus A16 Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:36.0
occ:1.00
 NH2 A:ARG236 3.2 18.2 1.0
NH1 A:ARG236 3.7 14.2 1.0
CZ A:ARG236 3.9 21.4 1.0
CB A:TRP171 4.5 8.8 1.0
O A:TRP171 4.6 21.4 1.0
C A:TRP171 5.0 15.1 1.0

Chlorine binding site 2 out of 7 in 5c9a

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Chlorine binding site 2 out of 7 in the Crystal Structure of Empty Coxsackievirus A16 Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Empty Coxsackievirus A16 Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:50.9
occ:1.00
 N A:HIS257 2.9 9.0 1.0
CA A:HIS257 3.4 9.2 1.0
N A:VAL258 3.4 11.1 1.0
NE2 B:GLN44 3.7 42.8 1.0
C A:LYS256 4.0 18.0 1.0
C A:HIS257 4.0 10.4 1.0
OE1 B:GLN44 4.0 74.6 1.0
CA A:GLY81 4.1 3.1 1.0
CB B:ALA41 4.1 16.4 1.0
CG1 A:VAL258 4.1 9.4 1.0
CA A:LYS256 4.2 14.2 1.0
CD B:GLN44 4.2 63.6 1.0
O B:ALA41 4.3 32.2 1.0
CA B:ALA41 4.5 22.8 1.0
CA A:VAL258 4.6 18.1 1.0
CB A:VAL258 4.8 19.5 1.0
C B:ALA41 4.8 27.8 1.0
CD2 A:HIS257 4.8 12.8 1.0
CB A:HIS257 4.8 3.1 1.0
O A:VAL258 4.9 22.4 1.0
C A:GLY81 4.9 14.2 1.0
O A:GLY81 4.9 17.1 1.0
CB A:LYS256 5.0 6.4 1.0

Chlorine binding site 3 out of 7 in 5c9a

Go back to Chlorine Binding Sites List in 5c9a
Chlorine binding site 3 out of 7 in the Crystal Structure of Empty Coxsackievirus A16 Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Empty Coxsackievirus A16 Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:47.8
occ:1.00
 N B:TYR233 3.5 18.2 1.0
CD B:PRO232 3.5 14.4 1.0
O C:HOH410 3.6 22.9 1.0
CG B:PRO232 3.6 15.4 1.0
CB B:TYR233 3.7 9.1 1.0
N B:PRO232 3.7 21.7 1.0
CA B:HIS231 3.8 19.5 1.0
C B:HIS231 3.8 23.7 1.0
CG C:MET66 3.9 19.2 1.0
CG C:PRO65 4.2 10.8 1.0
CA B:TYR233 4.2 14.2 1.0
CB B:HIS231 4.4 26.1 1.0
C B:PRO232 4.5 20.4 1.0
CA B:PRO232 4.5 18.3 1.0
O B:HIS231 4.5 29.0 1.0
CB B:PRO232 4.7 20.3 1.0
CD2 B:HIS231 4.7 24.1 1.0
O B:THR230 4.7 28.7 1.0
SD C:MET66 4.7 27.0 1.0
CD C:PRO65 4.8 21.6 1.0
CG B:HIS231 4.9 40.4 1.0
N B:HIS231 5.0 25.3 1.0
CG B:TYR233 5.0 13.3 1.0

Chlorine binding site 4 out of 7 in 5c9a

Go back to Chlorine Binding Sites List in 5c9a
Chlorine binding site 4 out of 7 in the Crystal Structure of Empty Coxsackievirus A16 Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Empty Coxsackievirus A16 Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:69.2
occ:1.00
 N B:SER139 3.3 23.0 1.0
CA B:LYS138 3.6 22.1 1.0
CB B:LYS138 3.8 3.1 1.0
CD B:LYS138 3.8 23.7 1.0
CE B:LYS138 3.9 34.2 1.0
C B:LYS138 4.0 20.8 1.0
CG B:LYS138 4.3 18.8 1.0
NE1 B:TRP147 4.4 36.2 1.0
CA B:SER139 4.4 17.9 1.0
O B:SER139 4.4 21.4 1.0
CB B:SER139 4.5 15.5 1.0
O B:THR137 4.7 35.5 1.0
C B:SER139 4.9 20.1 1.0
N B:LYS138 4.9 18.2 1.0

Chlorine binding site 5 out of 7 in 5c9a

Go back to Chlorine Binding Sites List in 5c9a
Chlorine binding site 5 out of 7 in the Crystal Structure of Empty Coxsackievirus A16 Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Empty Coxsackievirus A16 Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:55.7
occ:1.00
 N B:THR137 3.5 34.9 1.0
CB B:THR137 3.8 14.6 1.0
OG1 B:THR137 4.1 23.9 1.0
CA B:THR137 4.2 20.4 1.0
CA B:ASP136 4.3 42.3 1.0
C B:ASP136 4.4 35.9 1.0
CG B:ASP136 4.4 67.8 1.0
O B:THR137 4.4 35.5 1.0
OD2 B:ASP136 4.5 85.9 1.0
OD1 B:ASP136 4.6 49.0 1.0
CB B:ASP136 4.7 56.3 1.0
C B:THR137 4.8 22.6 1.0
CG2 B:THR137 5.0 3.1 1.0

Chlorine binding site 6 out of 7 in 5c9a

Go back to Chlorine Binding Sites List in 5c9a
Chlorine binding site 6 out of 7 in the Crystal Structure of Empty Coxsackievirus A16 Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Empty Coxsackievirus A16 Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:54.0
occ:1.00
 NZ B:LYS34 3.5 34.9 1.0
ND2 B:ASN15 3.7 41.0 1.0
CE B:LYS34 3.8 44.1 1.0
CD B:LYS34 3.9 28.1 1.0
CA C:GLY27 3.9 11.2 1.0
N C:GLY27 4.2 17.1 1.0
OD1 B:ASN15 4.3 73.1 1.0
CG B:ASN15 4.4 52.3 1.0
C C:PRO26 4.9 17.4 1.0
CG B:LYS34 4.9 38.6 1.0

Chlorine binding site 7 out of 7 in 5c9a

Go back to Chlorine Binding Sites List in 5c9a
Chlorine binding site 7 out of 7 in the Crystal Structure of Empty Coxsackievirus A16 Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Empty Coxsackievirus A16 Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl301

b:29.5
occ:1.00
 N C:GLY91 3.3 27.4 1.0
N C:ALA181 3.4 26.2 1.0
NE1 C:TRP111 3.5 28.3 1.0
CD C:PRO90 3.8 16.0 1.0
CA C:HIS180 3.8 25.0 1.0
CA C:GLY91 3.8 27.4 1.0
CB C:ASP89 3.9 19.9 1.0
N C:PRO90 3.9 17.6 1.0
N C:ARG92 4.0 29.8 1.0
CA C:ASP89 4.0 16.0 1.0
C C:ASP89 4.1 17.6 1.0
C C:GLY91 4.1 34.5 1.0
ND1 C:HIS180 4.1 23.2 1.0
C C:HIS180 4.1 27.7 1.0
CB C:ALA181 4.2 7.4 1.0
CG C:PRO90 4.2 3.1 1.0
O C:ALA179 4.3 18.7 1.0
CE2 C:TRP111 4.3 15.0 1.0
CA C:ALA181 4.4 20.5 1.0
CZ2 C:TRP111 4.4 24.7 1.0
C C:PRO90 4.4 19.5 1.0
CB C:HIS180 4.4 38.2 1.0
CD1 C:TRP111 4.5 24.1 1.0
CA C:PRO90 4.7 17.9 1.0
CB C:ARG92 4.7 14.3 1.0
CG C:ASP89 4.7 20.4 1.0
CG C:HIS180 4.7 38.7 1.0
N C:HIS180 4.8 32.0 1.0
O C:ASP89 4.8 31.3 1.0
O C:ALA181 4.8 30.4 1.0
O C:GLY91 4.9 34.4 1.0
OG1 C:THR191 4.9 35.6 1.0
C C:ALA179 4.9 22.7 1.0
CA C:ARG92 4.9 15.8 1.0
OD2 C:ASP89 4.9 42.8 1.0
O C:TYR189 5.0 26.2 1.0

Reference:

J.Ren, X.Wang, L.Zhu, Z.Hu, Q.Gao, P.Yang, X.Li, J.Wang, X.Shen, E.E.Fry, Z.Rao, D.I.Stuart. Structures of Coxsackievirus A16 Capsids with Native Antigenicity: Implications For Particle Expansion, Receptor Binding, and Immunogenicity. J.Virol. V. 89 10500 2015.
ISSN: ESSN 1098-5514
PubMed: 26269176
DOI: 10.1128/JVI.01102-15
Page generated: Sat Jul 12 00:44:13 2025

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