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Chlorine in PDB 2df7: Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle

Protein crystallography data

The structure of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle, PDB code: 2df7 was solved by T.P.Ko, C.C.Lee, M.Y.Wang, A.H.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.60
Space group P 21 3 2
Cell size a, b, c (Å), α, β, γ (°) 316.412, 316.412, 316.412, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 21.5

Other elements in 2df7:

The structure of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle also contains other interesting chemical elements:

Calcium (Ca) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle (pdb code 2df7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle, PDB code: 2df7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2df7

Go back to Chlorine Binding Sites List in 2df7
Chlorine binding site 1 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral 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 Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl5503

b:32.0
occ:1.00
 N F:ARG202 3.1 31.6 1.0
N A:ARG202 3.2 28.7 1.0
CA F:ARG202 3.7 30.5 1.0
CA A:ARG202 3.8 29.6 1.0
CD F:PRO203 3.9 27.4 1.0
CD A:PRO203 3.9 27.1 1.0
C F:ASP201 4.2 32.2 1.0
C A:ASP201 4.2 30.7 1.0
CA F:ASP201 4.3 33.0 1.0
CA A:ASP201 4.4 30.7 1.0
CG F:ARG202 4.6 27.7 1.0
CG A:ARG202 4.6 28.2 1.0
CB F:ARG202 4.7 30.5 1.0
N F:PRO203 4.7 28.9 1.0
CB A:ARG202 4.8 30.0 1.0
C F:ARG202 4.8 29.6 1.0
N A:PRO203 4.8 30.6 1.0
CB F:ASP201 4.8 34.2 1.0
CB A:ASP201 4.8 32.2 1.0
C A:ARG202 4.9 30.2 1.0
CG F:PRO203 5.0 27.6 1.0

Chlorine binding site 2 out of 8 in 2df7

Go back to Chlorine Binding Sites List in 2df7
Chlorine binding site 2 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral 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 Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl5501

b:26.5
occ:0.33
 N B:ARG202 3.1 27.8 1.0
CA B:ARG202 3.7 26.6 1.0
CD B:PRO203 3.9 23.5 1.0
C B:ASP201 4.2 29.4 1.0
CA B:ASP201 4.4 31.0 1.0
CG B:ARG202 4.5 22.8 1.0
CB B:ARG202 4.6 25.5 1.0
N B:PRO203 4.8 24.4 1.0
C B:ARG202 4.8 26.4 1.0
CB B:ASP201 4.9 32.4 1.0

Chlorine binding site 3 out of 8 in 2df7

Go back to Chlorine Binding Sites List in 2df7
Chlorine binding site 3 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral 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 Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl5504

b:30.2
occ:1.00
 N L:ARG202 3.1 33.0 1.0
N E:ARG202 3.2 29.7 1.0
N C:ARG202 3.2 31.9 1.0
O L:HOH470 3.5 36.2 1.0
CA L:ARG202 3.7 32.0 1.0
CA C:ARG202 3.7 30.7 1.0
CA E:ARG202 3.8 28.4 1.0
CD C:PRO203 4.0 29.8 1.0
CD L:PRO203 4.0 30.7 1.0
CD E:PRO203 4.1 27.9 1.0
C L:ASP201 4.1 33.0 1.0
C E:ASP201 4.2 30.6 1.0
C C:ASP201 4.3 32.0 1.0
CA L:ASP201 4.3 34.0 1.0
CA E:ASP201 4.4 30.7 1.0
CA C:ASP201 4.4 33.5 1.0
CG L:ARG202 4.5 31.1 1.0
CG E:ARG202 4.5 30.8 1.0
CG C:ARG202 4.6 30.1 1.0
CB L:ARG202 4.6 31.5 1.0
CB L:ASP201 4.7 37.0 1.0
CB E:ARG202 4.7 30.0 1.0
CB C:ARG202 4.7 30.0 1.0
CB E:ASP201 4.8 31.3 1.0
C L:ARG202 4.8 32.5 1.0
N L:PRO203 4.8 31.0 1.0
N C:PRO203 4.8 30.3 1.0
C C:ARG202 4.9 31.8 1.0
N E:PRO203 4.9 29.2 1.0
C E:ARG202 4.9 29.3 1.0
CB C:ASP201 4.9 36.7 1.0

Chlorine binding site 4 out of 8 in 2df7

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Chlorine binding site 4 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral 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 Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl5505

b:33.6
occ:1.00
 N M:ARG202 3.1 31.0 1.0
N G:ARG202 3.2 30.4 1.0
N K:ARG202 3.2 34.0 1.0
CA G:ARG202 3.7 29.7 1.0
CA M:ARG202 3.8 32.1 1.0
CA K:ARG202 3.8 33.6 1.0
CD M:PRO203 3.8 27.1 1.0
CD G:PRO203 3.9 26.3 1.0
CD K:PRO203 3.9 30.3 1.0
C M:ASP201 4.2 32.1 1.0
C G:ASP201 4.2 29.9 1.0
C K:ASP201 4.3 33.9 1.0
CA M:ASP201 4.3 33.2 1.0
CA G:ASP201 4.4 30.2 1.0
CA K:ASP201 4.4 35.1 1.0
CG M:ARG202 4.6 34.8 1.0
CG K:ARG202 4.7 33.9 1.0
CG G:ARG202 4.7 30.8 1.0
N G:PRO203 4.7 28.7 1.0
N M:PRO203 4.8 29.6 1.0
CB G:ARG202 4.8 31.5 1.0
CB M:ASP201 4.8 34.4 1.0
C G:ARG202 4.8 28.9 1.0
CB M:ARG202 4.8 32.6 1.0
N K:PRO203 4.8 31.6 1.0
CB K:ARG202 4.8 34.7 1.0
C M:ARG202 4.8 31.3 1.0
C K:ARG202 4.9 32.5 1.0
CB G:ASP201 4.9 31.8 1.0
CG G:PRO203 4.9 25.0 1.0
CB K:ASP201 4.9 37.1 1.0
CG M:PRO203 5.0 29.5 1.0

Chlorine binding site 5 out of 8 in 2df7

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Chlorine binding site 5 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral 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 Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl5506

b:31.2
occ:1.00
 N H:ARG202 3.1 29.9 1.0
N N:ARG202 3.2 30.9 1.0
N O:ARG202 3.2 32.4 1.0
CA H:ARG202 3.6 31.3 1.0
CA O:ARG202 3.8 32.2 1.0
CA N:ARG202 3.8 30.8 1.0
CD H:PRO203 3.8 33.1 1.0
CD O:PRO203 3.8 30.9 1.0
CD N:PRO203 3.9 29.9 1.0
C H:ASP201 4.1 29.9 1.0
C N:ASP201 4.2 31.4 1.0
C O:ASP201 4.3 33.1 1.0
CA H:ASP201 4.3 30.1 1.0
CA N:ASP201 4.4 31.4 1.0
CA O:ASP201 4.4 33.7 1.0
CG H:ARG202 4.6 31.1 1.0
CG N:ARG202 4.6 29.7 1.0
N H:PRO203 4.6 33.9 1.0
CB H:ARG202 4.7 32.3 1.0
CG O:ARG202 4.7 35.3 1.0
N O:PRO203 4.7 32.4 1.0
C H:ARG202 4.7 32.9 1.0
N N:PRO203 4.8 31.6 1.0
CB N:ARG202 4.8 30.5 1.0
CB O:ARG202 4.8 34.1 1.0
C O:ARG202 4.8 32.9 1.0
CB H:ASP201 4.9 31.9 1.0
CG H:PRO203 4.9 32.8 1.0
C N:ARG202 4.9 31.5 1.0
CB N:ASP201 4.9 33.2 1.0
CG O:PRO203 4.9 32.1 1.0
CB O:ASP201 4.9 35.8 1.0
CG N:PRO203 5.0 28.7 1.0

Chlorine binding site 6 out of 8 in 2df7

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Chlorine binding site 6 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral 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 Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl5507

b:33.5
occ:1.00
 N Q:ARG202 3.1 34.1 1.0
N J:ARG202 3.2 33.1 1.0
N I:ARG202 3.2 32.7 1.0
CA Q:ARG202 3.7 34.0 1.0
CA J:ARG202 3.7 33.5 1.0
CA I:ARG202 3.8 32.6 1.0
CD Q:PRO203 3.9 32.9 1.0
CD J:PRO203 3.9 33.2 1.0
CD I:PRO203 3.9 29.3 1.0
C Q:ASP201 4.2 35.3 1.0
C J:ASP201 4.2 34.6 1.0
C I:ASP201 4.2 32.2 1.0
CA Q:ASP201 4.3 36.7 1.0
CA I:ASP201 4.3 32.6 1.0
CA J:ASP201 4.4 35.8 1.0
CG Q:ARG202 4.6 36.7 1.0
CG J:ARG202 4.7 33.6 1.0
CG I:ARG202 4.7 32.6 1.0
N Q:PRO203 4.7 34.8 1.0
CB Q:ARG202 4.7 34.7 1.0
CB J:ARG202 4.8 35.2 1.0
N J:PRO203 4.8 34.5 1.0
CB Q:ASP201 4.8 39.4 1.0
CB I:ARG202 4.8 32.2 1.0
N I:PRO203 4.8 32.3 1.0
C Q:ARG202 4.8 34.1 1.0
C J:ARG202 4.8 35.2 1.0
CB I:ASP201 4.8 33.6 1.0
C I:ARG202 4.9 33.8 1.0
CB J:ASP201 4.9 38.8 1.0

Chlorine binding site 7 out of 8 in 2df7

Go back to Chlorine Binding Sites List in 2df7
Chlorine binding site 7 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral 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 Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Cl5502

b:26.0
occ:0.33
 N P:ARG202 3.1 33.6 1.0
CA P:ARG202 3.7 33.0 1.0
CD P:PRO203 3.9 34.3 1.0
C P:ASP201 4.2 33.5 1.0
CA P:ASP201 4.3 33.3 1.0
CG P:ARG202 4.5 36.2 1.0
CB P:ARG202 4.7 35.7 1.0
CB P:ASP201 4.8 36.3 1.0
N P:PRO203 4.8 35.0 1.0
C P:ARG202 4.8 33.6 1.0

Chlorine binding site 8 out of 8 in 2df7

Go back to Chlorine Binding Sites List in 2df7
Chlorine binding site 8 out of 8 in the Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Cl5508

b:27.7
occ:1.00
 N R:ARG202 3.1 31.2 1.0
N T:ARG202 3.1 28.0 1.0
N S:ARG202 3.2 27.2 1.0
O R:HOH5956 3.5 41.7 1.0
CA R:ARG202 3.7 30.0 1.0
CA T:ARG202 3.7 27.2 1.0
CA S:ARG202 3.8 26.7 1.0
CD R:PRO203 3.9 29.7 1.0
CD S:PRO203 3.9 23.7 1.0
CD T:PRO203 3.9 24.3 1.0
C R:ASP201 4.2 31.7 1.0
C T:ASP201 4.2 29.6 1.0
C S:ASP201 4.2 27.9 1.0
CA R:ASP201 4.4 32.7 1.0
CA S:ASP201 4.4 29.4 1.0
CA T:ASP201 4.4 30.0 1.0
CG R:ARG202 4.5 31.6 1.0
CG T:ARG202 4.6 30.6 1.0
CG S:ARG202 4.6 28.5 1.0
CB R:ARG202 4.7 31.5 1.0
CB T:ARG202 4.7 28.1 1.0
CB S:ARG202 4.7 27.0 1.0
N R:PRO203 4.8 29.4 1.0
C R:ARG202 4.8 29.5 1.0
CB T:ASP201 4.8 31.0 1.0
N T:PRO203 4.8 26.0 1.0
N S:PRO203 4.8 27.4 1.0
C T:ARG202 4.8 26.6 1.0
C S:ARG202 4.8 28.4 1.0
CB S:ASP201 4.9 31.9 1.0
CB R:ASP201 4.9 35.8 1.0
CG S:PRO203 5.0 22.1 1.0

Reference:

C.C.Lee, T.P.Ko, C.C.Chou, M.Yoshimura, S.R.Doong, M.Y.Wang, A.H.Wang. Crystal Structure of Infectious Bursal Disease Virus VP2 Subviral Particle at 2.6A Resolution: Implications in Virion Assembly and Immunogenicity. J.Struct.Biol. V. 155 74 2006.
ISSN: ISSN 1047-8477
PubMed: 16677827
DOI: 10.1016/J.JSB.2006.02.014
Page generated: Sat Dec 12 09:03:10 2020

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