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Zinc in PDB 4llf: Crystal Structure of Cucumber Necrosis Virus

Protein crystallography data

The structure of Crystal Structure of Cucumber Necrosis Virus, PDB code: 4llf was solved by T.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.31 / 2.89
Space group I 2 3 3
Cell size a, b, c (Å), α, β, γ (°) 384.000, 384.000, 384.000, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.2

Other elements in 4llf:

The structure of Crystal Structure of Cucumber Necrosis Virus also contains other interesting chemical elements:

Calcium (Ca) 15 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cucumber Necrosis Virus (pdb code 4llf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Cucumber Necrosis Virus, PDB code: 4llf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4llf

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Zinc binding site 1 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:97.0
occ:0.26
 ZN D:ZN401 0.0 97.0 0.3
NE2 D:HIS62 2.2 65.0 0.5
CE1 D:HIS62 2.3 65.6 0.5
ZN D:ZN401 2.8 1.0 0.7
CE1 D:HIS62 2.9 67.2 0.5
NE2 D:HIS62 3.1 67.9 0.5
ND1 D:HIS62 3.3 53.9 0.5
CD2 D:HIS62 3.4 53.2 0.5
ND1 D:HIS62 4.1 55.1 0.5
CD2 D:HIS62 4.3 54.8 0.5
CG D:HIS62 4.4 49.8 0.5
CG D:HIS62 4.4 50.2 0.5

Zinc binding site 2 out of 10 in 4llf

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Zinc binding site 2 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:1.0
occ:0.74
 ZN D:ZN401 0.0 1.0 0.7
NE2 D:HIS62 2.1 67.9 0.5
CE1 D:HIS62 2.2 67.2 0.5
CE1 D:HIS62 2.7 65.6 0.5
ZN D:ZN401 2.8 97.0 0.3
NE2 D:HIS62 3.0 65.0 0.5
CD2 D:HIS62 3.4 54.8 0.5
ND1 D:HIS62 3.4 55.1 0.5
ND1 D:HIS62 4.0 53.9 0.5
CD2 D:HIS62 4.2 53.2 0.5
CG D:HIS62 4.3 50.2 0.5
CG D:HIS62 4.4 49.8 0.5

Zinc binding site 3 out of 10 in 4llf

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Zinc binding site 3 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:99.2
occ:0.46
 ZN G:ZN401 0.0 99.2 0.5
NE2 G:HIS62 2.3 63.8 0.5
CE1 G:HIS62 2.3 64.3 0.5
ZN G:ZN401 2.6 0.5 0.5
CE1 G:HIS62 2.8 65.5 0.5
NE2 G:HIS62 3.0 66.0 0.5
ND1 G:HIS62 3.4 53.9 0.5
CD2 G:HIS62 3.5 52.7 0.5
ND1 G:HIS62 4.1 52.9 0.5
CD2 G:HIS62 4.2 52.8 0.5
CG G:HIS62 4.4 48.4 0.5
CG G:HIS62 4.4 48.2 0.5
CB G:ALA71 5.0 29.2 1.0

Zinc binding site 4 out of 10 in 4llf

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Zinc binding site 4 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn401

b:0.5
occ:0.54
 ZN G:ZN401 0.0 0.5 0.5
NE2 G:HIS62 2.2 66.0 0.5
CE1 G:HIS62 2.3 65.5 0.5
ZN G:ZN401 2.6 99.2 0.5
CE1 G:HIS62 2.8 64.3 0.5
NE2 G:HIS62 3.1 63.8 0.5
CD2 G:HIS62 3.5 52.8 0.5
ND1 G:HIS62 3.5 52.9 0.5
ND1 G:HIS62 4.0 53.9 0.5
CD2 G:HIS62 4.3 52.7 0.5
CG G:HIS62 4.4 48.4 0.5
CG G:HIS62 4.5 48.2 0.5

Zinc binding site 5 out of 10 in 4llf

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Zinc binding site 5 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn401

b:97.7
occ:0.27
 ZN J:ZN401 0.0 97.7 0.3
NE2 J:HIS62 2.3 61.3 0.5
CE1 J:HIS62 2.4 61.6 0.5
CE1 J:HIS62 2.7 61.4 0.5
ZN J:ZN401 2.7 0.7 0.7
NE2 J:HIS62 3.0 61.1 0.5
ND1 J:HIS62 3.5 52.7 0.5
CD2 J:HIS62 3.6 51.2 0.5
ND1 J:HIS62 4.0 51.7 0.5
CD2 J:HIS62 4.2 51.8 0.5
CG J:HIS62 4.4 49.5 0.5
CG J:HIS62 4.4 49.6 0.5

Zinc binding site 6 out of 10 in 4llf

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Zinc binding site 6 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn401

b:0.7
occ:0.73
 ZN J:ZN401 0.0 0.7 0.7
NE2 J:HIS62 2.3 61.1 0.5
CE1 J:HIS62 2.5 61.4 0.5
ZN J:ZN401 2.7 97.7 0.3
CE1 J:HIS62 3.1 61.6 0.5
NE2 J:HIS62 3.4 61.3 0.5
CD2 J:HIS62 3.5 51.8 0.5
ND1 J:HIS62 3.5 51.7 0.5
ND1 J:HIS62 4.3 52.7 0.5
CG J:HIS62 4.5 49.6 0.5
CD2 J:HIS62 4.6 51.2 0.5
CG J:HIS62 4.7 49.5 0.5

Zinc binding site 7 out of 10 in 4llf

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Zinc binding site 7 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:1.0
occ:0.50
 ZN M:ZN401 0.0 1.0 0.5
NE2 M:HIS62 2.2 62.6 0.5
CE1 M:HIS62 2.3 63.7 0.5
ZN M:ZN401 2.6 0.7 0.5
CE1 M:HIS62 2.7 64.0 0.5
NE2 M:HIS62 3.1 64.2 0.5
ND1 M:HIS62 3.3 53.8 0.5
CD2 M:HIS62 3.5 52.1 0.5
ND1 M:HIS62 4.0 51.9 0.5
CD2 M:HIS62 4.3 51.4 0.5
CG M:HIS62 4.4 47.8 0.5
CG M:HIS62 4.4 47.8 0.5

Zinc binding site 8 out of 10 in 4llf

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Zinc binding site 8 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn401

b:0.7
occ:0.50
 ZN M:ZN401 0.0 0.7 0.5
NE2 M:HIS62 2.3 64.2 0.5
CE1 M:HIS62 2.4 64.0 0.5
ZN M:ZN401 2.6 1.0 0.5
CE1 M:HIS62 2.8 63.7 0.5
NE2 M:HIS62 3.2 62.6 0.5
ND1 M:HIS62 3.4 51.9 0.5
CD2 M:HIS62 3.5 51.4 0.5
ND1 M:HIS62 4.0 53.8 0.5
CG M:HIS62 4.4 47.8 0.5
CD2 M:HIS62 4.4 52.1 0.5
CG M:HIS62 4.5 47.8 0.5

Zinc binding site 9 out of 10 in 4llf

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Zinc binding site 9 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn401

b:1.0
occ:0.07
 ZN P:ZN401 0.0 1.0 0.1
NE2 P:HIS62 2.2 63.9 0.5
CE1 P:HIS62 2.3 63.7 0.5
ZN P:ZN401 2.8 0.4 0.9
CE1 P:HIS62 2.9 63.1 0.5
NE2 P:HIS62 3.1 62.5 0.5
ND1 P:HIS62 3.4 54.4 0.5
CD2 P:HIS62 3.4 53.8 0.5
ND1 P:HIS62 4.1 51.3 0.5
CD2 P:HIS62 4.3 53.4 0.5
CG P:HIS62 4.4 49.4 0.5
CG P:HIS62 4.5 49.2 0.5

Zinc binding site 10 out of 10 in 4llf

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Zinc binding site 10 out of 10 in the Crystal Structure of Cucumber Necrosis Virus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Cucumber Necrosis Virus within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn401

b:0.4
occ:0.93
 ZN P:ZN401 0.0 0.4 0.9
NE2 P:HIS62 2.3 62.5 0.5
CE1 P:HIS62 2.3 63.1 0.5
ZN P:ZN401 2.8 1.0 0.1
CE1 P:HIS62 2.9 63.7 0.5
NE2 P:HIS62 3.1 63.9 0.5
ND1 P:HIS62 3.4 51.3 0.5
CD2 P:HIS62 3.5 53.4 0.5
ND1 P:HIS62 4.1 54.4 0.5
CD2 P:HIS62 4.3 53.8 0.5
CG P:HIS62 4.4 49.2 0.5
CG P:HIS62 4.5 49.4 0.5
CB P:ALA71 5.0 37.1 1.0

Reference:

M.Li, K.Kakani, U.Katpally, S.Johnson, D.Rochon, T.J.Smith. Atomic Structure of Cucumber Necrosis Virus and the Role of the Capsid in Vector Transmission. J.Virol. V. 87 12166 2013.
ISSN: ISSN 0022-538X
PubMed: 24006433
DOI: 10.1128/JVI.01965-13
Page generated: Sun Oct 27 01:58:37 2024

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