Atomistry » Zinc » PDB 4lep-4llg » 4llf
Atomistry »
  Zinc »
    PDB 4lep-4llg »
      4llf »

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

Go back to Zinc Binding Sites List in 4llf
Zinc binding site 1 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 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

Go back to Zinc Binding Sites List in 4llf
Zinc binding site 2 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 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

Go back to Zinc Binding Sites List in 4llf
Zinc binding site 3 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 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

Go back to Zinc Binding Sites List in 4llf
Zinc binding site 4 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 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

Go back to Zinc Binding Sites List in 4llf
Zinc binding site 5 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 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

Go back to Zinc Binding Sites List in 4llf
Zinc binding site 6 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 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

Go back to Zinc Binding Sites List in 4llf
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

Go back to Zinc Binding Sites List in 4llf
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

Go back to Zinc Binding Sites List in 4llf
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

Go back to Zinc Binding Sites List in 4llf
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy