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Zinc in PDB 6otf: Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry

Zinc Binding Sites:

The binding sites of Zinc atom in the Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry (pdb code 6otf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry, PDB code: 6otf:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6otf

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Zinc binding site 1 out of 3 in the Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:30.0
occ:1.00
OE1 B:GLN295 2.0 0.3 1.0
ND1 B:HIS299 2.2 96.7 1.0
NE2 B:HIS293 2.2 92.9 1.0
CE1 B:HIS299 3.0 96.7 1.0
CD2 B:HIS293 3.1 92.9 1.0
CD B:GLN295 3.1 0.3 1.0
CE1 B:HIS293 3.2 92.9 1.0
CG B:HIS299 3.3 96.7 1.0
CB B:ASP381 3.5 99.2 1.0
CB B:HIS299 3.7 96.7 1.0
O B:LEU294 3.9 96.6 1.0
NE2 B:GLN295 3.9 0.3 1.0
OD2 B:ASP381 4.0 99.2 1.0
NE2 B:HIS299 4.1 96.7 1.0
CA B:HIS299 4.2 96.7 1.0
CG B:GLN295 4.2 0.3 1.0
CB B:GLN295 4.2 0.3 1.0
CA B:GLN295 4.2 0.3 1.0
CG B:ASP381 4.3 99.2 1.0
CD2 B:HIS299 4.3 96.7 1.0
CG B:HIS293 4.3 92.9 1.0
ND1 B:HIS293 4.3 92.9 1.0
C B:LEU294 4.5 96.6 1.0
OH B:TYR301 4.6 90.6 1.0
N B:GLN295 4.6 0.3 1.0
CA B:ASP381 4.7 99.2 1.0

Zinc binding site 2 out of 3 in 6otf

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Zinc binding site 2 out of 3 in the Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:30.0
occ:1.00
NE2 A:HIS293 2.1 95.4 1.0
ND1 A:HIS299 2.1 96.8 1.0
CE1 A:HIS293 2.8 95.4 1.0
CG A:HIS299 2.8 96.8 1.0
CB A:HIS299 2.9 96.8 1.0
OE1 A:GLN295 3.1 1.0 1.0
CE1 A:HIS299 3.3 96.8 1.0
CD2 A:HIS293 3.3 95.4 1.0
CA A:HIS299 3.7 96.8 1.0
O A:LEU294 3.8 96.1 1.0
ND1 A:HIS293 4.0 95.4 1.0
CD2 A:HIS299 4.1 96.8 1.0
OH A:TYR301 4.2 93.2 1.0
NE2 A:HIS299 4.2 96.8 1.0
CG A:HIS293 4.3 95.4 1.0
CD A:GLN295 4.3 1.0 1.0
CZ A:TYR301 4.5 93.2 1.0
C A:HIS299 4.5 96.8 1.0
CB A:ASP381 4.6 98.4 1.0
N A:LEU300 4.6 94.7 1.0
CE2 A:TYR301 4.7 93.2 1.0
N A:HIS299 4.8 96.8 1.0
C A:LEU294 4.9 96.1 1.0

Zinc binding site 3 out of 3 in 6otf

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Zinc binding site 3 out of 3 in the Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Symmetric Reconstruction of Human Norovirus Gii.2 Snow Mountain Virus Strain Vlp in T=3 Symmetry within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn601

b:30.0
occ:1.00
ND1 C:HIS299 2.0 0.1 1.0
NE2 C:HIS293 2.1 0.8 1.0
CE1 C:HIS299 2.8 0.1 1.0
CD2 C:HIS293 3.0 0.8 1.0
CE1 C:HIS293 3.1 0.8 1.0
CG C:HIS299 3.1 0.1 1.0
CB C:GLN295 3.5 0.8 1.0
OE1 C:GLN295 3.5 0.8 1.0
O C:LEU294 3.6 0.5 1.0
CB C:HIS299 3.7 0.1 1.0
CG C:GLN295 3.9 0.8 1.0
NE2 C:HIS299 3.9 0.1 1.0
CD C:GLN295 4.0 0.8 1.0
OH C:TYR301 4.1 0.8 1.0
CA C:HIS299 4.1 0.1 1.0
CD2 C:HIS299 4.1 0.1 1.0
CG C:HIS293 4.1 0.8 1.0
ND1 C:HIS293 4.2 0.8 1.0
C C:LEU294 4.3 0.5 1.0
CA C:GLN295 4.3 0.8 1.0
CZ C:TYR301 4.5 0.8 1.0
N C:GLN295 4.6 0.8 1.0
CE2 C:TYR301 4.6 0.8 1.0
CB C:ASP381 5.0 0.4 1.0

Reference:

J.Jung, T.Grant, D.R.Thomas, C.W.Diehnelt, N.Grigorieff, L.Joshua-Tor. High-Resolution Cryo-Em Structures of Outbreak Strain Human Norovirus Shells Reveal Size Variations. Proc.Natl.Acad.Sci.Usa V. 116 12828 2019.
ISSN: ESSN 1091-6490
PubMed: 31182604
DOI: 10.1073/PNAS.1903562116
Page generated: Wed Dec 16 12:27:27 2020

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