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Zinc in PDB 3gzu: VP7 Recoated Rotavirus Dlp

Zinc Binding Sites:

The binding sites of Zinc atom in the VP7 Recoated Rotavirus Dlp (pdb code 3gzu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the VP7 Recoated Rotavirus Dlp, PDB code: 3gzu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 3gzu

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Zinc binding site 1 out of 5 in the VP7 Recoated Rotavirus Dlp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of VP7 Recoated Rotavirus Dlp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn398

b:42.6
occ:1.00
NE2 C:HIS153 2.5 88.6 1.0
NE2 D:HIS153 2.6 0.5 1.0
NE2 E:HIS153 2.8 92.1 1.0
CE1 C:HIS153 2.9 88.6 1.0
CE1 D:HIS153 3.2 0.5 1.0
CE1 E:HIS153 3.4 92.1 1.0
CD D:LYS154 3.5 73.5 1.0
CD2 D:HIS153 3.7 0.5 1.0
CD2 C:HIS153 3.8 88.6 1.0
CD C:LYS154 3.9 82.4 1.0
CD2 E:HIS153 4.1 92.1 1.0
ND1 C:HIS153 4.2 88.6 1.0
CD E:LYS154 4.3 75.6 1.0
NZ D:LYS154 4.4 73.5 1.0
NZ C:LYS154 4.4 82.4 1.0
ND1 D:HIS153 4.4 0.5 1.0
CG D:LYS154 4.5 73.5 1.0
CE D:LYS154 4.6 73.5 1.0
ND1 E:HIS153 4.6 92.1 1.0
CG C:HIS153 4.7 88.6 1.0
CG D:HIS153 4.7 0.5 1.0
CE C:LYS154 4.7 82.4 1.0
CG C:LYS154 4.9 82.4 1.0

Zinc binding site 2 out of 5 in 3gzu

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Zinc binding site 2 out of 5 in the VP7 Recoated Rotavirus Dlp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of VP7 Recoated Rotavirus Dlp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn398

b:42.6
occ:1.00
CE G:LYS154 0.9 73.5 1.0
CD G:LYS154 1.2 73.5 1.0
NZ G:LYS154 1.6 73.5 1.0
CG G:LYS154 2.5 73.5 1.0
CB G:LYS154 3.5 73.5 1.0
OG G:SER186 4.4 0.3 1.0
OE1 F:GLU327 4.9 0.8 1.0
CA G:LYS154 4.9 0.8 1.0

Zinc binding site 3 out of 5 in 3gzu

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Zinc binding site 3 out of 5 in the VP7 Recoated Rotavirus Dlp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of VP7 Recoated Rotavirus Dlp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn398

b:42.6
occ:1.00
CE1 J:HIS153 2.9 0.5 1.0
CD J:LYS154 2.9 73.5 1.0
NE2 J:HIS153 3.2 0.5 1.0
CD K:LYS154 3.4 75.6 1.0
NZ K:LYS154 3.5 75.6 1.0
CG J:LYS154 3.5 73.5 1.0
OE1 J:GLU327 3.7 0.9 1.0
NE2 K:HIS153 3.7 92.1 1.0
CE K:LYS154 4.0 75.6 1.0
ND1 J:HIS153 4.0 0.5 1.0
CE J:LYS154 4.2 73.5 1.0
NZ J:LYS154 4.4 73.5 1.0
CE1 K:HIS153 4.4 92.1 1.0
CD2 J:HIS153 4.4 0.5 1.0
CB K:ALA338 4.5 0.4 1.0
NE2 I:HIS153 4.5 88.6 1.0
CG K:LYS154 4.6 75.6 1.0
CD2 K:HIS153 4.6 92.1 1.0
CB J:LYS154 4.6 73.5 1.0
CG J:HIS153 4.9 0.5 1.0
CD J:GLU327 4.9 0.9 1.0
CE1 I:HIS153 4.9 88.6 1.0

Zinc binding site 4 out of 5 in 3gzu

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Zinc binding site 4 out of 5 in the VP7 Recoated Rotavirus Dlp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of VP7 Recoated Rotavirus Dlp within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn398

b:42.6
occ:1.00
NE2 N:HIS153 2.6 92.1 1.0
NE2 M:HIS153 2.6 0.5 1.0
CE1 M:HIS153 2.9 0.5 1.0
NE2 L:HIS153 3.1 88.6 1.0
CE1 N:HIS153 3.1 92.1 1.0
CD N:LYS154 3.5 75.6 1.0
CD M:LYS154 3.7 73.5 1.0
CD2 N:HIS153 3.7 92.1 1.0
CE1 L:HIS153 3.7 88.6 1.0
CD2 M:HIS153 3.9 0.5 1.0
ND1 M:HIS153 4.2 0.5 1.0
CD2 L:HIS153 4.3 88.6 1.0
ND1 N:HIS153 4.3 92.1 1.0
NZ N:LYS154 4.4 75.6 1.0
CG N:LYS154 4.4 75.6 1.0
CG M:LYS154 4.5 73.5 1.0
CE N:LYS154 4.5 75.6 1.0
CD L:LYS154 4.5 82.4 1.0
NZ L:LYS154 4.6 82.4 1.0
CG N:HIS153 4.7 92.1 1.0
CG M:HIS153 4.7 0.5 1.0
NZ M:LYS154 4.8 73.5 1.0
CE M:LYS154 4.9 73.5 1.0
CB N:LYS154 4.9 75.6 1.0
CB N:ALA338 5.0 0.4 1.0
ND1 L:HIS153 5.0 88.6 1.0

Zinc binding site 5 out of 5 in 3gzu

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Zinc binding site 5 out of 5 in the VP7 Recoated Rotavirus Dlp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of VP7 Recoated Rotavirus Dlp within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn398

b:42.6
occ:0.33
NE2 O:HIS153 3.0 0.6 1.0
CE1 O:HIS153 3.2 0.6 1.0
CD2 O:HIS153 3.5 0.6 1.0
ND1 O:HIS153 3.7 0.6 1.0
CG O:HIS153 3.9 0.6 1.0

Reference:

J.Z.Chen, E.C.Settembre, S.T.Aoki, X.Zhang, A.R.Bellamy, P.R.Dormitzer, S.C.Harrison, N.Grigorieff. Molecular Interactions in Rotavirus Assembly and Uncoating Seen By High-Resolution Cryo-Em. Proc.Natl.Acad.Sci.Usa V. 106 10644 2009.
ISSN: ISSN 0027-8424
PubMed: 19487668
DOI: 10.1073/PNAS.0904024106
Page generated: Wed Dec 16 04:22:19 2020

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