Zinc in PDB 3sjp: Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)

The structure of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05), PDB code: 3sjp was solved by S.Shanker, J.-M.Choi, B.Sankaran, R.L.Atmar, M.K.Estes, B.V.V.Prasad, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.11 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.001, 72.966, 55.610, 90.00, 97.78, 90.00
R / Rfree (%)	19.8 / 24.2

The binding sites of Zinc atom in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) (pdb code 3sjp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05), PDB code: 3sjp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:28.8 occ:1.00 ND1 A:HIS460 2.3 23.3 1.0 O A:HOH549 2.3 32.8 1.0 O A:HOH161 2.4 29.2 1.0 O A:HOH162 2.5 22.0 1.0 O A:HOH167 2.6 27.8 1.0 CE1 A:HIS460 3.3 21.6 1.0 CG A:HIS460 3.3 20.7 1.0 CB A:HIS460 3.5 23.9 1.0 CA A:HIS460 3.8 24.2 1.0 O A:HOH550 4.3 39.1 1.0 NE2 A:HIS460 4.4 20.2 1.0 CD2 A:HIS460 4.4 18.8 1.0 OE2 A:GLU464 4.5 41.6 1.0 N A:HIS460 4.7 22.2 1.0 CG A:PRO230 5.0 21.4 1.0 C A:HIS460 5.0 22.6 1.0

Zinc binding site 2 out of 7 in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:55.8 occ:1.00 O A:HOH193 2.4 39.1 1.0 O A:HOH20 3.5 32.6 1.0 O A:HOH90 3.8 28.1 1.0 N A:GLN306 3.9 27.5 1.0 O A:HOH100 4.0 36.3 1.0 CA A:SER305 4.2 27.4 1.0 N A:LEU321 4.3 23.0 1.0 CB A:SER305 4.3 31.0 1.0 CG A:LEU321 4.4 22.3 1.0 CB A:GLN306 4.4 33.3 1.0 CA A:PRO320 4.4 34.4 1.0 C A:SER305 4.6 30.0 1.0 CD1 A:ILE317 4.6 42.3 1.0 CA A:GLN306 4.7 27.6 1.0 CD1 A:LEU321 4.8 22.7 1.0 CB A:LEU321 4.9 23.3 1.0 CB A:PRO320 4.9 20.0 1.0 C A:PRO320 4.9 29.2 1.0 CD1 A:TYR311 4.9 32.7 1.0

Zinc binding site 3 out of 7 in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:37.6 occ:1.00 ND1 A:HIS492 2.9 25.4 1.0 O A:HOH163 3.0 38.7 1.0 O A:HOH177 3.0 38.1 1.0 O A:HOH79 3.0 31.2 1.0 O A:ASP471 3.2 25.8 1.0 CB A:HIS492 3.6 21.2 1.0 CG A:HIS492 3.7 27.1 1.0 CG2 A:VAL472 3.7 29.9 1.0 CB A:ASP471 3.7 34.3 1.0 C A:ASP471 3.9 26.1 1.0 CE1 A:HIS492 3.9 28.9 1.0 OE1 A:GLN523 4.1 56.0 1.0 CA A:HIS492 4.2 24.7 1.0 CA A:ASP471 4.4 27.4 1.0 CG A:ASP471 4.6 47.6 1.0 N A:LYS493 4.6 22.1 1.0 OD2 A:ASP471 4.7 60.9 1.0 NE2 A:GLN523 4.7 53.4 1.0 N A:VAL472 4.8 21.8 1.0 CD A:GLN523 4.8 53.8 1.0 C A:HIS492 4.9 26.1 1.0 CD2 A:HIS492 4.9 26.3 1.0 OH A:TYR496 5.0 25.0 1.0 CB A:VAL472 5.0 26.2 1.0 NE2 A:HIS492 5.0 26.2 1.0

Zinc binding site 4 out of 7 in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn4 b:74.9 occ:1.00 O A:HOH538 2.3 64.0 1.0 O A:HOH169 2.3 43.3 1.0 OE2 A:GLU464 2.5 41.6 1.0 OE1 A:GLU464 2.5 41.3 1.0 O A:HOH159 2.9 51.2 1.0 CD A:GLU464 2.9 38.2 1.0 O A:HOH93 3.8 48.5 1.0 O A:HOH167 4.2 27.8 1.0 NZ A:LYS225 4.3 22.5 1.0 CG A:GLU464 4.4 29.0 1.0 O A:HOH83 4.4 31.4 0.5 CE A:LYS225 4.8 19.5 1.0 CD A:LYS225 5.0 27.2 1.0

Zinc binding site 5 out of 7 in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn5 b:42.6 occ:1.00 OD1 A:ASP370 2.3 48.1 1.0 ND1 A:HIS347 2.3 41.7 1.0 O A:HOH216 2.3 42.4 1.0 OD2 A:ASP370 2.4 52.4 1.0 O A:HOH160 2.6 38.8 1.0 CG A:ASP370 2.6 51.3 1.0 CE1 A:HIS347 3.2 41.0 1.0 CG A:HIS347 3.2 39.1 1.0 CB A:HIS347 3.5 33.2 1.0 CA A:HIS347 4.1 31.3 1.0 CB A:ASP370 4.1 48.4 1.0 NE2 A:HIS347 4.2 37.8 1.0 CD2 A:HIS347 4.3 38.2 1.0 O A:ASP370 4.4 38.2 1.0 C A:ASP370 4.6 41.5 1.0 N A:LYS348 4.6 30.8 1.0 O A:GLY346 4.8 25.5 1.0 CA A:ASP370 4.8 42.1 1.0 C A:HIS347 4.9 31.0 1.0

Zinc binding site 6 out of 7 in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn6 b:59.4 occ:1.00 O A:HOH157 2.2 45.0 1.0 ND1 A:HIS292 2.4 48.6 1.0 O A:HOH200 2.4 64.2 1.0 O A:HOH117 2.7 58.7 1.0 CG A:HIS292 3.2 41.0 1.0 CB A:HIS292 3.4 34.6 1.0 CE1 A:HIS292 3.4 49.6 1.0 O A:HOH203 3.4 49.5 1.0 O A:SER372 4.1 48.2 1.0 CD2 A:HIS292 4.4 42.6 1.0 NE2 A:HIS292 4.5 49.9 1.0 CA A:HIS292 4.8 34.9 1.0

Zinc binding site 7 out of 7 in the Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Characterization of A Gii.4 2004 Norovirus Variant (TCH05) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn7 b:37.6 occ:1.00 OD2 A:ASP341 2.3 20.0 1.0 OE1 A:GLU376 2.4 45.5 1.0 O A:ARG339 2.5 31.0 1.0 OE2 A:GLU376 2.5 34.5 1.0 CD A:GLU376 2.7 44.8 1.0 CG A:ASP341 2.9 20.0 1.0 OD1 A:ASP341 3.1 20.0 1.0 C A:ARG339 3.6 36.4 1.0 CB A:ARG339 4.0 34.0 1.0 CB A:ASP341 4.1 20.0 1.0 CG A:GLU376 4.2 44.7 1.0 NH2 A:ARG345 4.3 32.1 1.0 C A:ARG340 4.3 42.1 1.0 O A:ARG340 4.3 36.0 1.0 CA A:ARG339 4.5 30.8 1.0 N A:ASP341 4.6 42.5 1.0 N A:ARG340 4.6 32.9 1.0 NE2 A:GLN336 4.6 38.3 1.0 CZ A:ARG345 4.7 39.5 1.0 CB A:GLU376 4.8 37.9 1.0 NE A:ARG345 4.8 34.6 1.0 CA A:ARG340 4.8 36.7 1.0 CA A:ASP341 4.9 52.2 1.0

S.Shanker, J.M.Choi, B.Sankaran, R.L.Atmar, M.K.Estes, B.V.Prasad. Structural Analysis of Histo-Blood Group Antigen Binding Specificity in A Norovirus Gii.4 Epidemic Variant: Implications For Epochal Evolution. J.Virol. V. 85 8635 2011.
ISSN: ISSN 0022-538X
PubMed: 21715503
DOI: 10.1128/JVI.00848-11