Zinc in PDB 5e6t: Crystal Structure of Bovine Norovirus P Domain

The structure of Crystal Structure of Bovine Norovirus P Domain, PDB code: 5e6t was solved by B.K.Singh, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.81 / 2.27
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.920, 63.860, 87.560, 90.00, 115.06, 90.00
R / Rfree (%)	19.5 / 24.1

The binding sites of Zinc atom in the Crystal Structure of Bovine Norovirus P Domain (pdb code 5e6t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Bovine Norovirus P Domain, PDB code: 5e6t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:56.4 occ:1.00 OE1 A:GLU336 2.0 37.1 1.0 CD A:GLU336 3.2 35.3 1.0 O B:HOH803 3.3 40.6 1.0 OE2 A:GLU336 3.8 37.6 1.0 CG A:GLU336 4.4 31.1 1.0 O A:HOH710 4.5 21.7 1.0 CB A:GLU336 4.6 27.6 1.0 N A:GLU336 4.7 25.5 1.0 OE1 B:GLU336 4.7 43.1 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:68.3 occ:1.00 OE2 A:GLU241 2.0 31.0 1.0 NE2 B:HIS368 2.0 34.1 1.0 CD2 B:HIS368 2.7 32.3 1.0 CD A:GLU241 3.0 27.9 1.0 CE1 B:HIS368 3.2 34.3 1.0 OE1 A:GLU241 3.3 28.7 1.0 NE B:ARG366 3.8 31.4 1.0 CG B:HIS368 3.9 29.9 1.0 CG A:PRO416 4.0 18.9 1.0 O A:HOH800 4.0 38.1 1.0 CD B:ARG366 4.0 29.9 1.0 CD A:PRO416 4.1 18.1 1.0 ND1 B:HIS368 4.1 32.6 1.0 CG A:GLU241 4.3 23.3 1.0 CG B:ARG366 4.4 26.8 1.0 CB B:ARG366 5.0 24.6 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:67.0 occ:1.00 NE2 A:HIS378 2.0 32.5 1.0 CD2 A:HIS378 3.0 30.1 1.0 CE1 A:HIS378 3.0 32.4 1.0 OE2 A:GLU377 3.6 43.1 1.0 ND1 A:HIS378 4.1 31.2 1.0 CG A:HIS378 4.2 29.3 1.0 CD A:GLU377 4.5 40.3 1.0 CG A:GLU377 4.6 34.5 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn604 b:60.8 occ:1.00 ND1 A:HIS437 2.3 22.1 1.0 ND1 B:HIS437 2.7 33.8 1.0 CE1 A:HIS437 2.8 23.7 1.0 CE1 B:HIS437 3.3 36.0 1.0 CG A:HIS437 3.6 20.0 1.0 CG B:HIS437 3.9 31.4 1.0 NE2 A:HIS437 4.1 20.8 1.0 CB A:HIS437 4.2 16.9 1.0 CB B:HIS437 4.4 27.1 1.0 CD2 A:HIS437 4.5 17.6 1.0 CA A:HIS437 4.6 16.5 1.0 NE2 B:HIS437 4.6 35.5 1.0 CA B:HIS437 4.7 25.1 1.0 CD2 B:HIS437 4.9 32.1 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:92.1 occ:1.00 NE2 A:HIS306 2.1 57.5 1.0 CB A:ASP304 2.5 46.4 1.0 CE1 A:HIS306 3.0 59.3 1.0 CD2 A:HIS306 3.1 53.8 1.0 CA A:ASP304 3.7 44.9 1.0 N A:ASP304 4.0 46.9 1.0 O A:ASP304 4.0 41.6 1.0 C A:ASP304 4.1 41.8 1.0 ND1 A:HIS306 4.2 57.7 1.0 CG A:HIS306 4.2 53.6 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:43.1 occ:1.00 O B:VAL507 2.3 42.3 1.0 C B:VAL507 2.7 41.0 1.0 O B:HOH771 4.1 24.8 1.0 CA B:VAL507 4.2 39.3 1.0 CG2 B:VAL507 4.5 38.8 1.0 CB B:VAL507 4.8 39.3 1.0 CG1 B:VAL507 4.8 40.2 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:25.0 occ:1.00 OE1 B:GLU296 2.0 22.5 1.0 ND1 B:HIS353 2.0 23.1 1.0 O B:HOH712 2.7 18.5 1.0 CD B:GLU296 2.8 24.1 1.0 CE1 B:HIS353 2.9 23.8 1.0 OE2 B:GLU296 3.0 24.9 1.0 CG B:HIS353 3.1 23.0 1.0 CB B:HIS353 3.5 20.3 1.0 O B:LEU351 3.9 22.7 1.0 O B:GLY352 4.1 16.9 1.0 NE2 B:HIS353 4.1 23.8 1.0 CD2 B:HIS353 4.2 23.3 1.0 C B:GLY352 4.2 18.5 1.0 CG B:GLU296 4.2 24.0 1.0 N B:HIS353 4.4 18.4 1.0 O B:HOH793 4.5 34.0 1.0 CA B:HIS353 4.6 18.4 1.0 CA B:GLY352 4.9 18.7 1.0 C B:LEU351 4.9 21.4 1.0 CB B:GLU296 4.9 22.8 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Bovine Norovirus P Domain


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 Bovine Norovirus P Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:27.3 occ:1.00 OD2 B:ASP304 2.0 28.7 1.0 OD1 B:ASP304 2.0 27.6 1.0 NE2 B:HIS306 2.0 29.4 1.0 CG B:ASP304 2.3 27.4 1.0 CE1 B:HIS306 3.0 31.0 1.0 CD2 B:HIS306 3.1 28.0 1.0 CB B:ASP304 3.8 24.3 1.0 ND1 B:HIS306 4.1 30.8 1.0 CG B:HIS306 4.2 27.8 1.0 O B:ASP304 4.3 21.9 1.0 CA B:ASP304 4.6 21.7 1.0 C B:ASP304 4.7 21.4 1.0 N B:ASP304 4.8 21.6 1.0

B.K.Singh, A.Koromyslova, G.S.Hansman. Structural Analysis of Bovine Norovirus Protruding Domain. Virology V. 487 296 2015.
ISSN: ISSN 0042-6822
PubMed: 26599362
DOI: 10.1016/J.VIROL.2015.10.022