Zinc in PDB 4f5x: Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles

All present enzymatic activity of Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles:
2.7.7.48;

The structure of Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles, PDB code: 4f5x was solved by L.F.Estrozi, E.C.Settembre, G.Goret, B.Mcclain, X.Zhang, J.Z.Chen, N.Grigorieff, S.C.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 5.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	740.750, 1198.070, 1345.410, 90.00, 90.00, 90.00
R / Rfree (%)	29.3 / 29.6

The binding sites of Zinc atom in the Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles (pdb code 4f5x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles, PDB code: 4f5x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:51.3 occ:1.00 NE2 D:HIS153 2.6 0.1 1.0 NE2 E:HIS153 2.6 0.7 1.0 NE2 C:HIS153 2.7 97.2 1.0 CE1 E:HIS153 3.0 0.7 1.0 CE1 D:HIS153 3.3 0.1 1.0 CE1 C:HIS153 3.3 97.2 1.0 CD D:LYS154 3.7 82.2 1.0 CD2 D:HIS153 3.8 0.1 1.0 CD2 C:HIS153 3.9 97.2 1.0 CD2 E:HIS153 3.9 0.7 1.0 CD C:LYS154 4.1 91.1 1.0 ND1 E:HIS153 4.3 0.7 1.0 NZ C:LYS154 4.3 91.1 1.0 CD E:LYS154 4.3 84.3 1.0 ND1 D:HIS153 4.5 0.1 1.0 ND1 C:HIS153 4.6 97.2 1.0 CG D:LYS154 4.6 82.2 1.0 CE C:LYS154 4.7 91.1 1.0 CG E:HIS153 4.8 0.7 1.0 NZ E:LYS154 4.8 84.3 1.0 CG D:HIS153 4.8 0.1 1.0 NZ D:LYS154 4.8 82.2 1.0 CG C:HIS153 4.9 97.2 1.0 CE D:LYS154 4.9 82.2 1.0 CE E:LYS154 5.0 84.3 1.0

Zinc binding site 2 out of 5 in the Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:51.3 occ:1.00 NE2 G:HIS153 2.6 0.9 1.0 NE2 H:HIS153 2.6 0.7 1.0 NE2 F:HIS153 2.8 1.0 1.0 CE1 H:HIS153 3.2 0.7 1.0 CE1 F:HIS153 3.3 1.0 1.0 CE1 G:HIS153 3.3 0.9 1.0 CD2 G:HIS153 3.7 0.9 1.0 CD2 H:HIS153 3.8 0.7 1.0 CD H:LYS154 3.9 0.0 1.0 CD G:LYS154 4.0 94.6 1.0 CD F:LYS154 4.0 93.2 1.0 CD2 F:HIS153 4.1 1.0 1.0 ND1 H:HIS153 4.5 0.7 1.0 ND1 G:HIS153 4.5 0.9 1.0 ND1 F:HIS153 4.5 1.0 1.0 CG G:HIS153 4.7 0.9 1.0 NZ G:LYS154 4.7 94.6 1.0 NZ H:LYS154 4.7 0.0 1.0 CG H:HIS153 4.8 0.7 1.0 NZ F:LYS154 4.9 93.2 1.0 CG G:LYS154 4.9 94.6 1.0 CG H:LYS154 4.9 0.0 1.0 CG F:LYS154 4.9 93.2 1.0 CE G:LYS154 4.9 94.6 1.0 CG F:HIS153 4.9 1.0 1.0 CE H:LYS154 5.0 0.0 1.0

Zinc binding site 3 out of 5 in the Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn401 b:51.3 occ:1.00 NE2 K:HIS153 2.5 0.1 1.0 NE2 J:HIS153 2.5 0.6 1.0 NE2 I:HIS153 2.6 0.6 1.0 CE1 K:HIS153 3.1 0.1 1.0 CE1 J:HIS153 3.2 0.6 1.0 CE1 I:HIS153 3.2 0.6 1.0 CD2 K:HIS153 3.6 0.1 1.0 CD2 J:HIS153 3.7 0.6 1.0 CD2 I:HIS153 3.8 0.6 1.0 CD I:LYS154 3.9 79.1 1.0 CD J:LYS154 3.9 83.8 1.0 CD K:LYS154 3.9 89.3 1.0 NZ I:LYS154 4.3 79.1 1.0 ND1 K:HIS153 4.3 0.1 1.0 NZ K:LYS154 4.4 89.3 1.0 ND1 J:HIS153 4.4 0.6 1.0 ND1 I:HIS153 4.5 0.6 1.0 NZ J:LYS154 4.5 83.8 1.0 CG K:HIS153 4.6 0.1 1.0 CE I:LYS154 4.7 79.1 1.0 CG J:HIS153 4.7 0.6 1.0 CE K:LYS154 4.7 89.3 1.0 CG I:HIS153 4.8 0.6 1.0 CE J:LYS154 4.8 83.8 1.0 CG I:LYS154 4.9 79.1 1.0 CG J:LYS154 4.9 83.8 1.0 CG K:LYS154 4.9 89.3 1.0

Zinc binding site 4 out of 5 in the Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn401 b:51.3 occ:1.00 NE2 L:HIS153 2.6 0.8 1.0 NE2 M:HIS153 2.6 0.8 1.0 NE2 N:HIS153 2.6 0.8 1.0 CE1 N:HIS153 3.0 0.8 1.0 CE1 M:HIS153 3.1 0.8 1.0 CE1 L:HIS153 3.2 0.8 1.0 CD2 L:HIS153 3.8 0.8 1.0 CD N:LYS154 3.8 84.0 1.0 CD2 M:HIS153 3.9 0.8 1.0 CD L:LYS154 3.9 91.6 1.0 CD2 N:HIS153 3.9 0.8 1.0 CD M:LYS154 4.0 94.8 1.0 NZ M:LYS154 4.3 94.8 1.0 ND1 N:HIS153 4.3 0.8 1.0 ND1 M:HIS153 4.3 0.8 1.0 ND1 L:HIS153 4.5 0.8 1.0 CE M:LYS154 4.6 94.8 1.0 NZ L:LYS154 4.6 91.6 1.0 NZ N:LYS154 4.7 84.0 1.0 CG N:LYS154 4.7 84.0 1.0 CG N:HIS153 4.7 0.8 1.0 CG M:HIS153 4.8 0.8 1.0 CG L:HIS153 4.8 0.8 1.0 CG L:LYS154 4.8 91.6 1.0 CE N:LYS154 4.9 84.0 1.0 CE L:LYS154 4.9 91.6 1.0

Zinc binding site 5 out of 5 in the Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles within 5.0Å range: probe atom residue distance (Å) B Occ O:Zn401 b:51.3 occ:1.00 NE2 O:HIS153 4.7 0.2 1.0 CD2 O:HIS153 4.8 0.2 1.0

L.F.Estrozi, E.C.Settembre, G.Goret, B.Mcclain, X.Zhang, J.Z.Chen, N.Grigorieff, S.C.Harrison. Location of the Dsrna-Dependent Polymerase, VP1, in Rotavirus Particles. J.Mol.Biol. V. 425 124 2013.
ISSN: ISSN 0022-2836
PubMed: 23089332
DOI: 10.1016/J.JMB.2012.10.011