Zinc in PDB 3kz4: Crystal Structure of the Rotavirus Double Layered Particle

The structure of Crystal Structure of the Rotavirus Double Layered Particle, PDB code: 3kz4 was solved by B.Mcclain, E.C.Settembre, A.R.Bellamy, S.C.Harrison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.80
Space group	P 21 21 21 31
Cell size a, b, c (Å), α, β, γ (°)	740.750, 1198.070, 1345.410, 90.00, 90.00, 90.00
R / Rfree (%)	32.8 / 33.9

The binding sites of Zinc atom in the Crystal Structure of the Rotavirus Double Layered Particle (pdb code 3kz4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of the Rotavirus Double Layered Particle, PDB code: 3kz4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of the Rotavirus Double Layered Particle


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 the Rotavirus Double Layered Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn398 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 Crystal Structure of the Rotavirus Double Layered Particle


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 the Rotavirus Double Layered Particle within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn398 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 Crystal Structure of the Rotavirus Double Layered Particle


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 the Rotavirus Double Layered Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn398 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 Crystal Structure of the Rotavirus Double Layered Particle


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 the Rotavirus Double Layered Particle within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn398 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 Crystal Structure of the Rotavirus Double Layered Particle


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 the Rotavirus Double Layered Particle within 5.0Å range: probe atom residue distance (Å) B Occ O:Zn398 b:51.3 occ:1.00 NE2 O:HIS153 4.7 0.2 1.0 CD2 O:HIS153 4.8 0.2 1.0

B.Mcclain, E.Settembre, B.R.Temple, A.R.Bellamy, S.C.Harrison. X-Ray Crystal Structure of the Rotavirus Inner Capsid Particle at 3.8 A Resolution. J.Mol.Biol. V. 397 587 2010.
ISSN: ISSN 0022-2836
PubMed: 20122940
DOI: 10.1016/J.JMB.2010.01.055