Zinc in PDB 4kfu: Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp

The structure of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp, PDB code: 4kfu was solved by L.J.Happonen, E.Oksanen, T.Kajander, A.Goldman, S.Butcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.72 / 1.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.558, 65.227, 72.118, 90.85, 93.77, 91.56
R / Rfree (%)	18.8 / 23.4

The structure of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp (pdb code 4kfu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp, PDB code: 4kfu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:24.0 occ:0.76 NE2 A:HIS108 2.0 22.6 1.0 OD2 A:ASP73 2.0 32.2 1.0 NE2 A:HIS41 2.1 29.8 1.0 OD2 A:ASP39 2.3 26.6 1.0 OD1 A:ASP39 2.4 31.3 1.0 CG A:ASP39 2.7 25.7 1.0 CG A:ASP73 3.0 32.8 1.0 CD2 A:HIS108 3.0 23.2 1.0 CE1 A:HIS108 3.0 25.7 1.0 CD2 A:HIS41 3.0 31.7 1.0 CE1 A:HIS41 3.0 29.2 1.0 CB A:ASP73 3.3 30.4 1.0 OD1 A:ASP73 4.1 31.2 1.0 ND1 A:HIS108 4.1 26.0 1.0 ND1 A:HIS41 4.1 31.3 1.0 CG A:HIS108 4.1 23.8 1.0 CD2 A:PHE80 4.1 29.4 1.0 CG A:HIS41 4.1 35.0 1.0 CB A:ASP39 4.2 23.1 1.0 CE2 A:PHE80 4.2 31.2 1.0 CA A:ASP73 4.8 32.1 1.0 CA A:LYS76 4.9 32.0 1.0

Zinc binding site 2 out of 2 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn308 b:44.7 occ:0.42 NE2 B:HIS41 2.0 49.7 1.0 OD2 B:ASP73 2.1 51.2 1.0 OD2 B:ASP39 2.2 36.0 1.0 NE2 B:HIS108 2.3 44.7 1.0 CE1 B:HIS41 2.6 47.2 1.0 CG B:ASP39 3.0 33.6 1.0 OD1 B:ASP39 3.1 42.0 1.0 CG B:ASP73 3.2 53.9 1.0 CD2 B:HIS41 3.2 50.0 1.0 CD2 B:HIS108 3.3 40.8 1.0 CE1 B:HIS108 3.3 42.5 1.0 CB B:ASP73 3.7 46.3 1.0 ND1 B:HIS41 3.8 48.6 1.0 CG B:HIS41 4.1 49.5 1.0 OD1 B:ASP73 4.3 55.8 1.0 CB B:ASP39 4.4 23.9 1.0 ND1 B:HIS108 4.4 38.2 1.0 CG B:HIS108 4.4 40.5 1.0 CG2 B:ILE102 4.7 17.9 1.0 CD1 B:PHE80 5.0 40.7 1.0

L.J.Happonen, E.Oksanen, L.Liljeroos, A.Goldman, T.Kajander, S.J.Butcher. The Structure of the Ntpase That Powers Dna Packaging Into Sulfolobus Turreted Icosahedral Virus 2. J.Virol. V. 87 8388 2013.
ISSN: ISSN 0022-538X
PubMed: 23698307
DOI: 10.1128/JVI.00831-13