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Zinc in PDB 4kft: Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas

Protein crystallography data

The structure of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas, PDB code: 4kft 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) 46.61 / 2.24
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.726, 65.185, 71.620, 90.55, 93.65, 91.59
R / Rfree (%) 18.1 / 24.6

Other elements in 4kft:

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

Magnesium (Mg) 8 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas (pdb code 4kft). 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 Atp-Gammas, PDB code: 4kft:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4kft

Go back to Zinc Binding Sites List in 4kft
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 Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn308

b:49.8
occ:0.33
OD2 B:ASP73 2.0 56.1 1.0
OD2 B:ASP39 2.1 45.3 1.0
NE2 B:HIS41 2.1 60.5 1.0
NE2 B:HIS108 2.1 44.1 1.0
CD2 B:HIS41 2.9 59.3 1.0
CG B:ASP39 3.0 45.6 1.0
CE1 B:HIS41 3.0 58.6 1.0
CD2 B:HIS108 3.0 40.2 1.0
OD1 B:ASP39 3.2 56.2 1.0
CE1 B:HIS108 3.2 45.5 1.0
CG B:ASP73 3.2 53.7 1.0
CB B:ASP73 3.9 54.7 1.0
ND1 B:HIS41 4.0 57.2 1.0
CG B:HIS41 4.0 61.2 1.0
OD1 B:ASP73 4.2 57.4 1.0
CE2 B:PHE80 4.2 47.4 1.0
CG B:HIS108 4.2 40.5 1.0
ND1 B:HIS108 4.3 41.0 1.0
O B:HOH465 4.4 43.4 1.0
CB B:ASP39 4.4 34.7 1.0
CD2 B:PHE80 4.5 44.1 1.0
CG2 B:ILE102 4.7 23.2 1.0

Zinc binding site 2 out of 2 in 4kft

Go back to Zinc Binding Sites List in 4kft
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 Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn303

b:42.7
occ:1.00
OD1 C:ASP73 2.0 48.8 1.0
NE2 C:HIS41 2.1 36.3 1.0
NE2 C:HIS108 2.1 39.8 1.0
OD2 C:ASP39 2.1 41.8 1.0
OD1 C:ASP39 2.2 38.6 1.0
CG C:ASP39 2.5 33.3 1.0
CG C:ASP73 2.9 42.9 1.0
CD2 C:HIS41 3.0 42.1 1.0
CE1 C:HIS41 3.0 39.8 1.0
CD2 C:HIS108 3.1 36.4 1.0
CE1 C:HIS108 3.1 39.6 1.0
CB C:ASP73 3.3 42.8 1.0
OD2 C:ASP73 4.0 42.0 1.0
CE2 C:PHE80 4.0 42.9 1.0
CB C:ASP39 4.1 31.0 1.0
ND1 C:HIS41 4.1 44.1 1.0
CD2 C:PHE80 4.1 44.5 1.0
CG C:HIS41 4.1 45.7 1.0
ND1 C:HIS108 4.2 37.8 1.0
CG C:HIS108 4.2 35.1 1.0
CA C:ASP73 4.8 41.0 1.0
O C:ASP39 4.8 31.6 1.0
CA C:LYS76 4.8 48.0 1.0
C C:ASP39 4.9 35.2 1.0
CA C:ASP39 4.9 28.9 1.0

Reference:

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
Page generated: Sun Oct 27 01:10:19 2024

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