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Nickel in PDB 3zf5: Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp).

Enzymatic activity of Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp).

All present enzymatic activity of Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp).:
3.6.1.23;

Protein crystallography data

The structure of Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp)., PDB code: 3zf5 was solved by M.A.Tormo-Mas, J.Donderis, M.Garcia-Caballer, A.Alt, I.Mir-Sanchis, A.Marina, J.R.Penades, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.71 / 3.20
Space group P 21 3
Cell size a, b, c (Å), α, β, γ (°) 88.240, 88.240, 88.240, 90.00, 90.00, 90.00
R / Rfree (%) 22.189 / 27.663

Other elements in 3zf5:

The structure of Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp). also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp). (pdb code 3zf5). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp)., PDB code: 3zf5:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3zf5

Go back to Nickel Binding Sites List in 3zf5
Nickel binding site 1 out of 2 in the Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp).


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1171

b:27.7
occ:1.00
NE2 A:HIS96 3.4 31.6 1.0
NH2 A:ARG107 3.4 37.6 1.0
NE2 A:HIS72 3.6 23.4 1.0
CD2 A:HIS96 3.9 31.6 1.0
NH1 A:ARG107 4.3 37.6 1.0
CZ A:ARG107 4.4 37.7 1.0
CE1 A:HIS72 4.4 23.4 1.0
CD2 A:HIS72 4.5 23.4 1.0
CE1 A:HIS96 4.6 31.6 1.0

Nickel binding site 2 out of 2 in 3zf5

Go back to Nickel Binding Sites List in 3zf5
Nickel binding site 2 out of 2 in the Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp).


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Phage Dutpases Control Transfer of Virulence Genes By A Proto- Oncogenic G Protein-Like Mechanism. (Staphylococcus Bacteriophage 80ALPHA Dutpase Y84F Mutant with Dupnhpp). within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1172

b:64.0
occ:0.33
O A:HOH2018 2.0 36.4 1.0
OD1 A:ASP95 2.9 30.6 1.0
OD2 A:ASP95 3.2 30.8 1.0
CG A:ASP95 3.3 30.7 1.0
O A:ASP95 4.2 30.9 1.0
NZ A:LYS93 4.3 26.8 1.0
O A:HOH2019 4.3 19.4 0.3
NE2 A:GLN40 4.7 25.4 1.0
CB A:ASP95 4.8 30.6 1.0
OE1 A:GLN40 4.9 25.4 1.0

Reference:

M.A.Tormo-Mas, J.Donderis, M.Garcia-Caballer, A.Alt, I.Mir-Sanchis, A.Marina, J.R.Penades. Phage Dutpases Control Transfer of Virulence Genes By A Proto-Oncogenic G Protein-Like Mechanism. Mol.Cell V. 49 947 2013.
ISSN: ISSN 1097-2765
PubMed: 23333307
DOI: 10.1016/J.MOLCEL.2012.12.013
Page generated: Wed Dec 16 01:28:44 2020

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