Nickel in PDB 1k26: Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method

The structure of Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method, PDB code: 1k26 was solved by S.Wang, C.Mura, M.R.Sawaya, D.Cascio, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.85 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.424, 71.655, 85.762, 90.00, 90.00, 90.00
R / Rfree (%)	18.3 / 21.9

The structure of Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method also contains other interesting chemical elements:

Iridium

(Ir)

4 atoms

The binding sites of Nickel atom in the Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method (pdb code 1k26). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method, PDB code: 1k26:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni207 b:71.8 occ:1.00 NH1 A:ARG21 3.5 63.7 1.0 CE1 A:HIS91 3.6 29.5 1.0 ND1 A:HIS89 3.6 54.2 1.0 OH A:TYR84 3.7 40.3 1.0 IR A:IR3206 3.8 43.9 0.2 CZ A:ARG21 3.9 63.7 1.0 NE2 A:HIS91 4.0 30.1 1.0 O A:HOH256 4.0 49.2 1.0 CE1 A:HIS89 4.1 57.2 1.0 NE2 A:HIS31 4.2 50.5 1.0 O3 A:GOL209 4.2 40.4 1.0 NE A:ARG21 4.4 57.3 1.0 CD A:ARG21 4.5 51.3 1.0 NH2 A:ARG21 4.6 62.9 1.0 CZ A:TYR84 4.6 37.2 1.0 CE1 A:TYR84 4.6 33.2 1.0 CE1 A:HIS19 4.7 26.3 1.0 O A:HOH264 4.7 37.0 1.0 ND1 A:HIS91 4.7 25.5 1.0 NE2 A:HIS19 4.8 33.4 1.0 CE1 A:HIS31 4.8 51.3 1.0 CG A:HIS89 4.8 44.8 1.0

Nickel binding site 2 out of 2 in the Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of A Nudix Protein From Pyrobaculum Aerophilum Solved By the Single Wavelength Anomolous Scattering Method within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni208 b:79.7 occ:1.00 O B:HOH267 2.3 50.3 1.0 O B:HOH268 2.3 47.4 1.0 NE2 B:HIS31 3.1 54.6 1.0 CE1 B:HIS31 3.5 54.7 1.0 OH B:TYR84 3.7 33.1 1.0 NE2 B:HIS91 3.9 19.7 1.0 CE1 B:HIS91 3.9 20.8 1.0 CD2 B:HIS31 4.4 52.0 1.0 CE1 B:TYR84 4.4 30.5 1.0 ND1 B:HIS89 4.4 43.1 1.0 CZ B:TYR84 4.5 30.2 1.0 SD B:MET1 4.8 59.2 1.0 ND1 B:HIS31 4.8 53.4 1.0 CE B:MET1 4.9 48.4 1.0 CE1 B:HIS89 4.9 44.3 1.0

S.Wang, C.Mura, M.R.Sawaya, D.Cascio, D.Eisenberg. Structure of A Nudix Protein From Pyrobaculum Aerophilum Reveals A Dimer with Two Intersubunit Beta-Sheets. Acta Crystallogr.,Sect.D V. 58 571 2002.
ISSN: ISSN 0907-4449
PubMed: 11914479
DOI: 10.1107/S0907444902001191