Iridium 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:

Nickel

(Ni)

2 atoms

The binding sites of Iridium 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 Iridium atom.
In total 4 binding sites of Iridium 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 Iridium binding site number: 1; 2; 3; 4;

Iridium binding site 1 out of 4 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 Iridium with other atoms in the Ir 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:Ir203 b:26.6 occ:0.23 O A:HOH308 2.3 45.8 1.0 O A:HOH267 2.3 31.8 1.0 O A:HOH301 2.4 40.9 1.0 O A:HOH257 2.5 22.3 1.0 O A:HOH270 2.6 32.4 1.0 NZ A:LYS18 4.1 27.7 1.0

Iridium binding site 2 out of 4 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 Iridium with other atoms in the Ir 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 A:Ir205 b:32.8 occ:0.16 O A:HOH229 2.3 22.8 1.0 OE1 A:GLU66 3.6 49.7 1.0 ND2 A:ASN67 4.0 13.8 1.0 O4 B:SO4202 4.3 36.6 1.0 OD2 A:ASP65 4.3 45.0 1.0 NZ B:LYS127 4.4 50.8 1.0 CD A:GLU66 4.6 45.1 1.0 CG A:ASP65 4.6 33.1 1.0 OE2 A:GLU66 4.9 50.2 1.0 CB A:ASP65 4.9 23.5 1.0

Iridium binding site 3 out of 4 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 Iridium with other atoms in the Ir binding site number 3 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:Ir206 b:43.9 occ:0.20 O A:HOH256 2.3 49.2 1.0 O A:HOH288 2.6 41.0 1.0 NE2 A:HIS31 3.4 50.5 1.0 NZ A:LYS20 3.4 55.6 1.0 CE A:LYS20 3.5 52.8 1.0 O3 A:GOL211 3.6 37.9 1.0 CD2 A:HIS31 3.8 51.2 1.0 NI A:NI207 3.8 71.8 1.0 CE1 A:HIS31 4.0 51.3 1.0 O3 A:GOL209 4.5 40.4 1.0 CG A:HIS31 4.6 43.0 1.0 ND1 A:HIS31 4.7 52.1 1.0 CA A:GLY30 4.8 21.2 1.0 O2 A:GOL211 4.9 33.3 1.0 C3 A:GOL211 4.9 35.0 1.0

Iridium binding site 4 out of 4 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 Iridium with other atoms in the Ir binding site number 4 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:Ir204 b:37.8 occ:0.21 O A:HOH287 2.4 47.6 1.0 OD2 B:ASP65 3.2 53.9 1.0 O1 A:SO4201 3.8 30.2 1.0 OE1 B:GLU66 3.9 66.3 1.0 CG B:ASP65 4.2 42.6 1.0 ND2 B:ASN67 4.3 25.6 1.0 CB B:ASP65 4.4 36.8 1.0 O B:HOH263 4.6 42.9 1.0 O A:HOH275 4.6 29.2 1.0 O A:HOH285 4.6 40.7 1.0 NZ A:LYS127 4.7 37.9 1.0 CD B:GLU66 5.0 59.1 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