Nickel in PDB 1k2e: Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum

The structure of Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum, PDB code: 1k2e 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)	19.74 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.712, 72.612, 85.175, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22

The binding sites of Nickel atom in the Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum (pdb code 1k2e). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum, PDB code: 1k2e:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni211 b:59.8 occ:1.00 O A:HOH504 1.8 30.2 1.0 CE1 A:HIS91 3.5 22.1 1.0 OH A:TYR84 3.7 27.9 1.0 ND1 A:HIS89 3.8 29.8 1.0 NE2 A:HIS91 4.0 22.0 1.0 NE2 A:HIS31 4.2 36.6 1.0 NH1 A:ARG21 4.2 43.3 1.0 CD A:ARG21 4.3 38.5 1.0 CE1 A:HIS89 4.3 33.0 1.0 O3 A:GOL203 4.4 31.5 1.0 CE1 A:TYR84 4.6 23.7 1.0 CZ A:TYR84 4.6 26.0 1.0 CE1 A:HIS19 4.7 22.5 1.0 ND1 A:HIS91 4.7 21.0 1.0 NE2 A:HIS19 4.7 21.6 1.0 CE1 A:HIS31 4.8 37.6 1.0 CG A:HIS89 4.9 25.4 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of A Nudix Protein From Pyrobaculum Aerophilum within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni212 b:71.9 occ:1.00 O B:HOH505 2.4 42.5 1.0 O B:HOH506 2.5 36.2 1.0 NE2 B:HIS31 3.3 37.1 1.0 OH B:TYR84 3.5 19.4 1.0 CE1 B:HIS31 3.9 38.2 1.0 CE1 B:HIS91 3.9 21.8 1.0 NE2 B:HIS91 4.3 22.5 1.0 CD2 B:HIS31 4.4 35.6 1.0 NE2 B:HIS19 4.5 23.7 1.0 CZ B:TYR84 4.5 18.1 1.0 CE1 B:TYR84 4.6 19.3 1.0 C1 B:GOL205 4.6 38.9 1.0 CE1 B:HIS19 4.9 21.7 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