Nickel in PDB 3rdq: Crystal Structure of R7-2 Streptavidin Complexed with Desthiobiotin

The structure of Crystal Structure of R7-2 Streptavidin Complexed with Desthiobiotin, PDB code: 3rdq was solved by V.N.Malashkevich, M.Magalhaes, C.M.Czecster, R.Guan, M.Levy, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 1.60
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	57.275, 57.275, 183.742, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 19

The structure of Crystal Structure of R7-2 Streptavidin Complexed with Desthiobiotin also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Nickel atom in the Crystal Structure of R7-2 Streptavidin Complexed with Desthiobiotin (pdb code 3rdq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of R7-2 Streptavidin Complexed with Desthiobiotin, PDB code: 3rdq:

Nickel binding site 1 out of 1 in the Crystal Structure of R7-2 Streptavidin Complexed with Desthiobiotin


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 R7-2 Streptavidin Complexed with Desthiobiotin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:25.6 occ:1.00 OI2 A:DTB300 1.9 20.2 1.0 O A:HOH163 2.1 35.3 1.0 O A:HOH259 2.4 28.9 1.0 C A:DTB300 2.7 19.2 1.0 OI1 A:DTB300 2.8 18.9 1.0 N A:ASN49 3.8 20.5 1.0 CB A:ASN49 3.9 24.1 1.0 CA A:DTB300 4.1 19.0 1.0 CA A:GLY48 4.5 18.6 1.0 CA A:ASN49 4.5 22.2 1.0 C A:GLY48 4.6 20.1 1.0 CB A:DTB300 4.8 18.4 1.0

M.L.Magalhaes, C.M.Czekster, R.Guan, V.N.Malashkevich, S.C.Almo, M.Levy. Evolved Streptavidin Mutants Reveal Key Role of Loop Residue in High-Affinity Binding. Protein Sci. V. 20 1145 2011.
ISSN: ISSN 0961-8368
PubMed: 21520321
DOI: 10.1002/PRO.642