Nickel in PDB 8qq3: Streptavidin with A Ni-Cofactor

The structure of Streptavidin with A Ni-Cofactor, PDB code: 8qq3 was solved by K.Zhang, R.P.Jakob, T.R.Ward, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.13 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	115.028, 88.712, 57.79, 90, 97.13, 90
R / Rfree (%)	16.2 / 19.1

The binding sites of Nickel atom in the Streptavidin with A Ni-Cofactor (pdb code 8qq3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Streptavidin with A Ni-Cofactor, PDB code: 8qq3:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Streptavidin with A Ni-Cofactor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Streptavidin with A Ni-Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:70.5 occ:0.31 N38 A:WKF201 1.9 68.6 0.8 N3 A:WKF201 1.9 65.0 0.8 N35 A:WKF201 1.9 68.2 0.8 N10 A:WKF201 1.9 82.7 0.8 C4 A:WKF201 2.6 51.0 0.8 C9 A:WKF201 2.6 84.4 0.8 C37 A:WKF201 2.7 67.8 0.8 C36 A:WKF201 2.7 68.1 0.8 C2 A:WKF201 2.9 67.6 0.8 C34 A:WKF201 3.0 74.7 0.8 OG A:SER112 3.0 32.5 1.0 C39 A:WKF201 3.0 60.8 0.8 C11 A:WKF201 3.0 52.1 0.8 C14 A:WKF201 3.2 60.3 0.8 C15 A:WKF201 3.2 40.9 0.8 CB A:SER112 3.7 27.2 1.0 C5 A:WKF201 3.9 40.8 0.8 C8 A:WKF201 4.0 85.2 0.8 O1 A:WKF201 4.0 75.1 0.8 O46 A:WKF201 4.1 97.1 0.8 C42 A:WKF201 4.1 71.3 0.8 C45 A:WKF201 4.1 76.9 0.8 C12 A:WKF201 4.2 57.9 0.8 C40 A:WKF201 4.3 60.9 0.8 C16 A:WKF201 4.3 34.7 0.8 C13 A:WKF201 4.6 80.0 0.8 C41 A:WKF201 4.7 65.7 0.8 C33 A:WKF201 4.7 47.8 0.8 C6 A:WKF201 4.9 41.7 0.8 C7 A:WKF201 4.9 66.5 0.8 OG A:SER88 5.0 24.9 0.4

Nickel binding site 2 out of 3 in the Streptavidin with A Ni-Cofactor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Streptavidin with A Ni-Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:33.4 occ:0.69 N38 B:WKF201 1.9 39.2 1.0 N3 B:WKF201 1.9 28.1 1.0 N10 B:WKF201 2.0 32.4 1.0 N35 B:WKF201 2.0 60.8 1.0 C4 B:WKF201 2.5 27.0 1.0 C9 B:WKF201 2.5 27.8 1.0 C37 B:WKF201 2.7 78.7 1.0 C36 B:WKF201 2.8 90.0 1.0 C2 B:WKF201 2.9 33.0 1.0 C39 B:WKF201 3.0 34.6 1.0 C34 B:WKF201 3.0 52.8 1.0 C11 B:WKF201 3.0 30.2 1.0 C14 B:WKF201 3.3 31.1 1.0 OG B:SER112 3.3 29.4 1.0 C15 B:WKF201 3.4 25.7 1.0 C5 B:WKF201 3.8 27.4 1.0 C8 B:WKF201 3.8 28.1 1.0 O1 B:WKF201 4.0 33.5 1.0 CB B:SER112 4.1 28.3 1.0 C42 B:WKF201 4.1 79.4 1.0 O46 B:WKF201 4.1 82.2 1.0 C45 B:WKF201 4.1 94.2 1.0 C12 B:WKF201 4.2 27.7 1.0 C40 B:WKF201 4.3 42.0 1.0 C13 B:WKF201 4.5 34.3 1.0 C16 B:WKF201 4.5 24.5 1.0 C41 B:WKF201 4.7 55.9 1.0 C6 B:WKF201 4.7 31.8 1.0 C7 B:WKF201 4.7 38.4 1.0 C33 B:WKF201 4.8 28.0 1.0

Nickel binding site 3 out of 3 in the Streptavidin with A Ni-Cofactor


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Streptavidin with A Ni-Cofactor within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni202 b:35.9 occ:0.42 N38 C:WKF201 1.9 57.1 1.0 N10 C:WKF201 1.9 57.1 1.0 N3 C:WKF201 2.0 38.4 1.0 N35 C:WKF201 2.0 47.8 1.0 C9 C:WKF201 2.5 65.5 1.0 C4 C:WKF201 2.5 42.3 1.0 C37 C:WKF201 2.7 55.0 1.0 C36 C:WKF201 2.7 62.2 1.0 C2 C:WKF201 2.9 49.5 1.0 C34 C:WKF201 3.0 49.1 1.0 C11 C:WKF201 3.0 43.1 1.0 C39 C:WKF201 3.0 61.7 1.0 OG C:SER112 3.1 31.2 1.0 C14 C:WKF201 3.3 46.0 1.0 C15 C:WKF201 3.4 35.0 1.0 C8 C:WKF201 3.7 68.1 1.0 C5 C:WKF201 3.8 37.7 1.0 CB C:SER112 3.9 29.2 1.0 O1 C:WKF201 4.0 60.7 1.0 C42 C:WKF201 4.1 57.9 1.0 C45 C:WKF201 4.1 66.0 1.0 C12 C:WKF201 4.1 37.1 1.0 O46 C:WKF201 4.1 69.1 1.0 C40 C:WKF201 4.3 58.0 1.0 C13 C:WKF201 4.4 60.1 1.0 O C:HOH318 4.5 57.5 1.0 C16 C:WKF201 4.5 31.3 1.0 C6 C:WKF201 4.7 39.4 1.0 C7 C:WKF201 4.7 51.8 1.0 C41 C:WKF201 4.7 63.3 1.0 O C:HOH380 4.7 58.2 1.0 C33 C:WKF201 4.8 41.7 1.0

K.Yu, K.Zhang, R.P.Jakob, T.Maier, T.R.Ward. An Artificial Nickel Chlorinase Based on the Biotin-Streptavidin Technology. Chem.Commun.(Camb.) 2024.
ISSN: ESSN 1364-548X
PubMed: 38277163
DOI: 10.1039/D3CC05847F