Nickel in PDB 6k4j: Crystal Structure of the the CD9

The structure of Crystal Structure of the the CD9, PDB code: 6k4j was solved by R.Umeda, T.Nishizawa, K.Sato, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.50 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	45.180, 125.210, 129.400, 90.00, 90.00, 90.00
R / Rfree (%)	26.2 / 28.9

The binding sites of Nickel atom in the Crystal Structure of the the CD9 (pdb code 6k4j). 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 the the CD9, PDB code: 6k4j:

Nickel binding site 1 out of 1 in the Crystal Structure of the the CD9


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 the the CD9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:62.0 occ:1.00 OE1 A:GLU187 1.9 66.0 1.0 OE1 A:GLU174 2.0 80.9 1.0 OE2 A:GLU187 2.2 65.7 1.0 CD A:GLU187 2.3 62.5 1.0 OE2 A:GLU174 2.4 69.7 1.0 CD A:GLU174 2.5 74.3 1.0 CG A:GLU187 3.7 55.5 1.0 CG A:GLU174 4.0 65.3 1.0 CB A:GLU187 4.4 60.8 1.0 O A:HOH407 4.7 59.3 1.0 CB A:GLU174 4.8 61.1 1.0 CA A:ALA184 4.8 54.0 1.0

R.Umeda, Y.Satouh, M.Takemoto, Y.Nakada-Nakura, K.Liu, T.Yokoyama, M.Shirouzu, S.Iwata, N.Nomura, K.Sato, M.Ikawa, T.Nishizawa, O.Nureki. Structural Insights Into Tetraspanin CD9 Function. Nat Commun V. 11 1606 2020.
ISSN: ESSN 2041-1723
PubMed: 32231207
DOI: 10.1038/S41467-020-15459-7