Nickel in PDB 6ds2: Crystal Structure of Ni(II)-Bound Human Calprotectin

The structure of Crystal Structure of Ni(II)-Bound Human Calprotectin, PDB code: 6ds2 was solved by E.M.Nolan, C.L.Drennan, T.G.Nakashige, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.48 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.145, 78.082, 223.787, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.2

The structure of Crystal Structure of Ni(II)-Bound Human Calprotectin also contains other interesting chemical elements:

Sodium

(Na)

10 atoms

The binding sites of Nickel atom in the Crystal Structure of Ni(II)-Bound Human Calprotectin (pdb code 6ds2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the Crystal Structure of Ni(II)-Bound Human Calprotectin, PDB code: 6ds2:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in the Crystal Structure of Ni(II)-Bound Human Calprotectin


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 Ni(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:30.0 occ:1.00 NE2 A:HIS27 2.1 28.6 1.0 NE2 B:HIS95 2.2 35.3 1.0 NE2 B:HIS105 2.2 29.4 1.0 NE2 A:HIS17 2.2 26.8 1.0 NE2 B:HIS103 2.3 38.0 1.0 NE2 B:HIS91 2.3 26.2 1.0 CE1 A:HIS27 3.1 30.2 1.0 CD2 B:HIS105 3.1 30.5 1.0 CE1 A:HIS17 3.1 25.0 1.0 CD2 B:HIS103 3.1 36.2 1.0 CE1 B:HIS95 3.1 35.6 1.0 CD2 A:HIS27 3.1 26.2 1.0 CD2 A:HIS17 3.2 24.5 1.0 CD2 B:HIS95 3.2 36.0 1.0 CD2 B:HIS91 3.2 26.0 1.0 CE1 B:HIS105 3.2 29.6 1.0 CE1 B:HIS91 3.3 27.1 1.0 CE1 B:HIS103 3.3 37.9 1.0 ND1 A:HIS27 4.2 30.4 1.0 ND1 A:HIS17 4.2 24.4 1.0 CG A:HIS27 4.3 28.2 1.0 CG B:HIS105 4.3 30.4 1.0 ND1 B:HIS95 4.3 37.8 1.0 ND1 B:HIS105 4.3 28.9 1.0 CG A:HIS17 4.3 24.8 1.0 CG B:HIS95 4.3 37.6 1.0 CG B:HIS103 4.3 38.1 1.0 CG B:HIS91 4.4 25.7 1.0 ND1 B:HIS91 4.4 25.1 1.0 ND1 B:HIS103 4.4 37.6 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of Ni(II)-Bound Human Calprotectin


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 Ni(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni101 b:27.6 occ:0.80 NE2 C:HIS87 1.9 28.8 1.0 OD1 D:ASP30 2.0 29.1 1.0 NE2 C:HIS83 2.1 26.6 1.0 NE2 D:HIS20 2.2 24.6 1.0 OD2 D:ASP30 2.3 32.3 1.0 CG D:ASP30 2.4 33.7 1.0 O D:HOH338 2.5 36.3 1.0 CE1 C:HIS87 2.8 32.7 1.0 CD2 C:HIS87 3.0 29.7 1.0 CE1 C:HIS83 3.1 26.1 1.0 CD2 D:HIS20 3.1 21.9 1.0 CD2 C:HIS83 3.1 27.4 1.0 CE1 D:HIS20 3.2 29.0 1.0 CB D:ASP30 3.9 34.3 1.0 ND1 C:HIS87 3.9 30.6 1.0 CG C:HIS87 4.1 31.1 1.0 ND1 C:HIS83 4.2 27.8 1.0 CG C:HIS83 4.2 28.0 1.0 CG D:HIS20 4.3 22.8 1.0 ND1 D:HIS20 4.3 22.9 1.0 O D:HOH373 4.5 54.5 1.0 CA D:ASP30 4.5 34.3 1.0 O D:HOH317 4.7 35.7 1.0 CE2 D:PHE19 4.9 26.1 1.0 OG C:SER86 4.9 28.2 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of Ni(II)-Bound Human Calprotectin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni201 b:37.9 occ:1.00 NE2 C:HIS27 2.1 37.7 1.0 NE2 D:HIS103 2.1 44.6 1.0 NE2 D:HIS95 2.2 41.5 1.0 NE2 D:HIS91 2.3 31.5 1.0 NE2 D:HIS105 2.3 40.4 1.0 NE2 C:HIS17 2.3 36.0 1.0 CD2 D:HIS103 3.0 43.5 1.0 CE1 C:HIS27 3.1 37.0 1.0 CE1 D:HIS95 3.1 41.8 1.0 CD2 C:HIS27 3.1 36.2 1.0 CD2 D:HIS105 3.2 39.6 1.0 CE1 C:HIS17 3.2 33.9 1.0 CE1 D:HIS103 3.2 44.4 1.0 CE1 D:HIS91 3.2 33.9 1.0 CD2 D:HIS91 3.2 31.5 1.0 CD2 D:HIS95 3.2 39.3 1.0 CD2 C:HIS17 3.2 35.4 1.0 CE1 D:HIS105 3.3 39.4 1.0 ND1 C:HIS27 4.2 37.1 1.0 CG D:HIS103 4.2 46.8 1.0 CG C:HIS27 4.3 36.6 1.0 ND1 D:HIS95 4.3 42.1 1.0 ND1 D:HIS103 4.3 45.2 1.0 ND1 C:HIS17 4.3 33.4 1.0 ND1 D:HIS91 4.3 30.3 1.0 CG D:HIS105 4.3 41.7 1.0 ND1 D:HIS105 4.3 40.3 1.0 CG D:HIS95 4.3 41.9 1.0 CG C:HIS17 4.4 35.8 1.0 CG D:HIS91 4.4 30.5 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of Ni(II)-Bound Human Calprotectin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:36.5 occ:0.80 OD1 F:ASP30 1.9 40.5 1.0 NE2 E:HIS87 2.0 39.8 1.0 NE2 F:HIS20 2.2 36.3 1.0 NE2 E:HIS83 2.2 32.2 1.0 O F:HOH307 2.4 48.8 1.0 CG F:ASP30 2.6 47.5 1.0 OD2 F:ASP30 2.9 54.9 1.0 CE1 E:HIS87 2.9 38.8 1.0 CD2 F:HIS20 3.0 31.2 1.0 CE1 E:HIS83 3.0 31.4 1.0 CD2 E:HIS87 3.1 39.0 1.0 CD2 E:HIS83 3.2 31.7 1.0 CE1 F:HIS20 3.2 29.8 1.0 CB F:ASP30 3.9 48.6 1.0 ND1 E:HIS87 4.1 39.9 1.0 CG E:HIS87 4.2 39.0 1.0 ND1 E:HIS83 4.2 29.0 1.0 CG F:HIS20 4.2 30.7 1.0 ND1 F:HIS20 4.3 29.9 1.0 CG E:HIS83 4.3 31.0 1.0 CA F:ASP30 4.4 48.0 1.0 O F:HOH321 4.5 38.6 1.0 CE2 F:PHE19 4.8 36.1 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of Ni(II)-Bound Human Calprotectin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni201 b:21.5 occ:1.00 NE2 F:HIS95 2.1 22.0 1.0 NE2 E:HIS27 2.2 20.6 1.0 NE2 E:HIS17 2.2 19.9 1.0 NE2 F:HIS105 2.2 24.6 1.0 NE2 F:HIS103 2.2 20.8 1.0 NE2 F:HIS91 2.3 22.4 1.0 CE1 F:HIS95 3.0 25.0 1.0 CE1 E:HIS17 3.1 19.9 1.0 CD2 F:HIS105 3.1 22.2 1.0 CE1 E:HIS27 3.1 20.9 1.0 CD2 E:HIS27 3.1 19.8 1.0 CE1 F:HIS103 3.2 21.6 1.0 CD2 F:HIS103 3.2 20.8 1.0 CD2 E:HIS17 3.2 19.6 1.0 CD2 F:HIS95 3.2 24.6 1.0 CE1 F:HIS105 3.2 25.1 1.0 CD2 F:HIS91 3.2 21.6 1.0 CE1 F:HIS91 3.2 21.2 1.0 ND1 F:HIS95 4.2 23.0 1.0 ND1 E:HIS17 4.2 19.5 1.0 ND1 E:HIS27 4.2 20.5 1.0 CG F:HIS105 4.3 22.4 1.0 CG E:HIS17 4.3 19.3 1.0 ND1 F:HIS105 4.3 21.8 1.0 ND1 F:HIS103 4.3 20.9 1.0 CG E:HIS27 4.3 19.9 1.0 CG F:HIS95 4.3 23.3 1.0 CG F:HIS103 4.3 26.2 1.0 ND1 F:HIS91 4.3 21.6 1.0 CG F:HIS91 4.4 24.4 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of Ni(II)-Bound Human Calprotectin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Ni(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni201 b:41.9 occ:1.00 NE2 H:HIS105 2.1 40.7 1.0 NE2 G:HIS27 2.2 41.9 1.0 NE2 H:HIS95 2.2 47.8 1.0 NE2 H:HIS103 2.2 50.2 1.0 NE2 H:HIS91 2.2 39.9 1.0 NE2 G:HIS17 2.3 51.2 1.0 CD2 H:HIS105 3.1 41.7 1.0 CE1 H:HIS105 3.1 45.5 1.0 CD2 G:HIS27 3.1 40.7 1.0 CE1 H:HIS95 3.2 49.3 1.0 CD2 H:HIS103 3.2 49.7 1.0 CD2 G:HIS17 3.2 51.5 1.0 CE1 H:HIS91 3.2 38.6 1.0 CE1 G:HIS17 3.2 49.5 1.0 CE1 G:HIS27 3.2 39.5 1.0 CD2 H:HIS91 3.2 39.2 1.0 CE1 H:HIS103 3.2 50.9 1.0 CD2 H:HIS95 3.2 46.9 1.0 ND1 H:HIS105 4.2 42.4 1.0 CG H:HIS105 4.2 48.6 1.0 ND1 G:HIS17 4.3 48.5 1.0 CG G:HIS27 4.3 41.8 1.0 ND1 G:HIS27 4.3 41.4 1.0 CG G:HIS17 4.3 51.0 1.0 ND1 H:HIS95 4.3 48.7 1.0 ND1 H:HIS91 4.3 37.5 1.0 ND1 H:HIS103 4.3 51.4 1.0 CG H:HIS103 4.3 53.8 1.0 CG H:HIS95 4.4 47.6 1.0 CG H:HIS91 4.4 38.2 1.0

T.G.Nakashige, S.E.J.Bowman, E.M.Zygiel, C.L.Drennan, E.M.Nolan. Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the Ef-Hand Domains and HIS3ASP Site. Biochemistry V. 57 4155 2018.
ISSN: ISSN 1520-4995
PubMed: 29890074
DOI: 10.1021/ACS.BIOCHEM.8B00415