Nickel in PDB 5w1f: Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin

The structure of Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin, PDB code: 5w1f was solved by T.G.Nakashige, C.L.Drennan, E.M.Nolan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.24 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.020, 77.611, 222.722, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.2

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

Calcium	(Ca)	10 atoms
Sodium	(Na)	6 atoms

The binding sites of Nickel atom in the Crystal Structure of Ni(II)- and Ca(II)-Bound Human Calprotectin (pdb code 5w1f). 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)- and Ca(II)-Bound Human Calprotectin, PDB code: 5w1f:
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)- and Ca(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)- and Ca(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:37.0 occ:1.00 NE2 B:HIS105 2.2 38.6 1.0 NE2 A:HIS27 2.2 39.4 1.0 NE2 A:HIS17 2.2 30.2 1.0 NE2 B:HIS103 2.3 54.9 1.0 NE2 B:HIS95 2.3 45.8 1.0 NE2 B:HIS91 2.4 43.1 1.0 CE1 B:HIS95 3.0 46.3 1.0 CD2 B:HIS105 3.1 39.2 1.0 CE1 A:HIS27 3.1 38.6 1.0 CE1 A:HIS17 3.1 34.5 1.0 CD2 A:HIS27 3.2 38.7 1.0 CE1 B:HIS105 3.2 38.7 1.0 CD2 A:HIS17 3.2 35.3 1.0 CD2 B:HIS103 3.2 55.0 1.0 CD2 B:HIS91 3.2 43.4 1.0 CE1 B:HIS103 3.2 55.8 1.0 CD2 B:HIS95 3.4 45.5 1.0 CE1 B:HIS91 3.5 42.2 1.0 ND1 A:HIS17 4.2 35.0 1.0 ND1 A:HIS27 4.2 37.9 1.0 ND1 B:HIS95 4.3 46.5 1.0 CG A:HIS17 4.3 35.4 1.0 ND1 B:HIS105 4.3 39.8 1.0 CG B:HIS105 4.3 40.6 1.0 CG A:HIS27 4.3 38.0 1.0 ND1 B:HIS103 4.4 56.2 1.0 CG B:HIS103 4.4 55.8 1.0 CG B:HIS95 4.5 46.1 1.0 CG B:HIS91 4.5 43.1 1.0 ND1 B:HIS91 4.6 42.4 1.0

Nickel binding site 2 out of 6 in the Crystal Structure of Ni(II)- and Ca(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)- and Ca(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni101 b:32.0 occ:0.75 OD1 D:ASP30 1.9 34.4 1.0 NE2 C:HIS83 2.1 32.8 1.0 NE2 C:HIS87 2.1 34.0 1.0 NE2 D:HIS20 2.1 31.6 1.0 CG D:ASP30 2.8 34.9 1.0 CE1 C:HIS83 2.9 32.7 1.0 CE1 C:HIS87 3.0 34.4 1.0 OD2 D:ASP30 3.0 34.4 1.0 CD2 C:HIS83 3.0 32.3 1.0 CD2 D:HIS20 3.1 31.3 1.0 CE1 D:HIS20 3.1 30.9 1.0 CD2 C:HIS87 3.2 33.7 1.0 ND1 C:HIS83 4.0 32.2 1.0 CG C:HIS83 4.1 32.1 1.0 ND1 C:HIS87 4.1 34.6 1.0 CB D:ASP30 4.2 34.8 1.0 ND1 D:HIS20 4.2 30.8 1.0 CG D:HIS20 4.2 31.4 1.0 CG C:HIS87 4.3 34.7 1.0 CE2 D:PHE19 4.4 40.3 1.0 CA D:ASP30 4.6 35.0 1.0 O D:ASP30 4.6 34.6 1.0 O D:HOH318 4.7 35.6 1.0 CD2 D:PHE19 4.7 39.6 1.0

Nickel binding site 3 out of 6 in the Crystal Structure of Ni(II)- and Ca(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)- and Ca(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni201 b:30.2 occ:1.00 NE2 C:HIS17 2.1 30.4 1.0 NE2 C:HIS27 2.2 29.6 1.0 NE2 D:HIS95 2.2 41.1 1.0 NE2 D:HIS103 2.3 38.6 1.0 NE2 D:HIS105 2.3 28.6 1.0 NE2 D:HIS91 2.3 29.4 1.0 CE1 D:HIS95 3.0 41.5 1.0 CE1 C:HIS17 3.0 30.4 1.0 CD2 C:HIS27 3.1 28.8 1.0 CD2 C:HIS17 3.1 30.6 1.0 CE1 C:HIS27 3.2 30.0 1.0 CD2 D:HIS105 3.2 29.2 1.0 CD2 D:HIS103 3.2 38.3 1.0 CD2 D:HIS91 3.2 29.1 1.0 CE1 D:HIS103 3.3 38.4 1.0 CD2 D:HIS95 3.3 41.4 1.0 CE1 D:HIS91 3.3 29.2 1.0 CE1 D:HIS105 3.3 28.2 1.0 ND1 C:HIS17 4.1 30.5 1.0 CG C:HIS17 4.2 31.1 1.0 ND1 D:HIS95 4.2 42.1 1.0 CG C:HIS27 4.2 28.3 1.0 ND1 C:HIS27 4.2 29.7 1.0 CG D:HIS95 4.4 42.5 1.0 ND1 D:HIS103 4.4 38.6 1.0 CG D:HIS105 4.4 28.8 1.0 CG D:HIS103 4.4 38.2 1.0 ND1 D:HIS105 4.4 28.5 1.0 CG D:HIS91 4.4 29.6 1.0 ND1 D:HIS91 4.4 29.3 1.0

Nickel binding site 4 out of 6 in the Crystal Structure of Ni(II)- and Ca(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)- and Ca(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni201 b:32.4 occ:1.00 NE2 H:HIS95 2.1 36.1 1.0 NE2 G:HIS27 2.1 35.6 1.0 NE2 H:HIS91 2.2 32.2 1.0 NE2 H:HIS103 2.3 43.4 1.0 NE2 G:HIS17 2.3 28.4 1.0 NE2 H:HIS105 2.5 46.9 1.0 CE1 G:HIS27 3.0 36.5 1.0 CE1 H:HIS95 3.1 36.1 1.0 CD2 H:HIS95 3.1 35.9 1.0 CE1 H:HIS91 3.1 31.3 1.0 CD2 G:HIS27 3.1 35.6 1.0 CD2 H:HIS91 3.2 32.6 1.0 CD2 H:HIS103 3.2 42.8 1.0 CD2 G:HIS17 3.2 28.4 1.0 CE1 H:HIS103 3.2 43.8 1.0 CD2 H:HIS105 3.3 47.1 1.0 CE1 G:HIS17 3.3 28.7 1.0 CE1 H:HIS105 3.5 47.2 1.0 ND1 G:HIS27 4.1 36.2 1.0 ND1 H:HIS95 4.2 36.2 1.0 CG G:HIS27 4.2 34.9 1.0 CG H:HIS95 4.2 36.4 1.0 ND1 H:HIS91 4.3 31.6 1.0 CG H:HIS91 4.3 32.8 1.0 ND1 H:HIS103 4.4 43.9 1.0 CG H:HIS103 4.4 43.7 1.0 CG G:HIS17 4.4 29.3 1.0 ND1 G:HIS17 4.4 28.6 1.0 CG H:HIS105 4.5 48.1 1.0 ND1 H:HIS105 4.5 48.0 1.0

Nickel binding site 5 out of 6 in the Crystal Structure of Ni(II)- and Ca(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)- and Ca(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni101 b:30.4 occ:0.75 OD1 F:ASP30 1.9 30.1 1.0 NE2 E:HIS83 2.0 30.2 1.0 NE2 F:HIS20 2.0 27.1 1.0 NE2 E:HIS87 2.1 33.4 1.0 CG F:ASP30 2.8 30.6 1.0 CD2 E:HIS83 2.9 31.0 1.0 CE1 E:HIS87 2.9 34.7 1.0 CE1 E:HIS83 2.9 30.2 1.0 OD2 F:ASP30 3.0 30.6 1.0 CE1 F:HIS20 3.0 26.9 1.0 CD2 F:HIS20 3.0 26.9 1.0 CD2 E:HIS87 3.2 34.5 1.0 ND1 E:HIS83 4.0 30.6 1.0 CG E:HIS83 4.0 30.9 1.0 ND1 E:HIS87 4.1 34.9 1.0 ND1 F:HIS20 4.1 27.6 1.0 CG F:HIS20 4.2 27.4 1.0 CB F:ASP30 4.2 29.4 1.0 CG E:HIS87 4.3 34.4 1.0 CE2 F:PHE19 4.3 31.2 1.0 CD2 F:PHE19 4.6 30.6 1.0 O F:ASP30 4.7 27.4 1.0 CA F:ASP30 4.7 28.8 1.0

Nickel binding site 6 out of 6 in the Crystal Structure of Ni(II)- and Ca(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)- and Ca(II)-Bound Human Calprotectin within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni201 b:39.6 occ:1.00 NE2 F:HIS103 2.2 43.9 1.0 NE2 F:HIS95 2.2 46.8 1.0 NE2 E:HIS17 2.2 35.2 1.0 NE2 F:HIS91 2.3 35.8 1.0 NE2 E:HIS27 2.3 44.2 1.0 NE2 F:HIS105 2.4 47.2 1.0 CD2 F:HIS103 3.1 45.1 1.0 CE1 F:HIS95 3.1 47.8 1.0 CE1 F:HIS103 3.1 44.8 1.0 CE1 E:HIS17 3.1 34.4 1.0 CE1 F:HIS91 3.2 35.9 1.0 CD2 E:HIS27 3.2 43.8 1.0 CD2 E:HIS17 3.2 35.6 1.0 CD2 F:HIS95 3.2 46.5 1.0 CE1 F:HIS105 3.3 47.0 1.0 CD2 F:HIS91 3.3 35.4 1.0 CE1 E:HIS27 3.3 44.6 1.0 CD2 F:HIS105 3.3 47.8 1.0 ND1 E:HIS17 4.2 34.5 1.0 ND1 F:HIS103 4.3 45.5 1.0 ND1 F:HIS95 4.3 48.0 1.0 CG F:HIS103 4.3 45.9 1.0 CG E:HIS17 4.3 35.0 1.0 ND1 F:HIS91 4.3 34.9 1.0 CG E:HIS27 4.4 43.7 1.0 CG F:HIS95 4.4 47.4 1.0 ND1 E:HIS27 4.4 44.2 1.0 ND1 F:HIS105 4.4 47.5 1.0 CG F:HIS91 4.4 34.9 1.0 CG F:HIS105 4.4 47.5 1.0

T.G.Nakashige, E.M.Zygiel, C.L.Drennan, E.M.Nolan. Nickel Sequestration By the Host-Defense Protein Human Calprotectin. J. Am. Chem. Soc. V. 139 8828 2017.
ISSN: ESSN 1520-5126
PubMed: 28573847
DOI: 10.1021/JACS.7B01212