Nickel in PDB 2y3y: Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH

The structure of Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH, PDB code: 2y3y was solved by S.Benini, M.Cianci, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.98 / 2.39
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	72.970, 72.970, 116.730, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 27.9

The binding sites of Nickel atom in the Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH (pdb code 2y3y). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH, PDB code: 2y3y:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1143 b:41.0 occ:1.00 ND1 A:HIS101 2.0 28.3 1.0 NE2 B:HIS88 2.0 43.4 1.0 NE2 A:HIS99 2.1 33.4 1.0 SG A:CYS107 2.2 34.6 1.0 CE1 A:HIS101 2.8 28.3 1.0 CE1 B:HIS88 2.9 41.2 1.0 CD2 A:HIS99 3.0 24.2 1.0 CD2 B:HIS88 3.0 40.6 1.0 CG A:HIS101 3.1 34.9 1.0 CE1 A:HIS99 3.1 31.4 1.0 CB A:CYS107 3.4 33.8 1.0 CA A:HIS101 3.4 35.1 1.0 CB A:HIS101 3.6 35.7 1.0 CG2 B:ILE84 3.7 35.2 1.0 CA A:CYS107 3.9 34.8 1.0 N A:HIS101 3.9 33.8 1.0 ND1 B:HIS88 4.0 44.5 1.0 NE2 A:HIS101 4.0 29.8 1.0 CG B:HIS88 4.1 44.6 1.0 O A:ILE100 4.1 33.4 1.0 CD2 A:HIS101 4.2 29.8 1.0 CG A:HIS99 4.2 27.6 1.0 ND1 A:HIS99 4.2 32.0 1.0 C A:ILE100 4.2 31.2 1.0 O A:ASN106 4.6 37.4 1.0 C A:HIS101 4.6 36.4 1.0 N A:CYS107 4.7 37.1 1.0 O A:HOH2003 5.0 44.7 1.0 CB B:ILE84 5.0 38.0 1.0 N A:MET102 5.0 36.5 1.0

Nickel binding site 2 out of 4 in the Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni1143 b:29.7 occ:1.00 NE2 A:HIS88 1.9 19.5 1.0 NE2 B:HIS99 2.0 26.2 1.0 ND1 B:HIS101 2.0 20.9 1.0 SG B:CYS107 2.2 31.4 1.0 CD2 A:HIS88 2.9 18.6 1.0 CE1 B:HIS101 2.9 19.9 1.0 CD2 B:HIS99 2.9 24.5 1.0 CE1 A:HIS88 3.0 27.3 1.0 CE1 B:HIS99 3.0 29.2 1.0 CG B:HIS101 3.1 19.3 1.0 CB B:CYS107 3.4 25.4 1.0 CA B:HIS101 3.4 25.1 1.0 CB B:HIS101 3.5 22.6 1.0 CG2 A:ILE84 3.9 27.0 1.0 CA B:CYS107 4.0 26.4 1.0 O B:ILE100 4.0 25.4 1.0 CG A:HIS88 4.0 22.5 1.0 N B:HIS101 4.0 24.4 1.0 ND1 A:HIS88 4.0 23.9 1.0 NE2 B:HIS101 4.1 20.2 1.0 ND1 B:HIS99 4.1 28.9 1.0 CG B:HIS99 4.1 25.8 1.0 CD2 B:HIS101 4.1 22.7 1.0 C B:ILE100 4.3 24.6 1.0 O B:ASN106 4.7 30.2 1.0 C B:HIS101 4.7 25.7 1.0 CD1 A:ILE84 4.8 41.2 1.0 N B:CYS107 4.8 28.4 1.0

Nickel binding site 3 out of 4 in the Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni1142 b:39.8 occ:1.00 ND1 C:HIS101 1.9 22.6 1.0 NE2 D:HIS88 2.0 47.5 1.0 NE2 C:HIS99 2.1 34.7 1.0 SG C:CYS107 2.1 30.1 1.0 CE1 C:HIS101 2.7 22.9 1.0 CD2 D:HIS88 3.0 41.6 1.0 CE1 C:HIS99 3.0 29.8 1.0 CG C:HIS101 3.0 31.3 1.0 CE1 D:HIS88 3.1 45.4 1.0 CD2 C:HIS99 3.1 29.5 1.0 CB C:CYS107 3.2 34.9 1.0 CA C:HIS101 3.4 33.3 1.0 CB C:HIS101 3.5 32.1 1.0 CG2 D:ILE84 3.6 37.9 1.0 CA C:CYS107 3.9 35.3 1.0 NE2 C:HIS101 3.9 27.8 1.0 N C:HIS101 4.0 32.3 1.0 CD2 C:HIS101 4.1 23.9 1.0 ND1 C:HIS99 4.1 32.3 1.0 CG D:HIS88 4.1 46.0 1.0 ND1 D:HIS88 4.2 46.4 1.0 CG C:HIS99 4.2 30.3 1.0 O C:ILE100 4.2 32.9 1.0 C C:ILE100 4.4 30.9 1.0 N C:CYS107 4.6 37.0 1.0 O C:ASN106 4.7 38.9 1.0 C C:HIS101 4.8 35.1 1.0 O C:HOH2003 4.8 37.7 1.0 CB D:ILE84 4.9 39.3 1.0 ND1 C:HIS74 4.9 41.1 1.0

Nickel binding site 4 out of 4 in the Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Holo-Ni(II) Hpnikr Is A Symmetric Tetramer Containing Four Canonic Square-Planar Ni(II) Ions at Physiological pH within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni1143 b:31.2 occ:1.00 NE2 C:HIS88 1.9 23.4 1.0 NE2 D:HIS99 1.9 30.4 1.0 ND1 D:HIS101 2.0 24.4 1.0 SG D:CYS107 2.2 30.0 1.0 CE1 C:HIS88 2.9 26.8 1.0 CE1 D:HIS99 2.9 28.4 1.0 CD2 C:HIS88 2.9 21.9 1.0 CE1 D:HIS101 2.9 19.6 1.0 CD2 D:HIS99 3.0 24.3 1.0 CG D:HIS101 3.1 20.1 1.0 CB D:CYS107 3.3 25.8 1.0 CA D:HIS101 3.4 23.7 1.0 CB D:HIS101 3.5 18.9 1.0 CG2 C:ILE84 3.7 28.9 1.0 O D:ILE100 3.9 26.1 1.0 CA D:CYS107 4.0 26.9 1.0 ND1 C:HIS88 4.0 27.0 1.0 N D:HIS101 4.0 22.9 1.0 ND1 D:HIS99 4.0 28.1 1.0 CG C:HIS88 4.0 26.8 1.0 NE2 D:HIS101 4.1 23.0 1.0 CG D:HIS99 4.1 24.9 1.0 CD2 D:HIS101 4.2 18.6 1.0 C D:ILE100 4.2 23.5 1.0 C D:HIS101 4.7 25.2 1.0 O D:ASN106 4.7 28.8 1.0 CD1 C:ILE84 4.8 41.4 1.0 N D:CYS107 4.8 27.9 1.0 N D:MET102 5.0 27.5 1.0

S.Benini, M.Cianci, S.Ciurli. Holo-Ni(2+)Helicobacter Pylori Nikr Contains Four Square-Planar Nickel-Binding Sites at Physiological pH. Dalton Trans V. 40 7831 2011.
ISSN: ISSN 1477-9226
PubMed: 21725560
DOI: 10.1039/C1DT11107H