Nickel in PDB 4i7h: Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes

The structure of Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes, PDB code: 4i7h was solved by M.Kumaraswami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.23 / 2.00
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	118.910, 118.910, 118.611, 90.00, 90.00, 120.00
R / Rfree (%)	22.9 / 26.5

The structure of Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes (pdb code 4i7h). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes, PDB code: 4i7h:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:36.0 occ:1.00 OD1 A:ASN15 2.4 33.4 1.0 CE1 A:HIS99 2.4 26.3 1.0 NE2 A:HIS19 2.4 34.8 1.0 NE2 A:HIS97 2.4 31.7 1.0 NE2 A:HIS6 2.4 38.5 1.0 NE2 A:HIS4 2.5 37.7 1.0 CD2 A:HIS6 3.1 35.8 1.0 CD2 A:HIS19 3.1 35.0 1.0 CD2 A:HIS97 3.2 34.5 1.0 ND1 A:HIS99 3.2 32.2 1.0 CG A:ASN15 3.3 37.6 1.0 CE1 A:HIS4 3.4 38.6 1.0 CD2 A:HIS4 3.4 37.3 1.0 NE2 A:HIS99 3.4 34.2 1.0 CE1 A:HIS97 3.5 39.9 1.0 CE1 A:HIS19 3.5 39.3 1.0 CE1 A:HIS6 3.6 43.2 1.0 ND2 A:ASN15 3.7 30.4 1.0 CG A:HIS6 4.4 40.5 1.0 CG A:HIS19 4.4 38.3 1.0 CG A:HIS97 4.4 37.8 1.0 CG A:HIS99 4.4 30.8 1.0 ND1 A:HIS4 4.5 38.0 1.0 CG A:HIS4 4.5 40.0 1.0 ND1 A:HIS97 4.5 36.4 1.0 ND1 A:HIS19 4.5 40.2 1.0 CD2 A:HIS99 4.5 29.7 1.0 ND1 A:HIS6 4.6 38.3 1.0 CB A:ASN15 4.6 36.4 1.0

Nickel binding site 2 out of 2 in the Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structural Basis For Peroxide Sensing and Gene Regulation By Perr From Streptococcus Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni202 b:35.5 occ:1.00 NE2 B:HIS99 2.4 31.6 1.0 OD1 B:ASN15 2.4 31.8 1.0 NE2 B:HIS4 2.4 36.5 1.0 NE2 B:HIS97 2.4 36.1 1.0 NE2 B:HIS19 2.5 36.5 1.0 NE2 B:HIS6 2.6 46.6 1.0 CD2 B:HIS99 3.1 28.5 1.0 CD2 B:HIS4 3.1 40.6 1.0 CD2 B:HIS19 3.1 36.9 1.0 CD2 B:HIS6 3.2 36.7 1.0 CD2 B:HIS97 3.2 33.0 1.0 CG B:ASN15 3.3 34.9 1.0 CE1 B:HIS99 3.5 36.8 1.0 CE1 B:HIS97 3.5 35.1 1.0 ND2 B:ASN15 3.6 30.1 1.0 CE1 B:HIS4 3.6 40.1 1.0 CE1 B:HIS19 3.6 45.8 1.0 CE1 B:HIS6 3.8 48.4 1.0 CG B:HIS99 4.3 31.4 1.0 CG B:HIS4 4.4 41.8 1.0 CG B:HIS19 4.4 40.8 1.0 CG B:HIS97 4.5 36.7 1.0 CG B:HIS6 4.5 39.5 1.0 ND1 B:HIS99 4.5 34.2 1.0 ND1 B:HIS4 4.6 42.6 1.0 ND1 B:HIS97 4.6 39.0 1.0 ND1 B:HIS19 4.6 43.5 1.0 CB B:ASN15 4.7 31.6 1.0 ND1 B:HIS6 4.7 47.8 1.0

N.Makthal, S.Rastegari, M.Sanson, Z.Ma, R.J.Olsen, J.D.Helmann, J.M.Musser, M.Kumaraswami. Crystal Structure of Peroxide Stress Regulator From Streptococcus Pyogenes Provides Functional Insights Into the Mechanism of Oxidative Stress Sensing. J.Biol.Chem. V. 288 18311 2013.
ISSN: ISSN 0021-9258
PubMed: 23645680
DOI: 10.1074/JBC.M113.456590