Zinc in PDB 5nl9: Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans

The structure of Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans, PDB code: 5nl9 was solved by F.A.Saul, A.Haouz, M.Picardeau, N.Benaroudj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.84 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.683, 56.100, 68.794, 90.00, 105.82, 90.00
R / Rfree (%)	20.3 / 23.4

The structure of Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans (pdb code 5nl9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans, PDB code: 5nl9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:33.1 occ:1.00 NE2 A:HIS36 2.0 25.6 1.0 OD2 A:ASP84 2.0 21.1 1.0 NE2 A:HIS92 2.1 27.0 1.0 NE2 A:HIS90 2.1 29.2 1.0 OD1 A:ASP103 2.2 28.2 1.0 CG A:ASP84 2.9 28.6 1.0 CD2 A:HIS36 3.0 26.5 1.0 CD2 A:HIS92 3.0 27.0 1.0 CD2 A:HIS90 3.0 30.0 1.0 OD1 A:ASP84 3.0 29.4 1.0 CG A:ASP103 3.1 33.6 1.0 CE1 A:HIS36 3.1 25.4 1.0 CE1 A:HIS92 3.1 26.9 1.0 CE1 A:HIS90 3.1 29.6 1.0 OD2 A:ASP103 3.4 34.1 1.0 O A:HOH319 3.7 33.0 1.0 O A:HOH304 4.1 33.3 1.0 CG A:HIS36 4.2 25.9 1.0 CG A:HIS92 4.2 25.5 1.0 CG A:HIS90 4.2 29.1 1.0 ND1 A:HIS92 4.2 27.5 1.0 ND1 A:HIS36 4.2 26.4 1.0 CB A:ASP84 4.2 29.0 1.0 ND1 A:HIS90 4.2 30.6 1.0 CB A:ASP103 4.4 26.6 1.0 CA A:ASP103 4.7 25.1 1.0 CB A:ASN86 4.8 29.1 1.0 CD2 A:LEU74 4.8 47.5 1.0 O A:HIS91 5.0 20.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Peroxide Stress Regulator From Leptospira Interrogans within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn200 b:40.7 occ:1.00 NE2 B:HIS92 2.1 33.9 1.0 O B:HOH304 2.1 36.4 1.0 NE2 B:HIS90 2.1 28.7 1.0 OD1 B:ASP103 2.2 36.4 1.0 UNK B:UNX201 2.3 37.1 1.0 UNK B:UNX202 2.4 39.9 1.0 CD2 B:HIS92 3.0 34.6 1.0 CG B:ASP103 3.1 37.0 1.0 CD2 B:HIS90 3.1 28.2 1.0 CE1 B:HIS92 3.1 33.2 1.0 CE1 B:HIS90 3.2 28.9 1.0 OD2 B:ASP103 3.4 43.6 1.0 CG B:HIS92 4.2 31.7 1.0 CG B:HIS90 4.3 29.6 1.0 ND1 B:HIS92 4.3 33.2 1.0 ND1 B:HIS90 4.3 31.0 1.0 CB B:ASP103 4.4 32.6 1.0 O B:HOH392 4.7 51.8 1.0 CA B:ASP103 4.8 31.1 1.0 CG2 B:ILE88 5.0 37.3 1.0

M.Kebouchi, F.Saul, R.Taher, A.Landier, B.Beaudeau, S.Dubrac, P.Weber, A.Haouz, M.Picardeau, N.Benaroudj. Structure and Function of the Leptospira Interrogans Peroxide Stress Regulator (Perr), An Atypical Perr Devoid of A Structural Metal-Binding Site. J. Biol. Chem. V. 293 497 2018.
ISSN: ESSN 1083-351X
PubMed: 29146596
DOI: 10.1074/JBC.M117.804443