Zinc in PDB 2xxg: Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans

The structure of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2xxg was solved by M.A.Hough, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 1.60
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	89.552, 89.552, 287.678, 90.00, 90.00, 120.00
R / Rfree (%)	16.75 / 21.074

The structure of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Copper

(Cu)

4 atoms

The binding sites of Zinc atom in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 2xxg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2xxg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1339 b:24.8 occ:1.00 OE2 C:GLU195 1.9 26.9 1.0 NE2 A:HIS165 2.0 21.4 1.0 O A:HOH2331 2.1 32.2 1.0 OD2 A:ASP167 2.2 19.4 1.0 OD1 A:ASP167 2.5 22.4 1.0 CG A:ASP167 2.6 20.7 1.0 CD C:GLU195 2.7 24.7 1.0 CE1 A:HIS165 2.9 19.8 1.0 OE1 C:GLU195 3.0 25.3 1.0 CD2 A:HIS165 3.0 19.9 1.0 O C:HOH2212 3.7 34.1 1.0 OG1 A:THR234 3.9 17.3 1.0 ND1 A:HIS165 4.0 19.1 1.0 O C:HOH2206 4.0 29.1 1.0 O A:HOH2337 4.1 32.8 1.0 CG C:GLU195 4.1 22.9 1.0 CG A:HIS165 4.1 18.9 1.0 CB A:ASP167 4.1 20.2 1.0 CB A:THR234 4.3 17.6 1.0 CB C:ALA191 4.5 20.0 1.0 N A:THR234 4.5 18.7 1.0 N A:ASP167 4.6 19.7 1.0 O A:GLY232 4.8 23.2 1.0 CA A:ASP167 4.9 20.9 1.0

Zinc binding site 2 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1341 b:39.2 occ:0.30 O A:HOH2332 1.6 63.6 1.0 O A:HOH2333 2.0 59.6 1.0 NE2 A:HIS8 2.0 36.0 1.0 CD2 A:HIS8 2.8 35.3 1.0 CE1 A:HIS8 3.0 35.2 1.0 O A:LEU6 3.5 34.7 1.0 O A:ASP4 3.6 47.8 1.0 CG A:HIS8 4.0 33.8 1.0 ND1 A:HIS8 4.0 33.7 1.0 C A:ASP4 4.1 47.0 1.0 O A:ALA3 4.3 47.1 1.0 CA A:ASP4 4.4 47.8 1.0 C A:LEU6 4.6 34.8 1.0 O A:HOH2106 4.7 51.9 1.0 CG2 A:VAL32 4.7 27.8 1.0 N A:LEU6 4.8 38.9 1.0

Zinc binding site 3 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1340 b:26.5 occ:1.00 O C:HOH2306 2.0 25.3 1.0 NE2 C:HIS165 2.0 20.0 1.0 OD2 C:ASP167 2.0 20.8 1.0 OD1 C:ASP167 2.4 22.5 1.0 CG C:ASP167 2.5 23.3 1.0 CE1 C:HIS165 2.9 21.0 1.0 CD2 C:HIS165 3.1 18.0 1.0 O C:HOH2245 3.9 40.8 1.0 OG1 C:THR234 3.9 20.0 1.0 CB C:ASP167 4.0 22.7 1.0 ND1 C:HIS165 4.1 20.2 1.0 CG C:HIS165 4.2 18.3 1.0 CB C:THR234 4.3 21.5 1.0 N C:THR234 4.4 21.7 1.0 N C:ASP167 4.6 21.9 1.0 O C:GLY232 4.7 26.1 1.0 CA C:ASP167 4.8 23.3 1.0

Zinc binding site 4 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1342 b:54.3 occ:0.50 O C:HOH2307 2.0 51.3 1.0 NE2 C:HIS8 2.5 38.8 1.0 O C:ASP4 3.4 50.9 1.0 CE1 C:HIS8 3.4 37.8 1.0 CD2 C:HIS8 3.4 38.3 1.0 C C:ASP4 3.8 50.0 1.0 CA C:ASP4 3.9 51.1 1.0 O C:ALA3 4.2 52.3 1.0 O C:HOH2095 4.3 48.2 1.0 O C:LEU6 4.3 38.3 1.0 ND1 C:HIS8 4.4 35.7 1.0 CG C:HIS8 4.5 37.4 1.0 CB C:ASP4 4.8 51.1 1.0 N C:LYS5 4.8 48.5 1.0 OD1 C:ASP4 4.8 51.4 1.0 N C:ASP4 4.9 51.7 1.0 C C:ALA3 4.9 52.3 1.0

M.A.Hough, R.R.Eady, S.S.Hasnain. Identification of the Proton Channel to the Active Site Type 2 Cu Centre of Nitrite Reductase: Structural and Enzymatic Properties of the HIS254PHE and ASN90SER Mutants Biochemistry V. 47 13547 2008.
ISSN: ISSN 0006-2960
PubMed: 19053252
DOI: 10.1021/BI801369Y