Zinc in PDB 2xxf: Cu Metallated H254F Mutant of Nitrite Reductase

The structure of Cu Metallated H254F Mutant of Nitrite Reductase, PDB code: 2xxf 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)	95.78 / 1.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	89.333, 89.333, 287.851, 90.00, 90.00, 120.00
R / Rfree (%)	14.462 / 17.65

The structure of Cu Metallated H254F Mutant of Nitrite Reductase also contains other interesting chemical elements:

Copper

(Cu)

4 atoms

The binding sites of Zinc atom in the Cu Metallated H254F Mutant of Nitrite Reductase (pdb code 2xxf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cu Metallated H254F Mutant of Nitrite Reductase, PDB code: 2xxf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cu Metallated H254F Mutant of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cu Metallated H254F Mutant of Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1339 b:15.8 occ:0.70 CU A:CU1338 0.6 14.6 0.3 NE2 A:HIS129 1.9 18.0 1.0 NE2 A:HIS94 2.0 16.6 1.0 O A:HOH2281 2.2 22.8 1.0 CD2 A:HIS129 2.8 16.5 1.0 CE1 A:HIS129 2.9 20.2 1.0 CE1 A:HIS94 3.0 17.9 1.0 CD2 A:HIS94 3.1 18.0 1.0 OD2 A:ASP92 3.6 26.7 1.0 CG A:HIS129 4.0 18.1 1.0 ND1 A:HIS129 4.0 19.1 1.0 ND1 A:HIS94 4.1 17.0 1.0 CG A:HIS94 4.2 18.0 1.0 CG A:ASP92 4.2 23.5 1.0 OD1 A:ASP92 4.5 25.4 1.0

Zinc binding site 2 out of 6 in the Cu Metallated H254F Mutant of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cu Metallated H254F Mutant of Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1341 b:26.7 occ:1.00 NE2 A:HIS165 1.9 21.7 1.0 OD2 A:ASP167 2.0 23.9 1.0 O A:HOH2283 2.1 28.7 1.0 OD1 A:ASP167 2.5 27.0 1.0 CG A:ASP167 2.5 26.0 1.0 CE1 A:HIS165 2.8 21.4 1.0 CD2 A:HIS165 3.0 22.4 1.0 OG1 A:THR234 3.9 22.8 1.0 ND1 A:HIS165 4.0 22.4 1.0 O A:HOH2288 4.0 43.0 1.0 CB A:ASP167 4.1 24.0 1.0 CG A:HIS165 4.1 20.6 1.0 CB A:THR234 4.3 21.4 1.0 N A:THR234 4.4 22.5 1.0 N A:ASP167 4.6 23.6 1.0 O A:GLY232 4.6 28.8 1.0 CA A:ASP167 4.8 24.7 1.0

Zinc binding site 3 out of 6 in the Cu Metallated H254F Mutant of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cu Metallated H254F Mutant of Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1345 b:70.1 occ:0.50 O A:HOH2290 1.9 66.2 0.5 NE2 A:HIS8 2.3 42.9 1.0 CE1 A:HIS8 3.2 42.4 1.0 CD2 A:HIS8 3.2 40.9 1.0 O A:ASP4 3.6 51.5 1.0 O A:ALA3 4.1 49.6 1.0 C A:ASP4 4.1 50.0 1.0 CA A:ASP4 4.2 51.1 1.0 O A:LEU6 4.2 39.2 1.0 O A:HOH2086 4.3 30.0 0.5 ND1 A:HIS8 4.3 37.3 1.0 CG A:HIS8 4.3 38.8 1.0 CG2 A:VAL32 5.0 30.1 1.0 OD1 A:ASP4 5.0 55.9 1.0 C A:ALA3 5.0 50.7 1.0

Zinc binding site 4 out of 6 in the Cu Metallated H254F Mutant of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cu Metallated H254F Mutant of Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1338 b:18.6 occ:0.70 CU B:CU1340 0.4 10.5 0.3 NE2 B:HIS129 1.9 15.0 1.0 O B:HOH2308 2.0 19.0 1.0 NE2 B:HIS94 2.1 15.3 1.0 CD2 B:HIS129 2.8 16.3 1.0 CE1 B:HIS129 2.9 16.9 1.0 CE1 B:HIS94 3.0 15.9 1.0 CD2 B:HIS94 3.2 15.4 1.0 OD2 B:ASP92 3.7 22.2 1.0 CG B:HIS129 4.0 15.5 1.0 ND1 B:HIS129 4.0 16.8 1.0 ND1 B:HIS94 4.2 15.8 1.0 CG B:ASP92 4.3 24.2 1.0 CG B:HIS94 4.3 16.3 1.0 OD1 B:ASP92 4.6 24.9 1.0

Zinc binding site 5 out of 6 in the Cu Metallated H254F Mutant of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cu Metallated H254F Mutant of Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1344 b:25.0 occ:1.00 OE2 A:GLU195 2.0 28.4 1.0 NE2 B:HIS165 2.0 23.6 1.0 OD2 B:ASP167 2.1 22.3 1.0 O B:HOH2312 2.1 28.0 1.0 OD1 B:ASP167 2.5 24.8 1.0 CG B:ASP167 2.6 21.1 1.0 CD A:GLU195 2.7 26.5 1.0 CE1 B:HIS165 2.9 22.3 1.0 OE1 A:GLU195 2.9 27.2 1.0 CD2 B:HIS165 3.0 22.9 1.0 O A:HOH2190 3.7 39.6 1.0 OG1 B:THR234 3.9 21.2 1.0 CB B:ASP167 4.0 21.7 1.0 O A:HOH2184 4.1 29.5 1.0 ND1 B:HIS165 4.1 21.0 1.0 CG A:GLU195 4.1 26.5 1.0 O B:HOH2309 4.1 33.6 1.0 CG B:HIS165 4.1 21.9 1.0 CB B:THR234 4.3 19.9 1.0 N B:THR234 4.5 19.7 1.0 CB A:ALA191 4.5 22.9 1.0 N B:ASP167 4.6 21.0 1.0 O B:GLY232 4.7 26.1 1.0 CA B:ASP167 4.8 21.8 1.0

Zinc binding site 6 out of 6 in the Cu Metallated H254F Mutant of Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cu Metallated H254F Mutant of Nitrite Reductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1348 b:46.5 occ:0.50 O B:HOH2319 2.0 31.4 0.5 NE2 B:HIS8 2.2 39.5 1.0 CE1 B:HIS8 3.1 37.7 1.0 CD2 B:HIS8 3.2 37.5 1.0 O B:ASP4 3.4 49.7 1.0 C B:ASP4 3.9 47.9 1.0 O B:ALA3 4.0 46.3 1.0 O B:LEU6 4.0 37.6 1.0 CA B:ASP4 4.0 48.8 1.0 ND1 B:HIS8 4.2 35.6 1.0 CG B:HIS8 4.3 34.8 1.0 O B:HOH2096 4.5 43.2 1.0 C B:ALA3 4.8 48.2 1.0 N B:ASP4 4.8 48.6 1.0 OD1 B:ASP4 4.9 53.2 1.0 CG2 B:VAL32 5.0 29.4 1.0 N B:LEU6 5.0 39.7 1.0

N.G.H.Leferink, C.Han, S.V.Antonyuk, D.J.Heyes, S.E.J.Rigby, M.A.Hough, R.R.Eady, N.S.Scrutton, S.S.Hasnain. Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry V. 50 4121 2011.
ISSN: ISSN 0006-2960
PubMed: 21469743
DOI: 10.1021/BI200246F