Copper in PDB 2vn3: Nitrite Reductase From Alcaligenes Xylosoxidans

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2vn3 was solved by K.Sato, S.J.Firbank, C.Li, M.J.Banfield, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.14 / 2.35
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	89.451, 89.451, 144.473, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 21.5

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Copper atom in the Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 2vn3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2vn3:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:42.8 occ:1.00 ND1 A:HIS139 2.0 38.2 1.0 SG A:CYS130 2.2 36.0 1.0 ND1 A:HIS89 2.2 39.0 1.0 SD A:MET144 2.5 34.2 1.0 CE1 A:HIS139 2.9 37.6 1.0 CG A:HIS139 3.1 37.1 1.0 CB A:CYS130 3.1 34.8 1.0 CG A:HIS89 3.2 39.8 1.0 CE1 A:HIS89 3.2 36.4 1.0 CE A:MET144 3.4 30.3 1.0 CB A:HIS89 3.5 40.6 1.0 CB A:HIS139 3.5 33.0 1.0 CA A:HIS89 3.8 40.7 1.0 CG A:PRO132 3.9 38.8 1.0 NE2 A:HIS139 4.0 39.6 1.0 CG A:MET144 4.1 32.3 1.0 O A:PRO88 4.1 42.0 1.0 CD2 A:HIS139 4.2 38.5 1.0 NE2 A:HIS89 4.3 40.7 1.0 CD2 A:HIS89 4.3 40.0 1.0 CD A:PRO132 4.4 37.7 1.0 CA A:CYS130 4.6 35.1 1.0 CB A:MET144 4.6 31.0 1.0 SD A:MET56 4.6 37.2 1.0 CA A:HIS139 4.7 32.7 1.0 N A:ASN90 4.8 40.0 1.0 N A:HIS89 4.8 41.8 1.0 C A:PRO88 4.9 42.6 1.0 C A:HIS89 4.9 40.4 1.0

Copper binding site 2 out of 2 in the Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:36.1 occ:1.00 O A:HOH2052 1.8 47.8 1.0 NE2 A:HIS129 2.0 32.8 1.0 NE2 A:HIS94 2.1 29.6 1.0 CD2 A:HIS129 2.9 32.3 1.0 CE1 A:HIS94 3.0 30.9 1.0 CE1 A:HIS129 3.0 33.4 1.0 CD2 A:HIS94 3.2 28.9 1.0 OD2 A:ASP92 3.7 35.0 1.0 CG A:HIS129 4.1 31.1 1.0 ND1 A:HIS129 4.1 35.0 1.0 ND1 A:HIS94 4.1 31.9 1.0 CG A:HIS94 4.3 31.9 1.0 CG A:ASP92 4.4 35.5 1.0 OD1 A:ASP92 4.8 35.5 1.0

K.Sato, S.J.Firbank, C.Li, M.J.Banfield, C.Dennison. The Importance of the Long Type 1 Copper-Binding Loop of Nitrite Reductase For Structure and Function. Chemistry V. 14 5820 2008.
ISSN: ISSN 0947-6539
PubMed: 18491346
DOI: 10.1002/CHEM.200701997