Copper in PDB 2dy2: Nitrite Reductase pH 6.0

All present enzymatic activity of Nitrite Reductase pH 6.0:
1.7.2.1;

The structure of Nitrite Reductase pH 6.0, PDB code: 2dy2 was solved by F.Jacobson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.77 / 2.26
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	74.996, 74.996, 153.611, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 24.1

The binding sites of Copper atom in the Nitrite Reductase pH 6.0 (pdb code 2dy2). 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 pH 6.0, PDB code: 2dy2:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in the Nitrite Reductase pH 6.0


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite Reductase pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:40.9 occ:1.00 ND1 A:HIS177 2.0 37.8 1.0 SG A:CYS167 2.2 39.6 1.0 ND1 A:HIS126 2.3 44.0 1.0 SD A:MET182 2.5 40.3 1.0 CE1 A:HIS177 2.9 39.5 1.0 CG A:HIS177 3.1 39.6 1.0 CG A:HIS126 3.2 43.2 1.0 CB A:CYS167 3.2 39.3 1.0 CE1 A:HIS126 3.3 42.4 1.0 CB A:HIS126 3.4 44.1 1.0 CB A:HIS177 3.5 38.1 1.0 CE A:MET182 3.5 39.8 1.0 CA A:HIS126 3.8 44.2 1.0 CG A:MET182 3.9 37.0 1.0 CG A:PRO169 4.1 43.2 1.0 NE2 A:HIS177 4.1 38.5 1.0 CD2 A:HIS177 4.2 38.0 1.0 O A:PRO125 4.2 45.7 1.0 CD2 A:HIS126 4.4 44.0 1.0 CB A:MET182 4.4 35.0 1.0 NE2 A:HIS126 4.4 45.3 1.0 CA A:CYS167 4.6 39.1 1.0 SD A:MET93 4.6 48.5 1.0 N A:ASN127 4.7 43.0 1.0 CA A:HIS177 4.7 37.5 1.0 CD A:PRO169 4.7 42.0 1.0 C A:HIS126 4.8 43.8 1.0 N A:HIS126 4.9 44.8 1.0 C A:PRO125 5.0 46.1 1.0 C A:CYS167 5.0 39.6 1.0

Copper binding site 2 out of 2 in the Nitrite Reductase pH 6.0


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite Reductase pH 6.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:35.3 occ:1.00 O A:HOH474 2.1 45.0 1.0 NE2 A:HIS338 2.2 23.3 1.0 CD2 A:HIS338 3.0 25.2 1.0 CE1 A:HIS338 3.2 25.6 1.0 NE2 A:HIS287 4.0 31.7 1.0 CG A:HIS338 4.2 24.1 1.0 ND1 A:HIS338 4.3 25.8 1.0 CD2 A:HIS287 4.3 29.4 1.0 CE1 A:HIS287 4.4 33.4 1.0 CG A:HIS287 4.9 31.0 1.0 ND1 A:HIS287 4.9 32.0 1.0

F.Jacobson, A.Pistorius, D.Farkas, W.De Grip, O.Hansson, L.Sjolin, R.Neutze. pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase J.Biol.Chem. V. 282 6347 2007.
ISSN: ISSN 0021-9258
PubMed: 17148448
DOI: 10.1074/JBC.M605746200