Copper in PDB 3wni: 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans

The structure of 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 3wni was solved by Y.Fukuda, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.91 / 1.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.017, 115.017, 84.543, 90.00, 90.00, 120.00
R / Rfree (%)	10.8 / 14.9

The binding sites of Copper atom in the 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 3wni). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 3wni:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:9.8 occ:0.90 ND1 A:HIS143 2.0 12.3 1.0 ND1 A:HIS95 2.0 11.4 1.0 SG A:CYS135 2.2 10.6 1.0 SD A:MET148 2.6 13.4 1.0 CE1 A:HIS143 2.9 11.2 1.0 CG A:HIS143 3.0 11.0 1.0 CG A:HIS95 3.1 8.5 1.0 CE1 A:HIS95 3.1 11.3 1.0 CB A:CYS135 3.2 9.1 1.0 CB A:HIS95 3.4 9.9 1.0 CB A:HIS143 3.5 9.8 1.0 CE A:MET148 3.5 11.9 1.0 CA A:HIS95 3.7 11.2 1.0 O A:PRO94 4.0 11.3 1.0 NE2 A:HIS143 4.0 12.5 1.0 CG A:MET148 4.1 10.5 1.0 CD2 A:HIS143 4.1 10.9 1.0 NE2 A:HIS95 4.2 10.3 1.0 CD2 A:HIS95 4.2 11.0 1.0 CB A:THR137 4.3 9.3 1.0 OG1 A:THR137 4.4 12.1 1.0 N A:SER96 4.5 13.1 1.0 CA A:HIS143 4.5 10.0 1.0 CB A:MET148 4.5 10.6 1.0 CE3 A:TRP63 4.6 9.4 1.0 CA A:CYS135 4.6 8.4 1.0 C A:HIS95 4.7 11.6 1.0 N A:HIS95 4.8 10.6 1.0 C A:PRO94 4.8 9.7 1.0 CZ3 A:TRP63 5.0 10.8 1.0

Copper binding site 2 out of 3 in the 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:10.5 occ:0.90 O2 A:OXY404 2.0 23.6 0.8 NE2 A:HIS100 2.0 8.8 1.0 NE2 A:HIS134 2.0 10.7 1.0 O A:HOH843 2.2 11.6 0.2 O1 A:OXY404 2.3 17.4 0.8 CE1 A:HIS100 2.9 10.9 1.0 CE1 A:HIS134 3.0 10.5 1.0 CD2 A:HIS100 3.0 7.9 1.0 CD2 A:HIS134 3.1 11.9 1.0 OD2 A:ASP98 3.9 14.2 1.0 ND1 A:HIS100 4.1 11.4 1.0 CG A:HIS100 4.2 8.3 1.0 ND1 A:HIS134 4.2 9.1 1.0 CG A:HIS134 4.2 9.0 1.0 CG A:ASP98 4.4 12.5 1.0 O A:HOH793 4.5 24.2 1.0 O A:HOH791 4.7 13.6 1.0 OD1 A:ASP98 4.7 11.7 1.0

Copper binding site 3 out of 3 in the 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of 1.50 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:10.9 occ:0.90 NE2 A:HIS42 2.0 10.6 1.0 ND1 A:HIS83 2.0 11.7 1.0 CE1 A:HIS83 2.9 11.8 1.0 CD2 A:HIS42 3.0 10.7 1.0 CE1 A:HIS42 3.0 11.6 1.0 CG A:HIS83 3.2 9.9 1.0 CB A:HIS83 3.6 10.8 1.0 O A:HOH603 4.1 18.2 1.0 NE2 A:HIS83 4.1 12.5 1.0 ND1 A:HIS42 4.2 12.0 1.0 CG A:HIS42 4.2 10.6 1.0 CD2 A:HIS83 4.2 14.5 1.0 O A:HOH550 4.4 16.2 1.0 CG2 A:VAL36 4.6 12.1 1.0

Y.Fukuda, T.Inoue. Crystallographic Evidence For Side-on Dioxygen Trapped on Type 2 Copper in Copper-Containing Nitrite Reductase To Be Published.