Copper in PDB 3wkp: C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite

The structure of C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite, PDB code: 3wkp 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)	25.18 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.866, 114.866, 84.039, 90.00, 90.00, 120.00
R / Rfree (%)	15.6 / 20.6

The binding sites of Copper atom in the C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite (pdb code 3wkp). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite, PDB code: 3wkp:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:17.0 occ:0.90 ND1 A:HIS143 2.0 15.5 1.0 SD A:MET148 2.1 27.4 1.0 ND1 A:HIS95 2.1 19.8 1.0 CE1 A:HIS143 2.8 16.6 1.0 CE1 A:HIS95 2.9 21.0 1.0 CG A:HIS143 3.0 16.2 1.0 CG A:HIS95 3.2 18.9 1.0 CE A:MET148 3.3 21.8 1.0 CG A:MET148 3.4 19.5 1.0 CB A:HIS143 3.5 14.3 1.0 CB A:ALA135 3.5 18.2 1.0 CB A:HIS95 3.7 16.0 1.0 CE3 A:TRP63 4.0 17.5 1.0 NE2 A:HIS143 4.0 16.9 1.0 CB A:MET148 4.1 17.4 1.0 NE2 A:HIS95 4.1 19.6 1.0 CD2 A:HIS143 4.1 16.1 1.0 CD2 A:HIS95 4.2 20.4 1.0 CA A:HIS95 4.2 17.0 1.0 CA A:HIS143 4.3 15.4 1.0 O A:PRO94 4.5 15.3 1.0 CZ3 A:TRP63 4.7 23.2 1.0 CB A:TRP63 4.8 16.4 1.0 CD2 A:TRP63 4.9 17.0 1.0 O A:HIS143 4.9 14.7 1.0

Copper binding site 2 out of 4 in the C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:16.7 occ:1.00 NE2 A:HIS134 1.9 18.2 1.0 O1 A:NO2405 2.0 19.7 1.0 NE2 A:HIS100 2.0 13.3 1.0 N A:NO2405 2.8 30.6 1.0 CE1 A:HIS100 2.9 13.0 1.0 CE1 A:HIS134 2.9 17.6 1.0 CD2 A:HIS134 3.0 17.0 1.0 CD2 A:HIS100 3.0 13.2 1.0 O2 A:NO2405 3.4 41.6 1.0 OD2 A:ASP98 3.7 15.6 1.0 ND1 A:HIS134 4.0 16.8 1.0 ND1 A:HIS100 4.0 13.3 1.0 CG A:HIS134 4.1 16.6 1.0 CG A:HIS100 4.1 13.2 1.0 CG A:ASP98 4.4 15.2 1.0 O A:HOH705 4.7 18.8 1.0 OD1 A:ASP98 4.7 15.9 1.0 O A:HOH531 4.9 31.8 1.0

Copper binding site 3 out of 4 in the C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:21.9 occ:1.00 O A:HOH658 1.9 35.9 1.0 ND1 A:HIS83 2.0 23.2 1.0 NE2 A:HIS42 2.1 15.1 1.0 O A:HOH708 2.4 19.1 1.0 CD2 A:HIS42 2.9 15.2 1.0 CE1 A:HIS83 3.0 23.6 1.0 CG A:HIS83 3.1 19.7 1.0 CE1 A:HIS42 3.1 16.9 1.0 CB A:HIS83 3.5 18.6 1.0 NE2 A:HIS83 4.1 19.6 1.0 CG A:HIS42 4.1 14.5 1.0 CD2 A:HIS83 4.2 22.7 1.0 ND1 A:HIS42 4.2 16.0 1.0 O A:HOH709 4.3 21.0 1.0 O A:HOH725 4.3 37.7 1.0 CG2 A:VAL36 4.6 17.9 1.0 O A:HOH576 4.6 23.6 1.0

Copper binding site 4 out of 4 in the C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:44.9 occ:0.50 NE2 A:HIS39 2.1 22.1 1.0 CD2 A:HIS39 3.0 20.5 1.0 CE1 A:HIS39 3.2 22.4 1.0 CG A:HIS39 4.3 19.7 1.0 ND1 A:HIS39 4.3 21.0 1.0 CB A:PRO38 4.7 20.5 1.0

Y.Fukuda, T.Inoue. C135A Mutant of Geobacillus Thermodenitrificans Copper-Containing Nitrite Reductase in Complex with Nitrite To Be Published.