Copper in PDB 3x1g: H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site

The structure of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site, PDB code: 3x1g 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)	28.82 / 1.30
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.275, 115.275, 84.691, 90.00, 90.00, 120.00
R / Rfree (%)	10.6 / 12.8

The binding sites of Copper atom in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site (pdb code 3x1g). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site, PDB code: 3x1g:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:8.2 occ:0.95 ND1 A:HIS143 2.0 8.8 1.0 ND1 A:HIS95 2.1 8.9 1.0 SG A:CYS135 2.2 8.7 1.0 SD A:MET148 2.6 8.7 1.0 CE1 A:HIS143 2.9 9.0 1.0 CE1 A:HIS95 3.0 9.5 1.0 CG A:HIS95 3.0 7.8 1.0 CG A:HIS143 3.1 8.1 1.0 CB A:CYS135 3.1 8.0 1.0 CB A:HIS95 3.4 9.0 1.0 CE A:MET148 3.4 10.3 1.0 CB A:HIS143 3.4 8.3 1.0 CA A:HIS95 3.7 9.1 1.0 NE2 A:HIS143 4.0 9.4 1.0 CG A:MET148 4.1 8.3 1.0 O A:PRO94 4.1 9.3 1.0 NE2 A:HIS95 4.1 8.9 1.0 CD2 A:HIS143 4.1 9.6 1.0 CD2 A:HIS95 4.2 9.5 1.0 CB A:THR137 4.4 8.0 1.0 OG1 A:THR137 4.4 8.9 1.0 N A:SER96 4.5 8.8 1.0 CB A:MET148 4.5 7.1 1.0 CA A:HIS143 4.5 7.8 1.0 CA A:CYS135 4.6 7.1 1.0 CE3 A:TRP63 4.6 8.3 1.0 C A:HIS95 4.6 8.9 1.0 N A:HIS95 4.7 8.8 1.0 C A:PRO94 4.8 8.7 1.0

Copper binding site 2 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:7.4 occ:0.45 CU A:CU402 0.0 7.4 0.5 CE1 A:HIS100 1.8 2.6 0.2 CU A:CU402 1.8 11.6 0.5 NE2 A:HIS100 1.8 2.4 0.2 NE2 A:HIS100 2.0 9.8 0.8 NE2 A:HIS134 2.1 6.6 0.5 O A:HOH867 2.2 3.4 0.3 O A:HOH867 2.4 6.2 0.7 NE2 A:HIS134 2.7 8.9 0.5 CE1 A:HIS100 2.9 9.9 0.8 CD2 A:HIS134 3.1 7.2 0.5 ND1 A:HIS100 3.1 2.8 0.2 CE1 A:HIS134 3.1 7.5 0.5 CD2 A:HIS100 3.1 8.6 0.8 CD2 A:HIS100 3.2 2.8 0.2 CD2 A:HIS134 3.2 8.0 0.5 CG A:HIS100 3.8 3.3 0.2 OD2 A:ASP98 3.8 10.4 0.5 CE1 A:HIS134 3.8 7.9 0.5 ND1 A:HIS100 4.0 9.5 0.8 OD2 A:ASP98 4.1 10.6 0.5 ND1 A:HIS134 4.2 6.5 0.5 CG A:HIS100 4.2 7.5 0.8 CG A:HIS134 4.2 7.0 0.5 OXT A:ACY407 4.3 28.4 1.0 CG A:HIS134 4.5 7.5 0.5 CG A:ASP98 4.6 10.1 0.5 ND1 A:HIS134 4.7 7.5 0.5 CG A:ASP98 4.7 9.0 0.5 OD1 A:ASP98 4.8 10.6 0.5 O A:HOH524 4.9 8.9 1.0 SD A:MET132 5.0 8.1 1.0 OD1 A:ASP98 5.0 10.7 0.5

Copper binding site 3 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:11.6 occ:0.45 CU A:CU402 0.0 11.6 0.5 O A:HOH867 1.4 3.4 0.3 CU A:CU402 1.8 7.4 0.5 NE2 A:HIS100 1.8 2.4 0.2 NE2 A:HIS134 1.9 6.6 0.5 OD2 A:ASP98 2.0 10.4 0.5 NE2 A:HIS134 2.0 8.9 0.5 O A:HOH867 2.1 6.2 0.7 CE1 A:HIS134 2.3 7.5 0.5 OD2 A:ASP98 2.3 10.6 0.5 CE1 A:HIS100 2.8 2.6 0.2 NE2 A:HIS100 2.9 9.8 0.8 CD2 A:HIS100 2.9 2.8 0.2 CG A:ASP98 2.9 10.1 0.5 CE1 A:HIS134 3.0 7.9 0.5 CD2 A:HIS134 3.0 8.0 0.5 CG A:ASP98 3.1 9.0 0.5 CD2 A:HIS134 3.2 7.2 0.5 OXT A:ACY407 3.3 28.4 1.0 CD2 A:HIS100 3.3 8.6 0.8 OD1 A:ASP98 3.4 10.6 0.5 ND1 A:HIS134 3.5 6.5 0.5 OD1 A:ASP98 3.6 10.7 0.5 O A:ACY407 3.8 19.1 1.0 ND1 A:HIS100 3.9 2.8 0.2 C A:ACY407 3.9 28.3 1.0 CB A:ASP98 3.9 9.0 0.5 CB A:ASP98 3.9 7.1 0.5 CG A:HIS134 4.0 7.0 0.5 CG A:HIS100 4.0 3.3 0.2 O A:HOH524 4.0 8.9 1.0 CE1 A:HIS100 4.1 9.9 0.8 ND1 A:HIS134 4.1 7.5 0.5 CG A:HIS134 4.2 7.5 0.5 CG A:HIS100 4.6 7.5 0.8 ND1 A:HIS100 5.0 9.5 0.8

Copper binding site 4 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:38.0 occ:0.50 NE2 A:HIS39 2.1 16.7 1.0 O A:HOH873 2.9 39.9 1.0 CE1 A:HIS39 3.1 15.8 1.0 CD2 A:HIS39 3.1 14.9 1.0 O A:HOH875 3.8 47.7 1.0 ND1 A:HIS39 4.2 13.3 1.0 CG A:HIS39 4.3 12.3 1.0 O A:HOH874 4.7 46.3 1.0 CB A:PRO38 4.8 11.4 0.5 CB A:PRO38 4.9 13.8 0.5

Copper binding site 5 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:17.3 occ:0.40 O A:HOH770 1.9 20.1 0.5 O A:HOH817 2.0 25.8 0.5 O A:HOH877 2.1 26.7 0.7 OD2 A:ASP167 2.1 13.2 1.0 O A:HOH769 2.3 24.3 1.0 O A:HOH701 2.7 30.8 0.5 CG A:ASP167 2.9 14.1 1.0 OD1 A:ASP167 3.0 18.6 1.0 O A:HOH877 3.6 29.1 0.3 O A:GLU165 4.1 15.8 1.0 O A:GLY225 4.1 13.8 1.0 N A:LYS227 4.2 10.4 1.0 O A:HOH701 4.3 29.7 0.5 CB A:ASP167 4.3 11.8 1.0 CA A:GLU226 4.5 10.9 1.0 CB A:LYS227 4.8 11.7 1.0 O A:HOH878 4.8 37.5 0.7 C A:GLU226 4.8 9.6 1.0

Copper binding site 6 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:7.3 occ:0.80 NE2 A:HIS42 2.0 9.8 1.0 ND1 A:HIS83 2.1 8.8 1.0 O A:HOH610 2.1 12.0 1.0 O A:HOH528 2.3 11.5 1.0 CE1 A:HIS83 2.9 9.5 1.0 CE1 A:HIS42 3.0 10.1 1.0 CD2 A:HIS42 3.0 9.1 1.0 CG A:HIS83 3.2 8.6 1.0 CB A:HIS83 3.6 9.2 1.0 O A:HOH556 4.1 15.7 1.0 NE2 A:HIS83 4.1 9.7 1.0 O A:HOH856 4.1 16.4 1.0 ND1 A:HIS42 4.1 10.2 1.0 CG A:HIS42 4.2 9.2 1.0 CD2 A:HIS83 4.2 11.7 1.0 O A:HOH549 4.4 14.1 1.0 O A:HOH530 4.6 11.7 1.0 O A:HOH868 4.6 24.9 1.0 CG2 A:VAL36 4.7 10.5 1.0

Copper binding site 7 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:18.0 occ:0.30 CU A:CU406 0.0 18.0 0.3 O A:HOH922 1.1 20.9 0.5 NE2 A:HIS298 2.2 7.4 1.0 CU A:CU406 2.2 15.2 0.2 O A:HOH915 2.8 16.6 1.0 OE2 A:GLU239 2.9 26.3 1.0 CD A:GLU239 3.1 16.1 1.0 OE1 A:GLU239 3.1 15.4 1.0 CE1 A:HIS298 3.1 8.8 1.0 CD2 A:HIS298 3.2 8.4 1.0 O A:HOH675 3.3 26.3 1.0 O A:HOH916 3.5 27.6 0.8 CD A:PRO191 3.6 8.8 1.0 CG A:PRO191 3.8 9.6 1.0 CG A:GLU239 4.0 12.0 1.0 O A:HOH518 4.1 9.4 1.0 O A:HOH917 4.2 35.1 1.0 ND2 A:ASN297 4.2 12.3 1.0 ND1 A:HIS298 4.3 8.0 1.0 CG A:HIS298 4.3 7.0 1.0 CG A:ASN297 4.7 8.4 1.0 OD1 A:ASN297 4.7 8.8 1.0 N A:PRO191 4.9 8.2 1.0

Copper binding site 8 out of 8 in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Showing Two Coordination Geometries at the T2CU Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:15.2 occ:0.20 CU A:CU406 0.0 15.2 0.2 O A:HOH916 1.6 27.6 0.8 O A:HOH922 1.9 20.9 0.5 CU A:CU406 2.2 18.0 0.3 OE2 A:GLU239 2.4 26.3 1.0 O A:HOH917 2.5 35.1 1.0 OE1 A:GLU239 3.0 15.4 1.0 CD A:GLU239 3.0 16.1 1.0 O A:HOH627 3.7 20.5 1.0 O A:HOH675 3.8 26.3 1.0 O A:HOH696 3.8 28.7 1.0 CD A:PRO191 3.9 8.8 1.0 O A:HOH915 4.2 16.6 1.0 NE2 A:HIS298 4.2 7.4 1.0 CG A:GLU239 4.4 12.0 1.0 CG1 A:VAL190 4.5 10.7 1.0 CA A:VAL190 4.7 8.2 1.0 CG A:PRO191 4.7 9.6 1.0 CB A:VAL190 4.7 9.6 1.0 CE1 A:HIS298 4.9 8.8 1.0

Y.Fukuda, T.Inoue. Structural Evidence of the Flexibility of the Cum Site To Be Published.