Copper in PDB 3x1f: H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans

The structure of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 3x1f 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)	18.36 / 1.35
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.977, 114.977, 84.138, 90.00, 90.00, 120.00
R / Rfree (%)	9.2 / 11.5

The binding sites of Copper atom in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 3x1f). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 3x1f:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in the H294M Mutant of 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 H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:8.9 occ:0.90 ND1 A:HIS143 2.0 10.7 1.0 ND1 A:HIS95 2.0 10.2 1.0 SG A:CYS135 2.2 9.9 1.0 SD A:MET148 2.6 10.9 1.0 CE1 A:HIS143 2.9 10.7 1.0 CE1 A:HIS95 3.0 9.9 1.0 CG A:HIS143 3.0 10.5 1.0 CG A:HIS95 3.1 9.5 1.0 CB A:CYS135 3.2 8.6 1.0 CB A:HIS95 3.4 9.2 1.0 CE A:MET148 3.4 12.0 1.0 CB A:HIS143 3.5 10.1 1.0 CA A:HIS95 3.7 9.3 1.0 NE2 A:HIS143 4.0 10.6 1.0 CG A:MET148 4.0 10.1 1.0 O A:PRO94 4.1 11.2 1.0 CD2 A:HIS143 4.1 9.5 1.0 NE2 A:HIS95 4.1 9.8 1.0 CD2 A:HIS95 4.2 10.4 1.0 CB A:THR137 4.4 9.7 1.0 OG1 A:THR137 4.4 10.4 1.0 N A:SER96 4.5 9.8 1.0 CA A:HIS143 4.5 8.8 1.0 CB A:MET148 4.5 9.7 1.0 CA A:CYS135 4.6 8.4 1.0 CE3 A:TRP63 4.6 10.1 1.0 C A:HIS95 4.7 9.7 1.0 N A:HIS95 4.7 10.6 1.0 C A:PRO94 4.8 11.0 1.0

Copper binding site 2 out of 9 in the H294M Mutant of 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 H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:8.0 occ:0.90 NE2 A:HIS100 2.0 7.8 1.0 NE2 A:HIS134 2.1 8.7 1.0 O A:HOH861 2.2 11.3 1.0 CE1 A:HIS100 3.0 8.8 1.0 CD2 A:HIS134 3.0 8.6 1.0 CD2 A:HIS100 3.1 8.3 1.0 CE1 A:HIS134 3.1 9.7 1.0 OD2 A:ASP98 4.0 10.0 1.0 ND1 A:HIS100 4.1 8.2 1.0 ND1 A:HIS134 4.2 8.4 1.0 CG A:HIS134 4.2 8.1 1.0 CG A:HIS100 4.2 8.2 1.0 OXT A:ACY408 4.3 13.8 1.0 CG A:ASP98 4.6 9.8 1.0 OD1 A:ASP98 4.8 9.8 1.0 O A:HOH862 4.8 9.1 1.0

Copper binding site 3 out of 9 in the H294M Mutant of 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 H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:35.4 occ:0.50 NE2 A:HIS39 2.0 16.7 1.0 O A:HOH838 2.7 89.8 1.0 CE1 A:HIS39 3.0 17.7 1.0 CD2 A:HIS39 3.0 15.5 1.0 ND1 A:HIS39 4.1 15.6 1.0 CG A:HIS39 4.2 13.9 1.0 CB A:PRO38 4.8 11.8 0.5 CB A:PRO38 4.9 13.7 0.5

Copper binding site 4 out of 9 in the H294M Mutant of 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 4 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:10.3 occ:0.90 ND1 A:HIS83 2.0 11.0 1.0 O A:HOH620 2.1 14.8 1.0 NE2 A:HIS42 2.1 9.9 1.0 O A:HOH559 2.3 13.2 1.0 CE1 A:HIS83 2.8 11.2 1.0 CE1 A:HIS42 3.0 11.8 1.0 CD2 A:HIS42 3.0 9.6 1.0 CG A:HIS83 3.1 10.8 1.0 CB A:HIS83 3.6 10.7 1.0 NE2 A:HIS83 4.0 12.1 1.0 O A:HOH587 4.0 17.1 1.0 O A:HOH791 4.1 17.5 1.0 ND1 A:HIS42 4.1 11.6 1.0 CD2 A:HIS83 4.2 13.7 1.0 CG A:HIS42 4.2 9.9 1.0 O A:HOH790 4.4 15.4 1.0 O A:HOH814 4.5 26.7 1.0 O A:HOH583 4.6 13.5 1.0 CG2 A:VAL36 4.6 11.2 1.0

Copper binding site 5 out of 9 in the H294M Mutant of 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 5 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:17.5 occ:0.30 CU A:CU405 0.0 17.5 0.3 O A:HOH849 1.2 16.1 0.3 NE2 A:HIS298 2.2 9.4 1.0 CU A:CU405 2.3 17.7 0.3 O A:HOH530 2.8 16.6 1.0 OE2 A:GLU239 2.8 26.9 1.0 CD A:GLU239 3.1 18.2 1.0 CD2 A:HIS298 3.1 8.4 1.0 CE1 A:HIS298 3.2 9.5 1.0 OE1 A:GLU239 3.2 18.5 1.0 O A:HOH602 3.4 24.9 1.0 CD A:PRO191 3.5 10.3 1.0 O A:HOH845 3.5 11.7 0.3 CG A:PRO191 3.8 11.4 1.0 CG A:GLU239 4.0 14.1 1.0 O A:HOH511 4.2 9.3 1.0 O A:HOH845 4.2 23.1 0.5 ND2 A:ASN297 4.2 12.9 1.0 ND1 A:HIS298 4.2 8.7 1.0 CG A:HIS298 4.3 7.5 1.0 CG A:ASN297 4.7 9.2 1.0 OD1 A:ASN297 4.8 9.1 1.0 N A:PRO191 4.9 9.2 1.0 CB A:VAL190 5.0 10.3 1.0

Copper binding site 6 out of 9 in the H294M Mutant of 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 6 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:17.7 occ:0.30 CU A:CU405 0.0 17.7 0.3 O A:HOH845 1.7 11.7 0.3 O A:HOH849 2.0 16.1 0.3 OE2 A:GLU239 2.2 26.9 1.0 CU A:CU405 2.3 17.5 0.3 O A:HOH845 2.4 23.1 0.5 CD A:GLU239 3.0 18.2 1.0 OE1 A:GLU239 3.0 18.5 1.0 O A:HOH611 3.8 22.0 1.0 CD A:PRO191 3.8 10.3 1.0 O A:HOH718 3.8 33.5 1.0 O A:HOH602 4.0 24.9 1.0 O A:HOH530 4.2 16.6 1.0 NE2 A:HIS298 4.2 9.4 1.0 CG A:GLU239 4.3 14.1 1.0 CG1 A:VAL190 4.5 11.5 1.0 CA A:VAL190 4.6 10.1 1.0 CB A:VAL190 4.7 10.3 1.0 CG A:PRO191 4.7 11.4 1.0 CE1 A:HIS298 4.9 9.5 1.0

Copper binding site 7 out of 9 in the H294M Mutant of 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 7 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:17.6 occ:0.40 CU A:CU406 0.0 17.6 0.4 O A:HOH502 1.9 30.2 1.0 O A:HOH830 2.0 25.9 0.4 OXT A:ACY412 2.1 16.4 0.3 OD2 A:ASP167 2.1 14.0 1.0 O A:HOH730 2.4 28.6 1.0 CU A:CU406 2.6 73.0 0.2 CG A:ASP167 2.9 16.9 1.0 OD1 A:ASP167 2.9 20.5 1.0 C A:ACY412 3.2 20.9 0.3 O A:ACY412 3.6 27.5 0.3 O A:GLU165 4.1 16.1 1.0 O A:GLY225 4.1 15.4 1.0 N A:LYS227 4.2 11.3 1.0 CB A:ASP167 4.3 13.4 1.0 O A:HOH856 4.5 18.5 0.2 CH3 A:ACY412 4.5 18.5 0.3 CA A:GLU226 4.5 12.8 1.0 CB A:LYS227 4.8 13.6 1.0 C A:GLU226 4.8 11.2 1.0 C A:GLY225 5.0 12.7 1.0

Copper binding site 8 out of 9 in the H294M Mutant of 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 8 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:73.0 occ:0.20 CU A:CU406 0.0 73.0 0.2 OD1 A:ASP167 2.1 20.5 1.0 O A:HOH856 2.3 18.5 0.2 O A:HOH502 2.5 30.2 1.0 CU A:CU406 2.6 17.6 0.4 O A:HOH830 3.0 25.9 0.4 CG A:ASP167 3.0 16.9 1.0 OD2 A:ASP167 3.3 14.0 1.0 OXT A:ACY412 3.8 16.4 0.3 O A:GLU165 4.1 16.1 1.0 O A:ACY412 4.2 27.5 0.3 O A:HOH501 4.2 18.9 0.3 CB A:ASP167 4.4 13.4 1.0 C A:ACY412 4.5 20.9 0.3 C A:GLU165 4.7 13.6 1.0 CA A:ASP167 4.7 12.0 1.0 O A:LYS164 4.8 21.1 1.0 O A:HOH730 4.8 28.6 1.0 N A:ASP167 4.9 12.0 1.0

Copper binding site 9 out of 9 in the H294M Mutant of 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 9 of H294M Mutant of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu407 b:3.8 occ:0.05 O A:HOH863 2.2 2.7 0.1 SD A:MET270 2.4 17.4 1.0 CG A:MET270 3.2 16.3 1.0 CE A:MET270 3.4 20.4 1.0 CB A:MET270 4.6 11.6 1.0 CG1 A:VAL240 4.8 10.2 1.0 CB A:VAL240 4.9 9.3 1.0 CG2 A:VAL240 4.9 10.9 1.0

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