Copper in PDB 3wnj: 1.20 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans

The structure of 1.20 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 3wnj 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)	28.73 / 1.20
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.903, 114.903, 84.022, 90.00, 90.00, 120.00
R / Rfree (%)	11.9 / 14.6

The structure of 1.20 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Copper atom in the 1.20 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 3wnj). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the 1.20 A Resolution Crystal Structure of Dioxygen Bound Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 3wnj:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the 1.20 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 1.20 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:8.6 occ:0.90 ND1 A:HIS95 2.0 8.8 1.0 ND1 A:HIS143 2.1 10.0 1.0 SG A:CYS135 2.2 8.9 1.0 SD A:MET148 2.6 8.8 0.8 CE1 A:HIS95 3.0 9.2 1.0 CE1 A:HIS143 3.0 9.5 1.0 CG A:HIS95 3.1 9.0 1.0 CG A:HIS143 3.1 9.1 1.0 CB A:CYS135 3.1 9.4 1.0 CE A:MET148 3.4 14.8 0.1 CB A:HIS95 3.5 9.7 1.0 CE A:MET148 3.5 11.1 0.8 CB A:HIS143 3.5 10.1 1.0 CA A:HIS95 3.7 9.2 1.0 CG A:MET148 3.8 9.8 0.1 SD A:MET148 3.9 14.8 0.1 O A:PRO94 4.0 10.0 1.0 NE2 A:HIS143 4.1 9.9 1.0 NE2 A:HIS95 4.1 8.9 1.0 CD2 A:HIS143 4.2 10.3 1.0 CD2 A:HIS95 4.2 9.5 1.0 CG A:MET148 4.2 10.0 0.8 OG1 A:THR137 4.3 10.1 1.0 CB A:THR137 4.3 10.3 1.0 N A:SER96 4.4 9.0 1.0 CA A:HIS143 4.5 9.2 1.0 CB A:MET148 4.5 11.2 0.1 CB A:MET148 4.5 9.2 0.8 CA A:CYS135 4.5 8.2 1.0 CE3 A:TRP63 4.6 9.1 1.0 C A:HIS95 4.6 9.2 1.0 N A:HIS95 4.7 9.7 1.0 C A:PRO94 4.8 10.4 1.0 CZ3 A:TRP63 5.0 9.6 1.0

Copper binding site 2 out of 8 in the 1.20 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 1.20 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:8.7 occ:0.90 NE2 A:HIS100 1.9 8.8 1.0 NE2 A:HIS134 2.0 8.2 1.0 O2 A:OXY408 2.1 21.9 0.8 O A:HOH856 2.2 8.2 0.2 O A:HOH821 2.2 6.4 0.2 O1 A:OXY408 2.4 14.0 0.8 CE1 A:HIS100 2.9 8.1 1.0 CD2 A:HIS134 3.0 8.8 1.0 CD2 A:HIS100 3.0 7.8 1.0 CE1 A:HIS134 3.0 8.1 1.0 OD2 A:ASP98 3.9 12.8 1.0 ND1 A:HIS100 4.1 8.0 1.0 CG A:HIS100 4.1 7.4 1.0 CG A:HIS134 4.2 8.3 1.0 ND1 A:HIS134 4.2 8.7 1.0 CG A:ASP98 4.4 9.7 1.0 OD1 A:ASP98 4.6 10.6 1.0 O A:HOH783 4.7 18.1 1.0 O A:HOH796 4.7 11.8 1.0

Copper binding site 3 out of 8 in the 1.20 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 1.20 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:11.1 occ:0.80 ND1 A:HIS83 2.0 11.4 1.0 NE2 A:HIS42 2.0 11.4 1.0 O A:HOH800 2.4 15.0 1.0 CE1 A:HIS83 2.8 11.7 1.0 CE1 A:HIS42 3.0 12.7 1.0 CG A:HIS83 3.0 10.1 1.0 CD2 A:HIS42 3.0 12.0 1.0 CB A:HIS83 3.5 10.6 1.0 NE2 A:HIS83 4.0 12.2 1.0 CD2 A:HIS83 4.1 13.9 1.0 O A:HOH571 4.1 18.9 1.0 ND1 A:HIS42 4.1 11.9 1.0 CG A:HIS42 4.2 10.7 1.0 O A:HOH782 4.4 15.4 1.0 CG2 A:VAL36 4.6 12.0 1.0

Copper binding site 4 out of 8 in the 1.20 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 4 of 1.20 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:Cu404 b:27.5 occ:0.40 NE2 A:HIS39 1.9 18.5 1.0 CE1 A:HIS39 2.9 16.7 1.0 CD2 A:HIS39 3.0 15.0 1.0 ND1 A:HIS39 4.0 13.9 1.0 CG A:HIS39 4.1 12.4 1.0 O A:HOH709 4.4 31.3 0.5 CB A:PRO38 4.8 10.4 0.3 CB A:PRO38 4.8 14.7 0.7

Copper binding site 5 out of 8 in the 1.20 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 5 of 1.20 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:Cu405 b:24.2 occ:0.20 CU A:CU405 0.0 24.2 0.2 OE2 A:GLU239 1.7 24.3 0.5 O A:HOH628 1.8 21.3 1.0 OE2 A:GLU239 2.0 13.8 0.5 CU A:CU405 2.2 17.7 0.3 CD A:GLU239 2.8 13.7 0.5 O A:HOH813 2.8 33.2 1.0 CD A:GLU239 2.9 10.8 0.5 OE1 A:GLU239 3.2 13.6 0.5 OE1 A:GLU239 3.3 14.2 0.5 O A:HOH641 3.7 32.3 1.0 O A:HOH814 3.9 17.7 1.0 CD A:PRO191 4.0 8.8 1.0 CG A:GLU239 4.1 11.1 0.5 CG A:GLU239 4.1 10.0 0.5 O A:HOH853 4.1 45.5 0.8 OH A:TYR178 4.3 8.0 1.0 O A:GLY189 4.4 10.5 1.0 O A:HOH514 4.4 11.5 1.0 CB A:ASN238 4.4 7.8 1.0 O A:HOH586 4.5 17.1 1.0 CA A:VAL190 4.8 9.0 1.0

Copper binding site 6 out of 8 in the 1.20 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 6 of 1.20 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:Cu405 b:17.7 occ:0.30 CU A:CU405 0.0 17.7 0.3 O A:HOH814 1.8 17.7 1.0 OE2 A:GLU239 2.0 13.8 0.5 CU A:CU405 2.2 24.2 0.2 O A:HOH853 2.2 45.5 0.8 O A:HOH813 2.5 33.2 1.0 OE2 A:GLU239 2.6 24.3 0.5 OE1 A:GLU239 2.7 13.6 0.5 CD A:GLU239 2.9 10.8 0.5 CD A:GLU239 3.0 13.7 0.5 OE1 A:GLU239 3.0 14.2 0.5 O A:HOH628 3.7 21.3 1.0 CD A:PRO191 3.7 8.8 1.0 O A:HOH853 3.8 18.7 0.2 O A:HOH770 4.0 24.2 1.0 NE2 A:HIS298 4.1 7.8 1.0 O A:HOH641 4.1 32.3 1.0 CG A:GLU239 4.3 11.1 0.5 CG A:GLU239 4.3 10.0 0.5 O A:HOH535 4.3 16.8 1.0 CG1 A:VAL190 4.5 12.3 1.0 CG A:PRO191 4.6 10.5 1.0 CA A:VAL190 4.7 9.0 1.0 CE1 A:HIS298 4.7 8.2 1.0 CB A:VAL190 4.8 10.2 1.0 N A:PRO191 5.0 8.5 1.0

Copper binding site 7 out of 8 in the 1.20 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 7 of 1.20 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:Cu406 b:16.6 occ:0.40 CU A:CU406 0.0 16.6 0.4 O A:HOH741 1.8 37.3 1.0 O A:HOH843 2.0 33.3 0.5 OD2 A:ASP167 2.1 14.9 1.0 O A:HOH806 2.4 69.4 1.0 O A:HOH693 2.4 28.0 1.0 CU A:CU406 2.5 26.9 0.1 CG A:ASP167 2.9 13.6 1.0 OD1 A:ASP167 3.0 20.2 1.0 O A:GLU165 4.1 15.7 1.0 N A:LYS227 4.1 10.8 1.0 O A:GLY225 4.2 15.5 1.0 CB A:ASP167 4.3 12.5 1.0 CA A:GLU226 4.5 11.7 1.0 CB A:LYS227 4.7 13.6 1.0 C A:GLU226 4.8 10.0 1.0

Copper binding site 8 out of 8 in the 1.20 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 8 of 1.20 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:Cu406 b:26.9 occ:0.10 CU A:CU406 0.0 26.9 0.1 OD1 A:ASP167 2.1 20.2 1.0 O A:HOH741 2.4 37.3 1.0 CU A:CU406 2.5 16.6 0.4 O A:HOH843 2.8 33.3 0.5 CG A:ASP167 3.0 13.6 1.0 OD2 A:ASP167 3.2 14.9 1.0 O A:HOH806 3.9 69.4 1.0 O A:GLU165 3.9 15.7 1.0 O A:HOH777 3.9 56.1 0.8 CB A:ASP167 4.3 12.5 1.0 C A:GLU165 4.5 13.0 1.0 CA A:ASP167 4.7 12.2 1.0 O A:LYS164 4.7 21.1 0.3 O A:LYS164 4.7 21.5 0.7 N A:ASP167 4.8 10.9 1.0 O A:HOH693 4.8 28.0 1.0 C A:VAL166 4.9 13.7 1.0 O A:VAL166 5.0 14.1 1.0 CA A:GLU165 5.0 15.0 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.