Copper in PDB 4zk8: Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)

The structure of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined), PDB code: 4zk8 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)	22.06 / 1.15
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.054, 115.054, 84.417, 90.00, 90.00, 120.00
R / Rfree (%)	12 / 14.6

The structure of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Copper atom in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) (pdb code 4zk8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 25 binding sites of Copper where determined in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined), PDB code: 4zk8:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:9.4 occ:0.95 ND1 A:HIS143 2.0 10.2 1.0 ND1 A:HIS95 2.0 9.1 1.0 SG A:CYS135 2.2 9.6 1.0 SD A:MET148 2.6 10.5 1.0 CE1 A:HIS143 2.9 10.9 1.0 CE1 A:HIS95 3.0 9.2 1.0 CG A:HIS95 3.1 9.7 1.0 CG A:HIS143 3.1 10.4 1.0 CB A:CYS135 3.2 9.0 1.0 CB A:HIS95 3.4 9.5 1.0 CB A:HIS143 3.4 10.1 1.0 CE A:MET148 3.4 11.4 1.0 CA A:HIS95 3.7 9.4 1.0 O A:PRO94 4.0 10.2 1.0 NE2 A:HIS143 4.1 10.8 1.0 NE2 A:HIS95 4.1 9.7 1.0 CG A:MET148 4.1 9.9 1.0 CD2 A:HIS95 4.2 10.3 1.0 CD2 A:HIS143 4.2 10.3 1.0 CB A:THR137 4.3 9.5 1.0 OG1 A:THR137 4.3 10.4 1.0 N A:SER96 4.5 9.7 1.0 CA A:HIS143 4.5 9.7 1.0 CB A:MET148 4.5 8.9 1.0 CA A:CYS135 4.6 8.3 1.0 CE3 A:TRP63 4.6 9.2 1.0 C A:HIS95 4.7 9.8 1.0 N A:HIS95 4.7 10.6 1.0 C A:PRO94 4.8 10.7 1.0

Copper binding site 2 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:9.2 occ:0.95 NE2 A:HIS100 2.0 8.2 1.0 NE2 A:HIS134 2.0 9.0 1.0 CL A:CL419 2.2 13.0 0.7 O A:HOH507 2.3 18.3 0.5 CE1 A:HIS100 2.9 8.2 1.0 CD2 A:HIS134 2.9 8.8 1.0 CE1 A:HIS134 3.0 8.7 1.0 CD2 A:HIS100 3.0 8.7 1.0 OD2 A:ASP98 3.9 12.9 1.0 ND1 A:HIS100 4.0 8.0 1.0 ND1 A:HIS134 4.1 8.5 1.0 CG A:HIS134 4.1 7.6 1.0 CG A:HIS100 4.1 7.5 1.0 CG A:ASP98 4.4 10.9 1.0 OD1 A:ASP98 4.6 11.0 1.0 O A:HOH802 4.7 19.3 1.0 O A:HOH691 4.7 11.9 1.0

Copper binding site 3 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:9.9 occ:0.80 ND1 A:HIS83 2.0 11.1 1.0 NE2 A:HIS42 2.0 11.5 1.0 O A:HOH750 2.3 13.7 1.0 CE1 A:HIS83 2.8 11.7 1.0 CE1 A:HIS42 3.0 11.0 1.0 CD2 A:HIS42 3.0 11.5 1.0 CG A:HIS83 3.1 10.5 1.0 CB A:HIS83 3.5 10.3 1.0 NE2 A:HIS83 4.0 12.2 1.0 O A:HOH683 4.1 17.7 1.0 ND1 A:HIS42 4.1 11.4 1.0 CD2 A:HIS83 4.2 13.7 1.0 CG A:HIS42 4.2 10.2 1.0 O A:HOH785 4.4 15.4 1.0 CG2 A:VAL36 4.7 12.4 1.0

Copper binding site 4 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:18.1 occ:0.30 O A:HOH646 1.8 35.3 1.0 OE1 A:GLU226 2.0 18.0 1.0 O A:HOH720 2.2 28.1 0.5 O A:HOH760 2.8 37.4 1.0 CD A:GLU226 3.0 16.5 1.0 CG A:GLU226 3.2 14.0 1.0 NH1 A:ARG168 4.0 20.8 1.0 OE2 A:GLU226 4.1 14.1 1.0 CB A:ASP167 4.1 13.8 1.0 CD A:LYS223 4.2 34.0 1.0 CG A:ASP167 4.6 15.7 1.0 CB A:GLU226 4.6 13.5 1.0 O A:ASP167 4.7 16.1 1.0 CB A:LYS223 4.7 16.1 1.0 OD1 A:ASP167 4.9 19.6 1.0 CG A:LYS223 4.9 20.9 1.0 CE A:LYS223 5.0 48.0 1.0

Copper binding site 5 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:17.8 occ:0.30 OXT A:ACY427 1.8 34.0 1.0 O A:HOH520 2.0 21.8 0.3 OE2 A:GLU169 2.0 18.7 1.0 O A:HOH732 2.3 21.9 0.3 O4 A:MPD421 2.4 35.4 1.0 CD A:GLU169 2.7 16.2 1.0 OE1 A:GLU169 2.7 16.6 1.0 C A:ACY427 2.8 33.2 1.0 O A:ACY427 3.2 34.7 1.0 C4 A:MPD421 3.8 33.9 1.0 OH A:TYR231 3.9 15.2 1.0 O2 A:MPD421 3.9 35.7 1.0 CH3 A:ACY427 4.2 22.2 1.0 CG A:GLU169 4.2 15.7 1.0 C5 A:MPD421 4.2 28.4 1.0 O A:HOH597 4.3 23.5 1.0 C3 A:MPD421 4.5 28.7 1.0 O A:HOH700 4.5 31.5 0.7 O A:HOH681 4.7 31.6 0.5 C2 A:MPD421 4.8 25.2 1.0 CZ A:TYR231 4.9 11.5 1.0 NH1 A:ARG229 4.9 14.5 1.0 CE1 A:TYR231 5.0 11.5 1.0

Copper binding site 6 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:31.2 occ:0.30 CU A:CU406 0.0 31.2 0.3 CU A:CU406 1.4 17.2 0.1 CU A:CU417 2.2 33.0 0.3 OD2 A:ASP40 2.2 15.9 1.0 CU A:CU417 2.4 31.7 0.2 O A:HOH637 2.7 37.4 1.0 O A:HOH515 2.8 40.9 1.0 CG A:ASP40 2.9 14.3 1.0 OD1 A:ASP40 3.1 12.8 1.0 O A:HOH522 3.8 14.8 1.0 CB A:ASP40 4.3 11.7 1.0 O A:HIS39 4.9 11.6 0.5 O A:HIS39 5.0 11.5 0.5

Copper binding site 7 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:17.2 occ:0.10 CU A:CU406 0.0 17.2 0.1 CU A:CU406 1.4 31.2 0.3 O A:HOH515 1.6 40.9 1.0 OD1 A:ASP40 2.0 12.8 1.0 CU A:CU417 2.1 33.0 0.3 OD2 A:ASP40 2.2 15.9 1.0 CG A:ASP40 2.3 14.3 1.0 CU A:CU417 2.4 31.7 0.2 O A:HOH637 2.7 37.4 1.0 CB A:ASP40 3.8 11.7 1.0 O A:HOH791 4.0 37.6 1.0 NE2 A:HIS83 4.2 12.2 1.0 CB A:THR81 4.5 11.3 1.0 O A:HIS39 4.6 11.6 0.5 O A:HOH522 4.6 14.8 1.0 O A:HIS39 4.6 11.5 0.5 CE1 A:HIS83 4.7 11.7 1.0 CG2 A:THR81 4.7 12.3 1.0 CA A:ASP40 4.8 10.3 1.0 OG1 A:THR81 4.9 14.6 1.0

Copper binding site 8 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu407 b:16.6 occ:0.30 O A:HOH508 1.7 33.7 1.0 O A:HOH516 1.9 20.6 0.5 O A:HOH516 1.9 17.9 0.5 OD2 A:ASP251 2.0 13.5 0.5 CU A:CU408 2.2 18.0 0.1 CG A:ASP251 2.8 12.9 0.5 OD1 A:ASP251 2.9 14.4 0.5 NZ A:LYS227 3.7 23.0 1.0 O A:HOH509 3.9 31.1 0.5 OD2 A:ASP252 3.9 14.7 1.0 O A:HOH535 4.0 35.4 1.0 OE1 A:GLU165 4.0 40.7 0.8 OE1 A:GLU165 4.1 19.7 0.2 CB A:ASP251 4.1 12.3 0.5 CB A:ASP251 4.2 10.3 0.5 O A:HOH502 4.3 20.4 0.6 CG A:ASP251 4.5 17.2 0.5 O A:HOH518 4.6 16.8 1.0 CD A:GLU165 4.9 20.2 0.2 OE2 A:GLU165 4.9 22.0 0.2 OD1 A:ASP251 4.9 17.5 0.5 OD2 A:ASP251 4.9 23.6 0.5 CU A:CU412 4.9 34.9 0.5 O A:HOH727 4.9 17.1 0.3 CG A:ASP252 5.0 13.2 1.0

Copper binding site 9 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu408 b:18.0 occ:0.10 OD1 A:ASP251 2.1 14.4 0.5 O A:HOH535 2.1 35.4 1.0 CU A:CU407 2.2 16.6 0.3 O A:HOH516 2.6 17.9 0.5 O A:HOH508 2.8 33.7 1.0 CG A:ASP251 2.9 12.9 0.5 OD2 A:ASP251 3.1 13.5 0.5 O A:HOH502 3.6 20.4 0.6 O A:HOH516 3.6 20.6 0.5 O A:HOH696 3.6 21.2 1.0 OD2 A:ASP252 4.2 14.7 1.0 O A:ASP251 4.3 10.9 0.5 CB A:ASP251 4.3 12.3 0.5 O A:ASP251 4.3 10.4 0.5 NE2 A:GLN264 4.4 19.2 0.5 CB A:ASP251 4.4 10.3 0.5 OE1 A:GLN264 4.6 21.9 0.5 OD1 A:ASP252 4.7 14.9 1.0 CA A:ASP251 4.8 10.4 0.5 C A:ASP251 4.8 10.2 0.5 C A:ASP251 4.8 10.0 0.5 CA A:ASP251 4.8 9.8 0.5 CG A:ASP252 4.8 13.2 1.0 CG A:ASP251 5.0 17.2 0.5 O A:HOH502 5.0 20.0 0.4

Copper binding site 10 out of 25 in the Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Copper-Containing Nitrite Reductase From Thermophilic Bacterium Geobacillus Thermodenitrificans (Re-Refined) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu409 b:16.4 occ:0.50 CU A:CU409 0.0 16.4 0.5 O A:HOH510 1.8 26.7 0.7 OD2 A:ASP55 1.8 14.2 1.0 O A:HOH786 1.9 19.4 0.5 O A:HOH526 2.1 32.0 1.0 CU A:CU409 2.6 21.4 0.3 O A:HOH673 2.7 21.1 0.5 CG A:ASP55 2.8 12.1 1.0 OD1 A:ASP55 3.1 17.0 1.0 O A:HOH778 3.9 28.3 0.5 CB A:ASP55 4.1 11.1 1.0 O A:LYS56 4.3 17.8 0.5 O A:LYS56 4.3 11.2 0.5 CE1 A:TYR193 4.5 13.8 1.0 O A:HOH523 4.5 14.3 0.5 OH A:TYR193 4.6 19.0 1.0 N A:LYS56 4.6 10.6 0.5 N A:LYS56 4.7 11.7 0.5 CE A:LYS58 4.9 17.9 0.3 CG A:LYS58 4.9 13.1 0.3

Y.Fukuda, K.M.Tse, M.Lintuluoto, Y.Fukunishi, E.Mizohata, H.Matsumura, H.Takami, M.Nojiri, T.Inoue. Structural Insights Into the Function of A Thermostable Copper-Containing Nitrite Reductase J.Biochem. V. 155 123 2014.
ISSN: ISSN 0021-924X
PubMed: 24293549
DOI: 10.1093/JB/MVT107