Copper in PDB 4yso: Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy

The structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy, PDB code: 4yso was solved by Y.Fukuda, K.M.Tse, M.Suzuki, K.Diederichs, K.Hirata, T.Nakane, M.Sugahara, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, H.Matsumura, T.Inoue, S.Iwata, E.Mizohata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.73 / 1.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.771, 114.771, 84.098, 90.00, 90.00, 120.00
R / Rfree (%)	12.9 / 17.7

The binding sites of Copper atom in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy (pdb code 4yso). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 7 binding sites of Copper where determined in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy, PDB code: 4yso:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:8.6 occ:0.90 ND1 A:HIS143 2.0 12.1 1.0 ND1 A:HIS95 2.0 9.8 1.0 SG A:CYS135 2.2 9.8 1.0 SD A:MET148 2.7 12.0 1.0 CE1 A:HIS143 2.9 11.8 1.0 CE1 A:HIS95 2.9 10.3 1.0 CG A:HIS143 3.0 10.5 1.0 CG A:HIS95 3.0 9.8 1.0 CB A:CYS135 3.2 9.1 1.0 CB A:HIS143 3.4 9.2 1.0 CB A:HIS95 3.4 9.6 1.0 CE A:MET148 3.6 10.6 1.0 CA A:HIS95 3.8 8.4 1.0 NE2 A:HIS143 4.0 10.0 1.0 O A:PRO94 4.0 9.2 1.0 NE2 A:HIS95 4.1 9.4 1.0 CD2 A:HIS143 4.1 9.9 1.0 CD2 A:HIS95 4.1 9.3 1.0 CG A:MET148 4.1 10.7 1.0 CB A:THR137 4.3 8.3 1.0 OG1 A:THR137 4.4 10.3 1.0 CA A:HIS143 4.4 8.1 1.0 N A:SER96 4.5 10.2 1.0 CB A:MET148 4.5 8.9 1.0 CA A:CYS135 4.6 8.8 1.0 CE3 A:TRP63 4.6 8.6 1.0 C A:HIS95 4.7 10.0 1.0 N A:HIS95 4.8 10.2 1.0 C A:PRO94 4.8 11.7 1.0 CZ3 A:TRP63 5.0 11.4 1.0

Copper binding site 2 out of 7 in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:8.7 occ:0.90 NE2 A:HIS100 2.1 7.5 1.0 NE2 A:HIS134 2.1 8.2 1.0 O A:HOH572 2.2 9.5 1.0 O A:HOH501 2.2 14.6 0.5 CE1 A:HIS100 3.0 7.4 1.0 CD2 A:HIS134 3.0 8.6 1.0 CE1 A:HIS134 3.1 9.6 1.0 CD2 A:HIS100 3.1 7.2 1.0 OD2 A:ASP98 3.9 12.2 1.0 ND1 A:HIS100 4.1 8.9 1.0 ND1 A:HIS134 4.2 8.1 1.0 CG A:HIS134 4.2 7.3 1.0 CG A:HIS100 4.2 6.9 1.0 O A:HOH588 4.4 19.2 1.0 CG A:ASP98 4.5 9.8 1.0 O A:HOH552 4.6 14.3 1.0 OD1 A:ASP98 4.7 10.7 1.0

Copper binding site 3 out of 7 in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:6.8 occ:0.80 NE2 A:HIS42 2.0 9.7 1.0 ND1 A:HIS83 2.0 9.1 1.0 O A:HOH554 2.0 14.1 1.0 O A:HOH566 2.2 12.4 1.0 CE1 A:HIS83 2.8 12.0 1.0 CE1 A:HIS42 3.0 11.9 1.0 CD2 A:HIS42 3.0 9.1 1.0 CG A:HIS83 3.1 9.5 1.0 CB A:HIS83 3.6 8.1 1.0 NE2 A:HIS83 4.0 9.1 1.0 O A:HOH559 4.1 16.2 1.0 ND1 A:HIS42 4.1 11.5 1.0 CG A:HIS42 4.2 7.6 1.0 CD2 A:HIS83 4.2 9.5 1.0 O A:HOH584 4.4 14.0 1.0 O A:HOH598 4.5 22.8 1.0 O A:HOH593 4.5 12.8 1.0 CG2 A:VAL36 4.7 10.1 1.0

Copper binding site 4 out of 7 in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:25.9 occ:0.30 NE2 A:HIS39 2.1 19.8 1.0 CD2 A:HIS39 3.0 15.8 1.0 CE1 A:HIS39 3.1 20.7 1.0 CG A:HIS39 4.2 11.7 1.0 ND1 A:HIS39 4.2 13.4 1.0 CB A:PRO38 4.7 13.2 1.0 O A:HOH758 4.8 29.2 0.3

Copper binding site 5 out of 7 in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:14.7 occ:0.30 O A:HOH701 1.9 16.9 0.5 O A:HOH832 2.0 27.4 0.5 OD2 A:ASP167 2.1 14.8 1.0 O A:HOH854 2.1 22.6 0.3 O A:HOH831 2.2 53.7 1.0 O A:HOH726 2.3 24.6 1.0 CG A:ASP167 2.8 14.5 1.0 OD1 A:ASP167 2.9 19.3 1.0 O A:HOH701 3.2 18.3 0.3 O A:GLU165 4.1 15.7 1.0 O A:GLY225 4.1 15.3 1.0 N A:LYS227 4.2 11.5 1.0 CB A:ASP167 4.3 13.8 1.0 CA A:GLU226 4.5 12.3 1.0 CB A:LYS227 4.8 13.7 1.0 C A:GLU226 4.8 11.3 1.0

Copper binding site 6 out of 7 in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:18.8 occ:0.20 O A:VAL249 1.9 9.3 1.0 O A:HOH516 2.0 10.5 1.0 N A:VAL249 2.1 8.3 1.0 OG1 A:THR248 2.2 9.7 1.0 C A:VAL249 2.6 8.8 1.0 CA A:VAL249 2.8 8.7 1.0 C A:THR248 3.2 8.5 1.0 CB A:THR248 3.3 10.6 1.0 CB A:VAL249 3.3 10.8 1.0 CA A:THR248 3.4 8.4 1.0 N A:PHE250 3.9 8.8 1.0 CG2 A:THR248 4.0 10.8 1.0 CG2 A:VAL249 4.1 12.8 1.0 CB A:PHE281 4.1 9.8 1.0 O A:THR282 4.2 12.0 1.0 N A:THR282 4.2 9.3 1.0 OD1 A:ASP251 4.3 14.3 1.0 O A:THR248 4.3 10.6 1.0 CG1 A:VAL249 4.5 9.5 1.0 CA A:PHE281 4.6 8.5 1.0 CA A:PHE250 4.6 6.8 1.0 N A:ASP251 4.7 8.7 1.0 C A:PHE250 4.8 7.2 1.0 CG A:ASP251 4.8 10.7 1.0 N A:THR248 4.8 9.0 1.0 C A:PHE281 4.9 10.1 1.0

Copper binding site 7 out of 7 in the Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 0.064 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu407 b:18.4 occ:0.30 O A:HOH517 1.7 38.7 1.0 O A:HOH521 1.8 15.4 1.0 OE2 A:GLU239 2.3 26.6 1.0 O A:HOH513 2.5 30.7 1.0 OE1 A:GLU239 3.0 14.6 1.0 CD A:GLU239 3.0 16.6 1.0 O A:HOH547 3.7 20.5 1.0 O A:HOH563 3.8 20.1 1.0 CD A:PRO191 3.8 10.5 1.0 O A:HOH578 3.8 32.8 1.0 NE2 A:HIS298 4.2 7.4 1.0 O A:HOH597 4.2 42.9 0.3 O A:HOH525 4.3 14.9 1.0 CG A:GLU239 4.4 11.2 1.0 CG1 A:VAL190 4.6 7.7 1.0 CG A:PRO191 4.7 10.7 1.0 CA A:VAL190 4.7 7.8 1.0 CE1 A:HIS298 4.8 9.0 1.0 CB A:VAL190 4.8 8.1 1.0

Y.Fukuda, K.M.Tse, M.Suzuki, K.Diederichs, K.Hirata, T.Nakane, M.Sugahara, E.Nango, K.Tono, Y.Joti, T.Kameshima, C.Song, T.Hatsui, M.Yabashi, O.Nureki, H.Matsumura, T.Inoue, S.Iwata, E.Mizohata. Redox-Coupled Structural Changes in Nitrite Reductase Revealed By Serial Femtosecond and Microfocus Crystallography J.Biochem. V. 159 527 2016.
ISSN: ISSN 0021-924X
PubMed: 26769972
DOI: 10.1093/JB/MVV133