Copper in PDB 4ysr: Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy

The structure of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy, PDB code: 4ysr 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)	50.00 / 1.34
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.047, 115.047, 84.335, 90.00, 90.00, 120.00
R / Rfree (%)	14.3 / 17.4

The binding sites of Copper atom in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy (pdb code 4ysr). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 7 binding sites of Copper where determined in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy, PDB code: 4ysr:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:9.8 occ:0.90 ND1 A:HIS143 2.0 11.0 1.0 ND1 A:HIS95 2.0 9.5 1.0 SG A:CYS135 2.3 10.2 1.0 SD A:MET148 2.6 12.3 1.0 CE1 A:HIS143 2.9 11.3 1.0 CE1 A:HIS95 3.0 9.7 1.0 CG A:HIS143 3.1 9.7 1.0 CG A:HIS95 3.1 9.3 1.0 CB A:CYS135 3.2 10.0 1.0 CB A:HIS143 3.5 10.5 1.0 CE A:MET148 3.5 10.0 1.0 CB A:HIS95 3.5 9.4 1.0 CA A:HIS95 3.7 9.2 1.0 O A:PRO94 4.0 11.7 1.0 NE2 A:HIS143 4.0 11.9 1.0 NE2 A:HIS95 4.1 9.7 1.0 CG A:MET148 4.1 10.8 1.0 CD2 A:HIS143 4.2 10.1 1.0 CD2 A:HIS95 4.2 10.1 1.0 CB A:THR137 4.3 10.7 1.0 OG1 A:THR137 4.4 11.8 1.0 N A:SER96 4.5 10.8 1.0 CA A:HIS143 4.5 9.6 1.0 CE3 A:TRP63 4.6 9.4 1.0 CA A:CYS135 4.6 8.7 1.0 CB A:MET148 4.6 10.0 1.0 C A:HIS95 4.7 9.9 1.0 N A:HIS95 4.7 10.5 1.0 C A:PRO94 4.8 10.0 1.0 CZ3 A:TRP63 5.0 11.8 1.0

Copper binding site 2 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:9.1 occ:0.90 NE2 A:HIS134 2.0 9.8 1.0 NE2 A:HIS100 2.1 8.4 1.0 O A:HOH734 2.3 12.8 1.0 CD2 A:HIS134 2.9 9.2 1.0 CE1 A:HIS100 3.0 7.4 1.0 CE1 A:HIS134 3.0 9.7 1.0 CD2 A:HIS100 3.1 7.6 1.0 OD2 A:ASP98 3.9 16.1 1.0 CG A:HIS134 4.1 7.4 1.0 ND1 A:HIS134 4.1 8.8 1.0 ND1 A:HIS100 4.1 9.1 1.0 CG A:HIS100 4.2 8.1 1.0 CG A:ASP98 4.4 12.3 1.0 O A:HOH755 4.5 22.3 1.0 OD1 A:ASP98 4.6 13.2 1.0 O A:HOH667 4.7 14.7 1.0 SD A:MET132 5.0 8.4 1.0

Copper binding site 3 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:18.4 occ:0.80 ND1 A:HIS83 2.0 14.5 1.0 NE2 A:HIS42 2.1 14.4 1.0 O A:HOH735 2.6 28.4 1.0 CE1 A:HIS83 2.8 18.2 1.0 CD2 A:HIS42 3.0 15.1 1.0 CE1 A:HIS42 3.0 17.9 1.0 CG A:HIS83 3.1 14.2 1.0 CB A:HIS83 3.5 13.0 1.0 NE2 A:HIS83 3.9 16.2 1.0 CD2 A:HIS83 4.0 20.7 1.0 ND1 A:HIS42 4.1 16.1 1.0 CG A:HIS42 4.1 12.4 1.0 O A:HOH685 4.2 30.5 1.0 O A:HOH746 4.3 21.0 1.0 O A:HOH754 4.6 23.1 1.0 CG2 A:VAL36 4.6 14.2 1.0 O A:HOH768 4.7 38.1 1.0

Copper binding site 4 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:32.0 occ:0.30 NE2 A:HIS39 2.0 20.1 1.0 CE1 A:HIS39 3.0 20.7 1.0 CD2 A:HIS39 3.0 19.4 1.0 ND1 A:HIS39 4.1 16.3 1.0 CG A:HIS39 4.1 16.5 1.0 CB A:PRO38 4.6 16.0 1.0

Copper binding site 5 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:23.2 occ:0.30 OD2 A:ASP167 2.1 15.5 1.0 O A:HOH518 2.1 34.8 1.0 CG A:ASP167 2.9 15.6 1.0 OD1 A:ASP167 3.0 21.2 1.0 O A:GLY225 4.1 15.5 1.0 N A:LYS227 4.1 12.1 1.0 O A:GLU165 4.1 17.2 1.0 CB A:ASP167 4.3 13.8 1.0 CA A:GLU226 4.4 13.1 1.0 C A:GLU226 4.8 12.2 1.0 CB A:LYS227 4.8 14.7 1.0 C A:GLY225 4.9 14.0 1.0

Copper binding site 6 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:24.0 occ:0.20 N A:VAL249 2.1 10.4 1.0 O A:VAL249 2.1 12.6 1.0 O A:HOH539 2.1 11.9 1.0 OG1 A:THR248 2.2 11.7 1.0 CA A:VAL249 2.8 10.2 1.0 C A:VAL249 2.8 11.6 1.0 C A:THR248 3.1 10.8 1.0 CB A:VAL249 3.2 12.1 1.0 CB A:THR248 3.3 12.0 1.0 CA A:THR248 3.3 10.9 1.0 CG2 A:VAL249 4.0 15.6 1.0 N A:PHE250 4.1 9.2 1.0 CG2 A:THR248 4.1 13.1 1.0 O A:THR248 4.2 11.6 1.0 O A:THR282 4.2 13.0 1.0 CB A:PHE281 4.3 10.7 1.0 OD1 A:ASP251 4.3 16.6 1.0 N A:THR282 4.4 11.0 1.0 CG1 A:VAL249 4.6 12.0 1.0 CA A:PHE281 4.7 9.7 1.0 CA A:PHE250 4.8 8.9 1.0 N A:THR248 4.8 10.2 1.0 N A:ASP251 4.9 10.3 1.0 C A:PHE250 4.9 10.0 1.0 CG A:ASP251 5.0 15.2 1.0

Copper binding site 7 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.6 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu407 b:31.7 occ:0.30 O A:HOH577 2.0 18.8 1.0 OE2 A:GLU239 2.2 24.3 1.0 O A:HOH599 2.6 41.5 1.0 CD A:GLU239 3.0 17.5 1.0 OE1 A:GLU239 3.1 15.4 1.0 O A:HOH564 3.3 25.6 1.0 CD A:PRO191 3.5 9.7 1.0 O A:HOH748 3.9 31.9 1.0 CA A:VAL190 4.2 9.1 1.0 O A:HOH541 4.3 16.7 1.0 NE2 A:HIS298 4.3 9.9 1.0 CG1 A:VAL190 4.3 12.3 1.0 CG A:GLU239 4.3 12.5 1.0 O A:HOH699 4.4 27.0 1.0 CG A:PRO191 4.4 12.5 1.0 CB A:VAL190 4.5 11.0 1.0 N A:PRO191 4.7 8.8 1.0 CE1 A:HIS298 5.0 10.0 1.0 C A:VAL190 5.0 8.7 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