Copper in PDB 4ysq: Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 Mgy

The structure of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 Mgy, PDB code: 4ysq 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)	34.35 / 1.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	114.951, 114.951, 84.225, 90.00, 90.00, 120.00
R / Rfree (%)	14 / 18.7

The binding sites of Copper atom in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 Mgy (pdb code 4ysq). 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 - 8.38 Mgy, PDB code: 4ysq:
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 - 8.38 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 - 8.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:14.0 occ:0.90 ND1 A:HIS95 2.0 15.9 1.0 ND1 A:HIS143 2.0 15.4 1.0 SG A:CYS135 2.2 14.7 1.0 SD A:MET148 2.7 17.6 1.0 CE1 A:HIS143 2.9 15.4 1.0 CE1 A:HIS95 2.9 17.9 1.0 CG A:HIS143 3.1 14.2 1.0 CG A:HIS95 3.1 14.2 1.0 CB A:CYS135 3.2 14.1 1.0 CB A:HIS143 3.5 13.1 1.0 CE A:MET148 3.5 15.6 1.0 CB A:HIS95 3.5 13.0 1.0 CA A:HIS95 3.8 12.6 1.0 O A:PRO94 4.0 15.0 1.0 NE2 A:HIS143 4.0 15.0 1.0 NE2 A:HIS95 4.0 14.8 1.0 CD2 A:HIS143 4.1 17.1 1.0 CD2 A:HIS95 4.2 14.8 1.0 CG A:MET148 4.2 14.3 1.0 CB A:THR137 4.3 13.8 1.0 OG1 A:THR137 4.3 14.9 1.0 N A:SER96 4.5 14.1 1.0 CA A:HIS143 4.5 12.5 1.0 CB A:MET148 4.6 13.4 1.0 CA A:CYS135 4.6 12.9 1.0 CE3 A:TRP63 4.6 13.3 1.0 C A:HIS95 4.7 14.2 1.0 N A:HIS95 4.7 14.1 1.0 C A:PRO94 4.8 13.7 1.0

Copper binding site 2 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 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 - 8.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:13.3 occ:0.90 NE2 A:HIS134 2.0 14.0 1.0 NE2 A:HIS100 2.1 15.1 1.0 O A:HOH740 2.3 21.9 1.0 CD2 A:HIS134 2.9 11.9 1.0 CE1 A:HIS100 3.0 14.1 1.0 CE1 A:HIS134 3.1 12.9 1.0 CD2 A:HIS100 3.1 11.9 1.0 OD2 A:ASP98 4.0 21.0 1.0 CG A:HIS134 4.1 13.0 1.0 ND1 A:HIS134 4.1 12.7 1.0 ND1 A:HIS100 4.1 14.4 1.0 CG A:HIS100 4.2 12.0 1.0 CG A:ASP98 4.4 16.6 1.0 O A:HOH771 4.5 25.8 1.0 OD1 A:ASP98 4.6 15.8 1.0 O A:HOH677 4.7 18.8 1.0

Copper binding site 3 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 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 - 8.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:20.9 occ:0.75 ND1 A:HIS83 2.0 20.6 1.0 NE2 A:HIS42 2.0 17.3 1.0 O A:HOH743 2.6 26.8 1.0 CE1 A:HIS83 2.8 26.5 1.0 CD2 A:HIS42 2.9 19.3 1.0 CG A:HIS83 3.0 19.7 1.0 CE1 A:HIS42 3.1 19.9 1.0 CB A:HIS83 3.4 14.9 1.0 NE2 A:HIS83 3.9 20.3 1.0 CD2 A:HIS83 4.0 20.8 1.0 CG A:HIS42 4.1 15.8 1.0 ND1 A:HIS42 4.1 21.2 1.0 O A:HOH698 4.2 37.0 1.0 O A:HOH761 4.4 24.4 1.0 O A:HOH774 4.5 24.1 1.0 CG2 A:VAL36 4.6 16.0 1.0 O A:HOH797 4.8 46.6 1.0 CA A:HIS83 5.0 15.3 1.0

Copper binding site 4 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 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 - 8.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:37.1 occ:0.30 NE2 A:HIS39 2.1 24.1 1.0 CD2 A:HIS39 3.0 22.0 1.0 CE1 A:HIS39 3.1 25.9 1.0 ND1 A:HIS39 4.2 23.3 1.0 CG A:HIS39 4.2 19.3 1.0 CB A:PRO38 4.6 20.4 1.0

Copper binding site 5 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 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 - 8.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:25.6 occ:0.30 O A:HOH655 1.9 26.0 0.5 OD2 A:ASP167 2.1 18.8 1.0 O A:HOH502 2.2 49.6 0.3 O A:HOH650 2.4 37.7 1.0 O A:HOH739 2.7 26.3 0.3 CG A:ASP167 2.8 19.4 1.0 OD1 A:ASP167 2.9 26.2 1.0 O A:HOH655 3.2 36.1 0.5 O A:GLY225 4.1 20.4 1.0 O A:GLU165 4.2 20.9 1.0 N A:LYS227 4.2 16.2 1.0 CB A:ASP167 4.3 20.8 1.0 CA A:GLU226 4.4 18.1 1.0 C A:GLU226 4.8 15.5 1.0 CB A:LYS227 4.8 18.4 1.0 C A:GLY225 4.9 18.3 1.0

Copper binding site 6 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 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 - 8.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:37.5 occ:0.30 O A:HOH599 2.2 23.1 1.0 OE2 A:GLU239 2.3 27.4 1.0 O A:HOH633 2.8 31.2 0.3 CD A:GLU239 3.1 22.6 1.0 O A:HOH529 3.2 30.3 1.0 OE1 A:GLU239 3.2 20.5 1.0 O A:HOH750 3.3 36.5 1.0 CD A:PRO191 3.5 14.7 1.0 CA A:VAL190 4.3 12.4 1.0 CG1 A:VAL190 4.3 14.6 1.0 O A:HOH726 4.3 32.0 1.0 CG A:GLU239 4.4 18.0 1.0 NE2 A:HIS298 4.4 13.8 1.0 CG A:PRO191 4.5 16.4 1.0 CB A:VAL190 4.5 14.3 1.0 N A:PRO191 4.7 12.3 1.0 O A:GLY189 4.9 15.2 1.0

Copper binding site 7 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 8.38 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 - 8.38 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu407 b:29.5 occ:0.20 N A:VAL249 2.1 12.8 1.0 O A:HOH570 2.1 15.2 1.0 O A:VAL249 2.1 14.8 1.0 OG1 A:THR248 2.2 15.1 1.0 C A:VAL249 2.8 15.3 1.0 CA A:VAL249 2.8 15.6 1.0 C A:THR248 3.1 17.3 1.0 CB A:VAL249 3.2 15.5 1.0 CB A:THR248 3.3 15.3 1.0 CA A:THR248 3.3 16.7 1.0 CG2 A:VAL249 4.0 20.4 1.0 N A:PHE250 4.1 13.2 1.0 CG2 A:THR248 4.1 18.4 1.0 O A:THR248 4.2 15.6 1.0 O A:THR282 4.2 17.1 1.0 OD1 A:ASP251 4.4 19.3 1.0 N A:THR282 4.4 14.1 1.0 CB A:PHE281 4.4 12.4 1.0 CG1 A:VAL249 4.5 15.4 1.0 N A:THR248 4.8 13.1 1.0 CA A:PHE281 4.8 12.8 1.0 CA A:PHE250 4.8 13.2 1.0 N A:ASP251 4.9 13.5 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