Copper in PDB 4ysu: Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 Mgy

The structure of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 Mgy, PDB code: 4ysu 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)	42.94 / 1.50
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.213, 115.213, 84.385, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 20.8

The binding sites of Copper atom in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 Mgy (pdb code 4ysu). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 Mgy, PDB code: 4ysu:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 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 - 25.0 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:10.8 occ:0.90 ND1 A:HIS143 2.0 13.3 1.0 ND1 A:HIS95 2.0 9.7 1.0 SG A:CYS135 2.2 11.4 1.0 SD A:MET148 2.7 15.0 1.0 CE1 A:HIS143 2.9 13.9 1.0 CE1 A:HIS95 3.0 11.0 1.0 CG A:HIS143 3.1 11.1 1.0 CG A:HIS95 3.1 9.9 1.0 CB A:CYS135 3.2 12.1 1.0 CB A:HIS143 3.4 10.3 1.0 CB A:HIS95 3.5 10.9 1.0 CE A:MET148 3.5 13.3 1.0 CA A:HIS95 3.8 10.1 1.0 O A:PRO94 4.0 11.1 1.0 NE2 A:HIS143 4.1 12.4 1.0 NE2 A:HIS95 4.1 12.5 1.0 CD2 A:HIS143 4.1 12.9 1.0 CD2 A:HIS95 4.2 10.9 1.0 CG A:MET148 4.2 9.9 1.0 CB A:THR137 4.3 12.5 1.0 OG1 A:THR137 4.4 11.9 1.0 CA A:HIS143 4.5 10.5 1.0 N A:SER96 4.5 12.3 1.0 CB A:MET148 4.6 10.4 1.0 CA A:CYS135 4.6 10.6 1.0 CE3 A:TRP63 4.6 9.4 1.0 C A:HIS95 4.7 12.5 1.0 N A:HIS95 4.7 10.5 1.0 C A:PRO94 4.8 11.7 1.0

Copper binding site 2 out of 5 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 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 - 25.0 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:10.6 occ:0.90 NE2 A:HIS134 2.0 10.2 1.0 NE2 A:HIS100 2.0 10.9 1.0 O A:HOH701 2.3 19.6 1.0 CE1 A:HIS100 2.9 12.6 1.0 CD2 A:HIS134 3.0 9.6 1.0 CE1 A:HIS134 3.0 10.7 1.0 CD2 A:HIS100 3.1 9.2 1.0 OD2 A:ASP98 3.8 23.6 1.0 ND1 A:HIS100 4.1 10.9 1.0 CG A:HIS134 4.1 7.1 1.0 ND1 A:HIS134 4.1 8.3 1.0 CG A:HIS100 4.2 10.0 1.0 CG A:ASP98 4.4 15.2 1.0 O A:HOH729 4.4 30.5 1.0 OD1 A:ASP98 4.6 16.9 1.0 O A:HOH671 4.8 16.3 1.0 SD A:MET132 5.0 10.4 1.0

Copper binding site 3 out of 5 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 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 - 25.0 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:25.4 occ:0.75 NE2 A:HIS42 2.0 18.6 1.0 ND1 A:HIS83 2.2 26.8 1.0 O A:HOH652 2.6 35.5 1.0 CD2 A:HIS42 2.9 17.0 1.0 CE1 A:HIS83 2.9 36.6 1.0 CG A:HIS83 2.9 22.1 1.0 CE1 A:HIS42 3.0 22.2 1.0 CB A:HIS83 3.4 14.3 1.0 NE2 A:HIS83 3.7 26.6 1.0 CD2 A:HIS83 3.8 27.5 1.0 O A:HOH539 4.0 31.7 0.7 CG A:HIS42 4.0 13.9 1.0 ND1 A:HIS42 4.1 19.8 1.0 O A:HOH726 4.3 27.7 1.0 O A:HOH737 4.4 27.0 1.0 CG2 A:VAL36 4.5 16.7 1.0 CA A:HIS83 5.0 10.7 1.0

Copper binding site 4 out of 5 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 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 - 25.0 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:36.9 occ:0.30 NE2 A:HIS39 2.2 25.0 1.0 CD2 A:HIS39 3.0 23.6 1.0 CE1 A:HIS39 3.2 25.1 1.0 CG A:HIS39 4.2 23.4 1.0 ND1 A:HIS39 4.3 22.2 1.0 CB A:PRO38 4.6 18.4 1.0 O A:HOH694 4.7 44.1 1.0

Copper binding site 5 out of 5 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 25.0 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 - 25.0 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:29.9 occ:0.30 O A:HOH501 2.1 43.6 1.0 OD2 A:ASP167 2.3 19.6 1.0 O A:HOH731 2.4 14.7 0.3 CG A:ASP167 3.0 17.3 1.0 OD1 A:ASP167 3.1 24.8 1.0 O A:HOH731 3.6 37.2 0.5 O A:GLY225 4.0 16.9 1.0 N A:LYS227 4.1 12.8 1.0 O A:GLU165 4.2 21.5 1.0 CA A:GLU226 4.5 16.8 1.0 CB A:ASP167 4.5 17.1 1.0 C A:GLU226 4.7 16.4 1.0 CB A:LYS227 4.8 16.6 1.0 C A:GLY225 4.9 13.9 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