Copper in PDB 4yst: Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 Mgy

The structure of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 Mgy, PDB code: 4yst 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)	20.12 / 1.34
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	115.177, 115.177, 84.376, 90.00, 90.00, 120.00
R / Rfree (%)	15.5 / 18.5

The binding sites of Copper atom in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 Mgy (pdb code 4yst). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 Mgy, PDB code: 4yst:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 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 - 24.9 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:12.2 occ:0.90 ND1 A:HIS143 2.0 14.6 1.0 ND1 A:HIS95 2.1 12.2 1.0 SG A:CYS135 2.2 12.7 1.0 SD A:MET148 2.6 14.4 1.0 CE1 A:HIS143 3.0 12.3 1.0 CE1 A:HIS95 3.0 11.6 1.0 CG A:HIS143 3.1 12.7 1.0 CG A:HIS95 3.1 11.3 1.0 CB A:CYS135 3.2 11.6 1.0 CB A:HIS143 3.4 13.4 1.0 CE A:MET148 3.5 12.6 1.0 CB A:HIS95 3.5 11.7 1.0 CA A:HIS95 3.8 11.5 1.0 O A:PRO94 4.0 13.8 1.0 NE2 A:HIS143 4.1 13.7 1.0 CG A:MET148 4.1 16.1 1.0 NE2 A:HIS95 4.1 13.3 1.0 CD2 A:HIS143 4.1 13.6 1.0 CD2 A:HIS95 4.2 11.9 1.0 CB A:THR137 4.3 12.5 1.0 OG1 A:THR137 4.4 14.2 1.0 CA A:HIS143 4.5 10.8 1.0 N A:SER96 4.6 13.1 1.0 CB A:MET148 4.6 12.1 1.0 CE3 A:TRP63 4.6 11.9 1.0 CA A:CYS135 4.6 11.4 1.0 C A:HIS95 4.7 12.5 1.0 N A:HIS95 4.8 12.7 1.0 C A:PRO94 4.8 12.7 1.0 CZ3 A:TRP63 4.9 14.1 1.0

Copper binding site 2 out of 6 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 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 - 24.9 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:11.7 occ:0.90 NE2 A:HIS134 2.0 12.9 1.0 NE2 A:HIS100 2.0 10.8 1.0 O A:HOH722 2.3 14.6 1.0 CD2 A:HIS134 2.9 11.6 1.0 CE1 A:HIS100 3.0 11.0 1.0 CE1 A:HIS134 3.0 10.5 1.0 CD2 A:HIS100 3.1 10.2 1.0 OD2 A:ASP98 3.8 18.9 1.0 CG A:HIS134 4.1 10.5 1.0 ND1 A:HIS100 4.1 11.3 1.0 ND1 A:HIS134 4.1 11.8 1.0 CG A:HIS100 4.2 9.8 1.0 CG A:ASP98 4.4 13.7 1.0 O A:HOH744 4.5 28.8 1.0 OD1 A:ASP98 4.6 16.8 1.0 O A:HOH648 4.7 18.3 1.0 SD A:MET132 5.0 11.1 1.0

Copper binding site 3 out of 6 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 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 - 24.9 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:24.0 occ:0.80 NE2 A:HIS42 2.0 18.3 1.0 ND1 A:HIS83 2.0 15.3 0.7 O A:HOH501 2.4 9.3 0.2 O A:HOH720 2.6 27.8 0.8 CE1 A:HIS83 2.8 17.7 0.7 CE1 A:HIS42 3.0 19.7 1.0 CD2 A:HIS42 3.0 17.8 1.0 CG A:HIS83 3.0 15.2 0.3 CG A:HIS83 3.0 17.7 0.7 ND1 A:HIS83 3.1 20.8 0.3 CB A:HIS83 3.5 15.8 0.7 CB A:HIS83 3.5 15.4 0.3 CD2 A:HIS83 3.5 18.4 0.3 CE1 A:HIS83 3.5 15.8 0.3 NE2 A:HIS83 3.7 17.4 0.3 NE2 A:HIS83 3.9 20.6 0.7 CD2 A:HIS83 4.0 19.6 0.7 ND1 A:HIS42 4.0 17.9 1.0 CG A:HIS42 4.1 14.2 1.0 O A:HOH734 4.3 25.2 1.0 O A:HOH569 4.5 19.7 0.5 CG2 A:VAL36 4.5 15.9 1.0 O A:HOH758 4.8 45.7 1.0 CA A:HIS83 5.0 14.1 0.3 CA A:HIS83 5.0 13.5 0.7

Copper binding site 4 out of 6 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 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 - 24.9 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:36.0 occ:0.30 NE2 A:HIS39 2.0 23.2 1.0 CE1 A:HIS39 3.0 23.9 1.0 CD2 A:HIS39 3.0 22.0 1.0 ND1 A:HIS39 4.1 20.3 1.0 CG A:HIS39 4.1 19.8 1.0 CB A:PRO38 4.6 17.1 1.0 O A:HOH621 5.0 35.9 0.5

Copper binding site 5 out of 6 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 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 - 24.9 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:27.9 occ:0.30 OD2 A:ASP167 2.0 18.5 1.0 O A:HOH509 2.1 19.2 0.3 O A:HOH666 2.6 34.3 1.0 CG A:ASP167 2.8 19.0 1.0 OD1 A:ASP167 3.0 24.4 1.0 O A:HOH509 3.3 22.1 0.3 O A:GLY225 4.0 18.6 1.0 N A:LYS227 4.1 14.4 1.0 O A:GLU165 4.1 19.3 1.0 CB A:ASP167 4.3 16.8 1.0 CA A:GLU226 4.4 15.3 1.0 O A:HOH679 4.6 37.9 0.5 C A:GLU226 4.7 15.1 1.0 CB A:LYS227 4.7 16.1 1.0 C A:GLY225 4.9 16.6 1.0

Copper binding site 6 out of 6 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 24.9 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 - 24.9 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:30.9 occ:0.20 O A:HOH576 2.1 22.8 1.0 OE2 A:GLU239 2.2 28.2 1.0 CD A:GLU239 3.1 21.5 1.0 OE1 A:GLU239 3.3 19.1 1.0 O A:HOH580 3.3 25.8 1.0 CD A:PRO191 3.5 12.3 1.0 O A:HOH736 3.8 37.8 1.0 CA A:VAL190 4.2 10.6 1.0 CG1 A:VAL190 4.2 15.7 1.0 O A:HOH588 4.3 19.4 1.0 O A:HOH691 4.4 31.3 1.0 CG A:PRO191 4.4 15.6 1.0 CB A:VAL190 4.4 13.6 1.0 NE2 A:HIS298 4.4 12.7 1.0 CG A:GLU239 4.5 15.1 1.0 N A:PRO191 4.6 10.4 1.0 O A:GLY189 4.9 14.1 1.0 C A:VAL190 4.9 11.3 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