Copper in PDB 4ysa: Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans

The structure of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 4ysa 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)	34.75 / 1.43
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	116.197, 116.197, 85.553, 90.00, 90.00, 120.00
R / Rfree (%)	13.7 / 14.9

The structure of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Copper atom in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 4ysa). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 4ysa:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:20.4 occ:1.00 ND1 A:HIS143 1.9 21.5 1.0 ND1 A:HIS95 2.0 18.7 1.0 SG A:CYS135 2.3 20.9 1.0 SD A:MET148 2.7 21.7 1.0 CE1 A:HIS143 2.8 18.9 1.0 CE1 A:HIS95 2.9 19.4 1.0 CG A:HIS143 3.0 21.6 1.0 CG A:HIS95 3.1 21.4 1.0 CB A:CYS135 3.3 17.8 1.0 CB A:HIS95 3.4 17.5 1.0 CB A:HIS143 3.5 19.7 1.0 CE A:MET148 3.6 19.9 1.0 CA A:HIS95 3.8 21.6 1.0 NE2 A:HIS143 4.0 21.6 1.0 CD2 A:HIS143 4.1 19.9 1.0 O A:PRO94 4.1 22.7 1.0 NE2 A:HIS95 4.1 21.2 1.0 CG A:MET148 4.2 18.7 1.0 CD2 A:HIS95 4.2 22.9 1.0 CB A:THR137 4.4 21.6 1.0 OG1 A:THR137 4.4 22.1 1.0 CA A:HIS143 4.5 17.7 1.0 N A:SER96 4.6 23.3 1.0 CE3 A:TRP63 4.6 19.7 1.0 CB A:MET148 4.6 18.0 1.0 CA A:CYS135 4.7 19.8 1.0 C A:HIS95 4.8 25.6 1.0 N A:HIS95 4.8 21.9 1.0 C A:PRO94 4.8 22.8 1.0 CZ3 A:TRP63 4.9 20.3 1.0

Copper binding site 2 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:17.9 occ:0.95 NE2 A:HIS100 2.1 18.0 1.0 O A:HOH509 2.1 36.5 0.9 NE2 A:HIS134 2.1 16.4 1.0 O A:HOH620 2.3 31.4 1.0 CE1 A:HIS100 3.0 15.0 1.0 CD2 A:HIS134 3.1 18.0 1.0 CE1 A:HIS134 3.1 18.3 1.0 CD2 A:HIS100 3.1 18.0 1.0 NA A:NA408 3.2 32.2 0.4 CU A:CU407 3.6 35.3 0.2 OD2 A:ASP98 4.1 21.2 1.0 ND1 A:HIS100 4.1 16.5 1.0 ND1 A:HIS134 4.2 19.6 1.0 CG A:HIS134 4.2 14.0 1.0 CG A:HIS100 4.2 17.1 1.0 CG A:ASP98 4.5 21.1 1.0 O A:HOH574 4.6 30.8 0.8 O A:HOH626 4.6 37.9 1.0 OD1 A:ASP98 4.7 23.2 1.0

Copper binding site 3 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:32.5 occ:0.40 CU A:CU403 0.0 32.5 0.4 O A:HOH568 2.0 38.8 0.4 OD2 A:ASP167 2.0 26.1 1.0 CU A:CU403 2.0 34.5 0.2 O A:HOH533 2.0 38.4 0.4 CG A:ASP167 2.7 26.9 1.0 OD1 A:ASP167 2.9 32.8 1.0 O A:GLU165 4.0 27.0 1.0 CB A:ASP167 4.1 24.9 1.0 N A:LYS227 4.2 21.8 1.0 O A:GLY225 4.2 28.3 1.0 CA A:GLU226 4.5 25.3 1.0 C A:GLU226 4.8 22.1 1.0 CB A:LYS227 4.9 21.0 1.0

Copper binding site 4 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu403 b:34.5 occ:0.20 CU A:CU403 0.0 34.5 0.2 OD1 A:ASP167 1.9 32.8 1.0 CU A:CU403 2.0 32.5 0.4 O A:HOH568 2.7 38.8 0.4 CG A:ASP167 2.7 26.9 1.0 OD2 A:ASP167 2.9 26.1 1.0 O A:HOH533 3.2 38.4 0.4 CB A:ASP167 4.1 24.9 1.0 O A:GLU165 4.4 27.0 1.0 CA A:ASP167 4.8 29.2 1.0

Copper binding site 5 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu404 b:22.2 occ:1.00 NE2 A:HIS42 1.9 18.8 1.0 ND1 A:HIS83 2.0 20.4 1.0 O A:HOH572 2.1 33.2 1.0 O A:HOH612 2.3 34.4 1.0 CE1 A:HIS83 2.9 19.0 1.0 CE1 A:HIS42 2.9 18.5 1.0 CD2 A:HIS42 3.0 18.0 1.0 CG A:HIS83 3.2 18.7 1.0 CB A:HIS83 3.6 20.1 1.0 O A:HOH629 4.0 38.6 1.0 ND1 A:HIS42 4.0 18.9 1.0 NE2 A:HIS83 4.1 22.4 1.0 CG A:HIS42 4.1 16.8 1.0 O A:HOH592 4.2 36.7 1.0 CD2 A:HIS83 4.2 20.6 1.0 O A:HOH625 4.3 37.5 1.0 CG2 A:VAL36 4.7 26.7 1.0 O A:HOH630 4.8 35.0 0.5

Copper binding site 6 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu405 b:41.1 occ:0.30 NE2 A:HIS39 2.1 46.8 1.0 CE1 A:HIS39 3.1 39.4 1.0 CD2 A:HIS39 3.1 33.6 1.0 ND1 A:HIS39 4.2 38.8 1.0 CG A:HIS39 4.3 31.3 1.0 CB A:PRO38 4.8 28.5 1.0

Copper binding site 7 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu406 b:24.2 occ:0.25 O A:HOH631 2.4 34.5 1.0 SD A:MET270 2.7 35.9 1.0 CG A:MET270 2.9 37.2 1.0 O A:HOH633 2.9 66.1 0.2 CB A:MET270 3.7 20.4 1.0 CE A:MET270 4.4 32.2 1.0

Copper binding site 8 out of 8 in the Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Completely Oxidized Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu407 b:35.3 occ:0.20 O A:HOH574 1.4 30.8 0.8 O A:HOH509 2.2 36.5 0.9 CD2 A:HIS100 3.0 18.0 1.0 NE2 A:HIS100 3.2 18.0 1.0 CU A:CU402 3.6 17.9 0.9 OD1 A:ASP98 3.6 23.2 1.0 CG A:HIS100 3.7 17.1 1.0 OD2 A:ASP98 3.8 21.2 1.0 NA A:NA408 3.9 32.2 0.4 CE1 A:HIS100 4.0 15.0 1.0 CG A:ASP98 4.1 21.1 1.0 O A:HOH620 4.2 31.4 1.0 ND1 A:HIS100 4.3 16.5 1.0 O A:HOH529 4.3 34.1 1.0 CA A:HIS100 4.4 14.1 1.0 CB A:HIS100 4.5 15.4 1.0 N A:HIS100 5.0 18.0 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