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Copper in PDB 4yss: Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 Mgy

Protein crystallography data

The structure of Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 Mgy, PDB code: 4yss was solved by Y.Fukuda, K.M.Tse, M.Suzuki, K.Diedrichs, 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) 33.23 / 1.50
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.098, 115.098, 84.305, 90.00, 90.00, 120.00
R / Rfree (%) 14.8 / 19.2

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 Mgy (pdb code 4yss). 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 - 16.7 Mgy, PDB code: 4yss:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7;

Copper binding site 1 out of 7 in 4yss

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Copper binding site 1 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 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 - 16.7 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:11.4
occ:0.90
ND1 A:HIS95 2.0 10.3 1.0
ND1 A:HIS143 2.0 12.7 1.0
SG A:CYS135 2.3 11.9 1.0
SD A:MET148 2.7 15.1 1.0
CE1 A:HIS95 2.9 13.0 1.0
CE1 A:HIS143 2.9 11.9 1.0
CG A:HIS143 3.1 12.2 1.0
CG A:HIS95 3.1 12.2 1.0
CB A:CYS135 3.2 9.8 1.0
CB A:HIS143 3.5 12.0 1.0
CB A:HIS95 3.5 11.3 1.0
CE A:MET148 3.5 12.2 1.0
CA A:HIS95 3.8 11.4 1.0
O A:PRO94 4.0 12.7 1.0
NE2 A:HIS95 4.1 13.8 1.0
NE2 A:HIS143 4.1 12.7 1.0
CD2 A:HIS143 4.1 13.1 1.0
CD2 A:HIS95 4.2 13.2 1.0
CG A:MET148 4.2 11.4 1.0
CB A:THR137 4.3 13.6 1.0
OG1 A:THR137 4.4 12.5 1.0
N A:SER96 4.5 10.5 1.0
CA A:HIS143 4.5 10.6 1.0
CE3 A:TRP63 4.6 9.4 1.0
CB A:MET148 4.6 10.5 1.0
CA A:CYS135 4.6 8.7 1.0
C A:HIS95 4.7 11.0 1.0
N A:HIS95 4.8 10.0 1.0
C A:PRO94 4.8 11.4 1.0
CZ3 A:TRP63 5.0 11.1 1.0

Copper binding site 2 out of 7 in 4yss

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Copper binding site 2 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 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 - 16.7 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:10.7
occ:0.90
NE2 A:HIS134 2.0 11.2 1.0
NE2 A:HIS100 2.0 12.7 1.0
O A:HOH730 2.3 19.8 1.0
CD2 A:HIS134 2.9 9.2 1.0
CE1 A:HIS100 2.9 14.2 1.0
CE1 A:HIS134 3.0 14.2 1.0
CD2 A:HIS100 3.1 12.0 1.0
OD2 A:ASP98 3.9 18.1 1.0
CG A:HIS134 4.1 7.9 1.0
ND1 A:HIS100 4.1 12.7 1.0
ND1 A:HIS134 4.1 11.1 1.0
CG A:HIS100 4.2 10.7 1.0
CG A:ASP98 4.4 14.2 1.0
O A:HOH755 4.5 25.9 1.0
OD1 A:ASP98 4.6 13.9 1.0
O A:HOH686 4.8 18.5 1.0
SD A:MET132 5.0 10.4 1.0

Copper binding site 3 out of 7 in 4yss

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Copper binding site 3 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 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 - 16.7 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:24.2
occ:0.75
NE2 A:HIS42 2.0 17.0 1.0
ND1 A:HIS83 2.1 22.8 1.0
O A:HOH718 2.6 33.4 1.0
CE1 A:HIS83 2.8 22.5 1.0
CD2 A:HIS42 2.9 16.8 1.0
CG A:HIS83 3.0 18.1 1.0
CE1 A:HIS42 3.0 21.8 1.0
CB A:HIS83 3.4 13.6 1.0
NE2 A:HIS83 3.8 22.6 1.0
CD2 A:HIS83 3.9 22.6 1.0
CG A:HIS42 4.0 14.4 1.0
ND1 A:HIS42 4.0 18.8 1.0
O A:HOH514 4.2 38.7 1.0
O A:HOH751 4.3 23.1 1.0
O A:HOH759 4.5 27.1 1.0
CG2 A:VAL36 4.5 15.3 1.0
CA A:HIS83 5.0 11.8 1.0

Copper binding site 4 out of 7 in 4yss

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Copper binding site 4 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 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 - 16.7 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:36.9
occ:0.30
NE2 A:HIS39 2.1 25.7 1.0
CE1 A:HIS39 3.0 23.0 1.0
CD2 A:HIS39 3.1 20.5 1.0
ND1 A:HIS39 4.2 20.9 1.0
CG A:HIS39 4.2 18.8 1.0
CB A:PRO38 4.7 19.1 1.0

Copper binding site 5 out of 7 in 4yss

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Copper binding site 5 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 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 - 16.7 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:28.6
occ:0.30
O A:HOH526 1.9 47.9 1.0
OD2 A:ASP167 2.2 17.9 1.0
O A:HOH631 2.7 18.0 0.3
CG A:ASP167 2.9 16.0 1.0
OD1 A:ASP167 3.0 25.9 1.0
O A:HOH733 3.2 27.8 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 19.2 1.0
CB A:ASP167 4.3 15.3 1.0
CA A:GLU226 4.5 14.6 1.0
O A:HOH599 4.5 29.9 0.5
C A:GLU226 4.8 13.0 1.0
CB A:LYS227 4.8 15.5 1.0
C A:GLY225 4.9 15.9 1.0

Copper binding site 6 out of 7 in 4yss

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Copper binding site 6 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 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 - 16.7 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:42.7
occ:0.30
O A:HOH576 2.3 19.9 1.0
OE2 A:GLU239 2.5 34.6 1.0
CD A:GLU239 3.2 21.9 1.0
O A:HOH507 3.2 29.0 1.0
OE1 A:GLU239 3.3 20.1 1.0
CD A:PRO191 3.5 11.3 1.0
O A:HOH746 3.5 34.6 1.0
CA A:VAL190 4.1 9.1 1.0
CG1 A:VAL190 4.2 12.3 1.0
O A:HOH549 4.3 17.8 1.0
CB A:VAL190 4.4 11.5 1.0
CG A:PRO191 4.5 13.1 1.0
NE2 A:HIS298 4.5 12.9 1.0
O A:HOH703 4.5 27.9 1.0
CG A:GLU239 4.5 17.3 1.0
N A:PRO191 4.6 10.0 1.0
O A:GLY189 4.8 12.8 1.0
C A:VAL190 4.9 9.1 1.0

Copper binding site 7 out of 7 in 4yss

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Copper binding site 7 out of 7 in the Structure of Copper Nitrite Reductase From Geobacillus Thermodenitrificans - 16.7 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 - 16.7 Mgy within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:29.4
occ:0.20
O A:HOH553 2.0 11.0 1.0
O A:VAL249 2.1 13.8 1.0
N A:VAL249 2.2 11.8 1.0
OG1 A:THR248 2.3 13.2 1.0
C A:VAL249 2.8 12.3 1.0
CA A:VAL249 2.9 12.0 1.0
C A:THR248 3.3 11.3 1.0
CB A:VAL249 3.3 13.2 1.0
CB A:THR248 3.4 13.0 1.0
CA A:THR248 3.5 11.3 1.0
N A:PHE250 4.1 11.1 1.0
CG2 A:VAL249 4.1 18.1 1.0
CG2 A:THR248 4.1 13.5 1.0
O A:THR282 4.2 13.9 1.0
OD1 A:ASP251 4.3 20.2 1.0
N A:THR282 4.3 10.4 1.0
CB A:PHE281 4.3 11.8 1.0
O A:THR248 4.4 12.3 1.0
CG1 A:VAL249 4.6 11.2 1.0
CA A:PHE281 4.8 9.8 1.0
CA A:PHE250 4.8 10.5 1.0
N A:ASP251 4.9 11.4 1.0
CG A:ASP251 4.9 16.5 1.0
N A:THR248 4.9 10.7 1.0

Reference:

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
Page generated: Sun Dec 13 11:16:26 2020

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