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

Protein crystallography data

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

Copper Binding Sites:

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 4ysq

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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 4ysq

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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 4ysq

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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 4ysq

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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 4ysq

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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 4ysq

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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 4ysq

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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

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 11:16:23 2020

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