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Copper in PDB 3x1e: Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride

Protein crystallography data

The structure of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride, PDB code: 3x1e was solved by Y.Fukuda, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.34 / 1.25
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 114.880, 114.880, 84.233, 90.00, 90.00, 120.00
R / Rfree (%) 14.1 / 17.1

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride (pdb code 3x1e). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 10 binding sites of Copper where determined in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride, PDB code: 3x1e:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 10 in 3x1e

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Copper binding site 1 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


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Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:9.3
occ:0.90
 ND1 A:HIS143 2.0 10.4 1.0
ND1 A:HIS95 2.1 9.3 1.0
SG A:CYS135 2.2 10.3 1.0
SD A:MET148 2.6 11.9 1.0
CE1 A:HIS143 2.9 8.6 1.0
CE1 A:HIS95 3.0 9.4 1.0
CG A:HIS143 3.1 11.0 1.0
CG A:HIS95 3.1 9.9 1.0
CB A:CYS135 3.1 7.8 1.0
CB A:HIS95 3.5 10.6 1.0
CB A:HIS143 3.5 11.4 1.0
CE A:MET148 3.5 11.9 1.0
CA A:HIS95 3.7 9.5 1.0
O A:PRO94 4.0 10.2 1.0
NE2 A:HIS143 4.0 9.5 1.0
NE2 A:HIS95 4.1 10.4 1.0
CD2 A:HIS143 4.1 9.6 1.0
CG A:MET148 4.2 11.0 1.0
CD2 A:HIS95 4.2 10.3 1.0
CB A:THR137 4.3 10.7 1.0
OG1 A:THR137 4.3 11.4 1.0
N A:SER96 4.5 9.1 1.0
CA A:HIS143 4.5 10.5 1.0
CA A:CYS135 4.6 8.4 1.0
CB A:MET148 4.6 8.4 1.0
CE3 A:TRP63 4.6 9.6 1.0
C A:HIS95 4.7 10.6 1.0
N A:HIS95 4.8 10.4 1.0
C A:PRO94 4.8 10.5 1.0

Copper binding site 2 out of 10 in 3x1e

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Copper binding site 2 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


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Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:8.1
occ:0.90
 NE2 A:HIS100 2.0 7.7 1.0
NE2 A:HIS134 2.1 8.4 1.0
O A:HOH841 2.2 22.3 0.8
O A:HOH503 2.3 13.2 1.0
CE1 A:HIS100 2.9 7.4 1.0
CD2 A:HIS134 3.0 8.6 1.0
CD2 A:HIS100 3.0 6.3 1.0
CE1 A:HIS134 3.1 8.2 1.0
CU A:CU407 3.9 10.5 0.1
OD2 A:ASP98 3.9 12.5 1.0
ND1 A:HIS100 4.0 6.7 1.0
CG A:HIS100 4.1 6.3 1.0
ND1 A:HIS134 4.2 8.9 1.0
CG A:HIS134 4.2 7.0 1.0
CG A:ASP98 4.4 10.8 1.0
O A:HOH838 4.6 20.7 1.0
OD1 A:ASP98 4.6 12.2 1.0
O A:HOH837 4.7 11.3 0.9

Copper binding site 3 out of 10 in 3x1e

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Copper binding site 3 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


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Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:12.0
occ:0.75
 ND1 A:HIS83 2.0 13.1 1.0
NE2 A:HIS42 2.1 13.4 1.0
O A:HOH543 2.3 20.2 1.0
O A:HOH765 2.3 28.0 1.0
CE1 A:HIS83 2.8 14.5 1.0
CE1 A:HIS42 3.0 13.0 1.0
CD2 A:HIS42 3.0 13.3 1.0
CG A:HIS83 3.1 12.2 1.0
CB A:HIS83 3.5 10.5 1.0
NE2 A:HIS83 4.0 13.7 1.0
O A:HOH620 4.1 23.1 1.0
ND1 A:HIS42 4.1 11.5 1.0
CD2 A:HIS83 4.1 14.2 1.0
CG A:HIS42 4.1 11.2 1.0
O A:HOH583 4.3 15.0 1.0
O A:HOH707 4.5 33.8 1.0
CG2 A:VAL36 4.6 11.8 1.0
O A:HOH818 4.7 19.4 1.0

Copper binding site 4 out of 10 in 3x1e

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Copper binding site 4 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


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-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:24.0
occ:0.30
 NE2 A:HIS39 1.9 24.1 1.0
CE1 A:HIS39 2.9 21.4 1.0
CD2 A:HIS39 2.9 15.1 1.0
O A:HOH858 3.0 46.6 0.3
ND1 A:HIS39 4.0 14.8 1.0
CG A:HIS39 4.1 13.7 1.0
CB A:PRO38 4.7 14.7 1.0

Copper binding site 5 out of 10 in 3x1e

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Copper binding site 5 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


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-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:13.7
occ:0.30
 O A:HOH738 1.7 38.3 1.0
OD2 A:ASP167 2.0 15.4 1.0
O A:HOH815 2.1 28.6 0.5
O A:HOH859 2.1 34.2 0.5
O A:HOH737 2.2 38.7 1.0
CG A:ASP167 2.8 15.8 1.0
OD1 A:ASP167 2.9 21.4 1.0
O A:HOH791 2.9 56.8 1.0
O A:HOH859 3.5 41.0 0.5
O A:HOH805 3.7 26.3 0.3
O A:GLU165 4.0 15.7 1.0
N A:LYS227 4.1 12.4 1.0
O A:GLY225 4.1 15.2 1.0
CB A:ASP167 4.2 13.9 1.0
O A:HOH809 4.3 23.4 0.3
CA A:GLU226 4.5 12.0 1.0
C A:GLU226 4.7 11.3 1.0
CB A:LYS227 4.8 12.8 1.0
C A:GLY225 5.0 13.3 1.0

Copper binding site 6 out of 10 in 3x1e

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Copper binding site 6 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


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Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:20.3
occ:0.30
 CU A:CU406 0.0 20.3 0.3
O A:HOH816 1.8 38.5 1.0
O A:HOH842 1.9 18.1 1.0
OE2 A:GLU239 2.3 26.3 1.0
CU A:CU406 2.4 36.7 0.3
O A:HOH868 2.4 17.0 0.3
OE1 A:GLU239 3.0 15.1 1.0
CD A:GLU239 3.0 12.5 1.0
CD A:PRO191 3.7 9.8 1.0
O A:HOH615 3.8 18.2 0.7
O A:HOH646 4.1 31.8 1.0
O A:HOH660 4.1 26.4 1.0
NE2 A:HIS298 4.1 8.2 1.0
O A:HOH502 4.3 16.6 1.0
CG A:GLU239 4.3 9.3 1.0
CG1 A:VAL190 4.4 12.8 1.0
CA A:VAL190 4.5 8.5 1.0
CG A:PRO191 4.5 11.1 1.0
CB A:VAL190 4.7 9.4 1.0
CE1 A:HIS298 4.8 8.3 1.0
N A:PRO191 4.9 9.6 1.0

Copper binding site 7 out of 10 in 3x1e

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Copper binding site 7 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


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-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:36.7
occ:0.30
 CU A:CU406 0.0 36.7 0.3
O A:HOH615 1.5 18.2 0.7
OE2 A:GLU239 2.0 26.3 1.0
O A:HOH816 2.1 38.5 1.0
CU A:CU406 2.4 20.3 0.3
CD A:GLU239 3.1 12.5 1.0
O A:HOH868 3.1 17.0 0.3
OE1 A:GLU239 3.5 15.1 1.0
O A:HOH646 3.7 31.8 1.0
CD A:PRO191 3.9 9.8 1.0
OH A:TYR178 4.0 7.8 1.0
O A:GLY189 4.1 10.6 1.0
CG A:GLU239 4.1 9.3 1.0
O A:HOH842 4.1 18.1 1.0
O A:HOH537 4.2 11.9 1.0
CB A:ASN238 4.3 6.5 1.0
O A:HOH565 4.4 19.7 1.0
CA A:VAL190 4.6 8.5 1.0
N A:PRO191 4.8 9.6 1.0
CG A:PRO191 4.9 11.1 1.0
ND2 A:ASN238 4.9 9.5 1.0

Copper binding site 8 out of 10 in 3x1e

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Copper binding site 8 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:10.5
occ:0.10
 O A:HOH837 1.3 11.3 0.9
O A:HOH841 2.5 22.3 0.8
CD2 A:HIS100 2.9 6.3 1.0
NE2 A:HIS100 3.3 7.7 1.0
O A:HOH604 3.5 14.2 0.7
OD1 A:ASP98 3.7 12.2 1.0
CG A:HIS100 3.7 6.3 1.0
OD2 A:ASP98 3.8 12.5 1.0
O A:HOH604 3.8 9.8 0.3
CU A:CU402 3.9 8.1 0.9
CE1 A:HIS100 4.1 7.4 1.0
CG A:ASP98 4.2 10.8 1.0
O A:HOH532 4.2 10.4 1.0
ND1 A:HIS100 4.2 6.7 1.0
CA A:HIS100 4.2 8.2 1.0
O A:HOH503 4.3 13.2 1.0
CB A:HIS100 4.3 7.2 1.0
N A:HIS100 4.9 7.2 1.0

Copper binding site 9 out of 10 in 3x1e

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Copper binding site 9 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu408

b:17.8
occ:0.20
 O A:HOH539 2.0 9.9 1.0
O A:VAL249 2.1 10.7 1.0
N A:VAL249 2.1 8.1 1.0
OG1 A:THR248 2.1 10.3 1.0
C A:VAL249 2.7 10.4 1.0
CA A:VAL249 2.8 8.4 1.0
C A:THR248 3.1 7.8 1.0
CB A:THR248 3.2 9.7 1.0
CB A:VAL249 3.3 9.8 1.0
CA A:THR248 3.3 8.5 1.0
CG2 A:THR248 4.0 11.4 1.0
N A:PHE250 4.0 7.9 1.0
O A:THR282 4.1 13.1 1.0
CB A:PHE281 4.2 9.6 1.0
CG2 A:VAL249 4.2 12.5 1.0
N A:THR282 4.2 10.5 1.0
O A:THR248 4.3 9.5 1.0
OD1 A:ASP251 4.4 16.1 1.0
CA A:PHE281 4.6 9.2 1.0
CG1 A:VAL249 4.6 9.9 1.0
CA A:PHE250 4.7 7.6 1.0
N A:THR248 4.7 7.8 1.0
N A:ASP251 4.9 9.3 1.0
C A:PHE250 4.9 8.4 1.0
C A:PHE281 4.9 9.7 1.0
CG A:ASP251 4.9 13.3 1.0

Copper binding site 10 out of 10 in 3x1e

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Copper binding site 10 out of 10 in the Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans Without Chloride within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu409

b:26.2
occ:0.20
 ND1 A:HIS262 2.3 16.3 0.5
O A:HOH701 2.8 37.6 1.0
CE1 A:HIS262 3.2 13.7 0.5
CG A:HIS262 3.3 11.3 0.5
ND1 A:HIS262 3.4 14.3 0.5
CG A:HIS262 3.5 14.6 0.5
CB A:HIS262 3.6 10.3 0.5
CB A:HIS262 3.6 12.1 0.5
O A:HIS262 3.9 13.8 0.5
CE1 A:HIS262 4.0 13.8 0.5
CD2 A:HIS262 4.3 13.3 0.5
OE1 A:GLN264 4.3 29.3 1.0
NE2 A:HIS262 4.3 11.7 0.5
O A:HOH746 4.4 34.3 1.0
CD2 A:HIS262 4.4 11.3 0.5
O A:HIS262 4.5 13.2 0.5
NE2 A:HIS262 4.5 15.6 0.5
C A:HIS262 4.7 12.0 0.5
CA A:HIS262 4.8 8.9 0.5
CA A:HIS262 4.8 9.2 0.5
C A:HIS262 4.8 11.4 0.5

Reference:

Y.Fukuda, T.Inoue. Structural Evidence of the Flexibility of the Cum Site To Be Published.
Page generated: Wed Jul 31 02:24:47 2024

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