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Copper in PDB 3wkq: Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate

Protein crystallography data

The structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate, PDB code: 3wkq 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) 26.25 / 1.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 114.981, 114.981, 84.431, 90.00, 90.00, 120.00
R / Rfree (%) 11.8 / 13.7

Other elements in 3wkq:

The structure of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate also contains other interesting chemical elements:

Sodium (Na) 1 atom

Copper Binding Sites:

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

Copper binding site 1 out of 6 in 3wkq

Go back to Copper Binding Sites List in 3wkq
Copper binding site 1 out of 6 in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:6.9
occ:0.90
 ND1 A:HIS143 2.0 8.1 1.0
ND1 A:HIS95 2.0 7.7 1.0
SG A:CYS135 2.2 7.1 1.0
SD A:MET148 2.6 6.8 0.8
CE1 A:HIS143 2.9 7.9 1.0
CE1 A:HIS95 2.9 7.2 1.0
CG A:HIS95 3.1 7.1 1.0
CG A:HIS143 3.1 8.1 1.0
CB A:CYS135 3.2 7.1 1.0
CB A:HIS95 3.5 7.8 1.0
CB A:HIS143 3.5 8.0 1.0
CE A:MET148 3.5 8.0 0.8
CE A:MET148 3.5 14.1 0.1
CA A:HIS95 3.7 7.1 1.0
SD A:MET148 3.7 13.0 0.1
O A:PRO94 4.0 8.6 0.7
CG A:MET148 4.0 9.9 0.1
O A:PRO94 4.1 8.3 0.3
NE2 A:HIS143 4.1 8.7 1.0
CG A:MET148 4.1 7.8 0.8
NE2 A:HIS95 4.1 7.2 1.0
CD2 A:HIS143 4.1 7.9 1.0
CD2 A:HIS95 4.2 7.8 1.0
CB A:THR137 4.3 8.2 1.0
OG1 A:THR137 4.3 8.3 1.0
N A:SER96 4.5 7.3 1.0
CA A:HIS143 4.5 7.3 1.0
CB A:MET148 4.5 9.1 0.1
CB A:MET148 4.5 7.1 0.8
CE3 A:TRP63 4.6 7.3 1.0
CA A:CYS135 4.6 6.2 1.0
C A:HIS95 4.7 7.1 1.0
N A:HIS95 4.7 8.0 1.0
C A:PRO94 4.8 7.2 0.7
C A:PRO94 4.8 7.8 0.3
CZ3 A:TRP63 5.0 8.3 1.0

Copper binding site 2 out of 6 in 3wkq

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Copper binding site 2 out of 6 in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:7.6
occ:0.90
 NE2 A:HIS100 2.0 6.3 1.0
NE2 A:HIS134 2.0 7.4 1.0
O A:HOH872 2.2 15.8 0.5
O A:HOH872 2.2 21.7 0.5
O2 A:FMT408 2.2 16.6 0.5
CE1 A:HIS100 2.9 6.4 1.0
CD2 A:HIS134 3.0 6.7 1.0
CE1 A:HIS134 3.0 6.7 1.0
CD2 A:HIS100 3.0 6.5 1.0
C A:FMT408 3.3 18.2 0.5
OD2 A:ASP98 3.9 12.7 1.0
ND1 A:HIS100 4.1 6.5 1.0
O1 A:FMT408 4.1 18.1 0.5
CG A:HIS134 4.1 5.9 1.0
ND1 A:HIS134 4.2 6.4 1.0
CG A:HIS100 4.2 5.3 1.0
CG A:ASP98 4.4 8.4 1.0
OD1 A:ASP98 4.5 10.2 1.0
O A:HOH873 4.6 30.7 0.5
O A:HOH818 4.7 9.8 1.0

Copper binding site 3 out of 6 in 3wkq

Go back to Copper Binding Sites List in 3wkq
Copper binding site 3 out of 6 in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:9.3
occ:0.80
 ND1 A:HIS83 2.0 10.2 1.0
NE2 A:HIS42 2.0 9.0 1.0
O A:HOH844 2.3 26.1 0.5
O2 A:FMT410 2.3 7.5 0.5
CE1 A:HIS83 2.8 10.9 1.0
CE1 A:HIS42 3.0 9.6 1.0
CD2 A:HIS42 3.0 9.2 1.0
CG A:HIS83 3.0 8.6 1.0
C A:FMT410 3.1 13.0 0.5
O1 A:FMT410 3.4 20.0 0.5
CB A:HIS83 3.5 9.3 1.0
NE2 A:HIS83 4.0 10.1 1.0
ND1 A:HIS42 4.1 9.4 1.0
CD2 A:HIS83 4.1 10.8 1.0
CG A:HIS42 4.2 8.3 1.0
O A:HOH700 4.2 17.7 0.5
O A:HOH803 4.3 13.1 1.0
CG2 A:VAL36 4.6 9.6 1.0
O A:HOH546 4.7 36.6 1.0

Copper binding site 4 out of 6 in 3wkq

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Copper binding site 4 out of 6 in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:23.1
occ:0.50
 NE2 A:HIS39 1.9 15.8 1.0
CD2 A:HIS39 2.9 12.9 1.0
CE1 A:HIS39 3.0 15.4 1.0
ND1 A:HIS39 4.1 12.0 1.0
CG A:HIS39 4.1 10.8 1.0
O A:HOH698 4.7 32.5 0.5
CB A:PRO38 4.8 14.0 0.5
CB A:PRO38 4.8 10.0 0.5
O A:HOH751 5.0 42.9 1.0

Copper binding site 5 out of 6 in 3wkq

Go back to Copper Binding Sites List in 3wkq
Copper binding site 5 out of 6 in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:10.3
occ:0.40
 O A:HOH784 1.5 30.2 0.8
O2 A:FMT413 1.9 25.8 0.5
NE2 A:HIS298 2.0 7.0 1.0
O A:HOH716 2.5 20.4 0.5
OE2 A:GLU239 2.7 19.1 0.7
C A:FMT413 2.8 16.6 0.5
O1 A:FMT413 2.9 12.4 0.5
O A:HOH847 2.9 13.5 0.5
CD A:GLU239 3.0 12.5 0.7
OE1 A:GLU239 3.0 9.1 0.3
CD2 A:HIS298 3.0 6.7 1.0
CE1 A:HIS298 3.0 8.1 1.0
OE1 A:GLU239 3.2 14.4 0.7
O A:HOH784 3.3 16.1 0.2
CD A:GLU239 3.3 11.1 0.3
CD A:PRO191 3.6 7.6 1.0
O A:HOH716 3.6 23.5 0.5
OE2 A:GLU239 3.7 20.8 0.3
CG A:PRO191 3.8 9.1 1.0
O A:HOH800 3.9 42.2 1.0
CG A:GLU239 4.0 7.1 0.3
O A:HOH542 4.1 9.9 1.0
CG A:GLU239 4.1 10.7 0.7
O A:HOH824 4.2 26.9 1.0
ND1 A:HIS298 4.2 7.1 1.0
ND2 A:ASN297 4.2 11.7 1.0
CG A:HIS298 4.2 5.9 1.0
CG A:ASN297 4.7 7.0 1.0
OD1 A:ASN297 4.8 7.5 1.0
N A:PRO191 5.0 6.9 1.0

Copper binding site 6 out of 6 in 3wkq

Go back to Copper Binding Sites List in 3wkq
Copper binding site 6 out of 6 in the Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:13.8
occ:0.30
 O A:HOH823 1.9 28.2 1.0
O2 A:FMT411 2.0 29.4 0.5
OD2 A:ASP167 2.1 12.3 1.0
O A:HOH797 2.2 36.7 1.0
O A:HOH718 2.5 26.0 1.0
CG A:ASP167 2.8 12.4 1.0
C A:FMT411 2.9 27.2 0.5
OD1 A:ASP167 2.9 16.5 1.0
O1 A:FMT411 3.1 53.9 0.5
O A:HOH730 3.2 86.0 0.5
O A:GLY225 4.1 12.0 1.0
O A:GLU165 4.2 13.1 1.0
N A:LYS227 4.2 9.2 1.0
CB A:ASP167 4.3 11.2 1.0
CA A:GLU226 4.4 9.9 1.0
C A:GLU226 4.8 8.7 1.0
CB A:LYS227 4.8 10.9 1.0
O A:HOH799 4.9 68.3 0.5
C A:GLY225 5.0 10.4 1.0

Reference:

Y.Fukuda, T.Inoue. Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans in Complex with Formate To Be Published.
Page generated: Mon Jul 14 03:13:10 2025

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