Atomistry » Copper » PDB 3t6w-3x1n » 3wkq
Atomistry »
  Copper »
    PDB 3t6w-3x1n »
      3wkq »

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

Go back to Copper Binding Sites List in 3wkq
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

Go back to Copper Binding Sites List in 3wkq
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: Wed Jul 31 02:22:09 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy