Atomistry » Copper » PDB 3t6w-3x1n » 3x1e
Atomistry »
  Copper »
    PDB 3t6w-3x1n »
      3x1e »

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

Go back to Copper Binding Sites List in 3x1e
Copper binding site 1 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 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

Go back to Copper Binding Sites List in 3x1e
Copper binding site 2 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 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

Go back to Copper Binding Sites List in 3x1e
Copper binding site 3 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 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

Go back to Copper Binding Sites List in 3x1e
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

Go back to Copper Binding Sites List in 3x1e
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

Go back to Copper Binding Sites List in 3x1e
Copper binding site 6 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 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

Go back to Copper Binding Sites List in 3x1e
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

Go back to Copper Binding Sites List in 3x1e
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

Go back to Copper Binding Sites List in 3x1e
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

Go back to Copper Binding Sites List in 3x1e
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: Sun Dec 13 11:12:50 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy