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Copper in PDB 9kws: D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans

Enzymatic activity of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans

All present enzymatic activity of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans:
1.7.2.1;

Protein crystallography data

The structure of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 9kws was solved by Y.Fukuda, M.Lintuluoto, Y.Hirano, K.Kusaka, T.Inoue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.26 / 1.05
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 115.038, 115.038, 84.403, 90, 90, 120
R / Rfree (%) 9 / 10.1

Other elements in 9kws:

The structure of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 9kws). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 9kws:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 9kws

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Copper binding site 1 out of 5 in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:10.2
occ:0.97
 ND1 A:HIS95 2.0 9.7 1.0
ND1 A:HIS143 2.1 10.9 1.0
SG A:CYS135 2.2 9.3 1.0
SD A:MET148 2.6 9.3 0.8
HB3 A:HIS143 2.9 12.9 1.0
CE1 A:HIS143 2.9 11.0 1.0
CE1 A:HIS95 3.0 9.6 1.0
HA A:HIS95 3.0 11.6 1.0
CG A:HIS143 3.1 10.6 1.0
CG A:HIS95 3.1 9.7 1.0
HE1 A:HIS143 3.1 13.2 0.6
HE1 A:HIS95 3.1 11.5 0.6
HB3 A:HIS95 3.2 12.1 0.9
CB A:CYS135 3.2 9.1 1.0
HB2 A:CYS135 3.2 10.9 1.0
HE2 A:MET148 3.2 15.3 0.2
HB3 A:CYS135 3.2 10.9 1.0
HE3 A:MET148 3.3 11.1 0.8
CB A:HIS95 3.5 10.1 1.0
CB A:HIS143 3.5 10.8 1.0
CE A:MET148 3.5 9.2 0.8
HB A:THR137 3.5 12.6 0.9
SD A:MET148 3.6 12.3 0.2
HE1 A:MET148 3.7 11.1 0.8
CA A:HIS95 3.7 9.7 1.0
CE A:MET148 3.7 12.8 0.2
H A:SER96 3.8 11.6 1.0
HE3 A:TRP63 3.9 11.6 0.7
HE3 A:MET148 3.9 15.3 0.2
O A:PRO94 4.0 10.8 1.0
NE2 A:HIS143 4.1 11.0 1.0
HB2 A:HIS143 4.1 12.9 1.0
NE2 A:HIS95 4.1 9.9 1.0
CG A:MET148 4.1 9.4 0.8
CD2 A:HIS143 4.1 10.8 1.0
HB2 A:MET148 4.2 12.6 0.2
CD2 A:HIS95 4.2 10.1 1.0
CB A:THR137 4.3 10.5 1.0
OG1 A:THR137 4.3 10.8 1.0
HA A:HIS143 4.3 12.2 1.0
H A:THR137 4.3 12.2 1.0
HE2 A:MET148 4.3 11.1 0.8
HB2 A:MET148 4.4 10.8 0.8
HG3 A:MET148 4.4 11.3 0.8
HB2 A:HIS95 4.4 12.1 1.0
HB3 A:MET148 4.4 10.8 0.8
N A:SER96 4.5 9.7 1.0
CA A:HIS143 4.5 10.1 1.0
HB3 A:MET148 4.6 12.6 0.2
CB A:MET148 4.6 9.0 0.8
CA A:CYS135 4.6 8.6 1.0
CE3 A:TRP63 4.6 9.7 1.0
HZ3 A:TRP63 4.6 12.8 0.9
HE1 A:MET148 4.6 15.3 0.2
C A:HIS95 4.7 10.0 1.0
CB A:MET148 4.7 10.5 0.2
N A:HIS95 4.7 10.0 1.0
HG23 A:THR137 4.8 13.3 0.9
CG A:MET148 4.8 11.3 0.2
C A:PRO94 4.8 10.2 1.0
HE2 A:HIS143 4.8 13.2 0.8
HA A:CYS135 4.8 10.3 0.7
HG2 A:MET148 4.8 11.3 0.8
HE2 A:HIS95 4.9 11.9 0.9
HB3 A:TRP63 4.9 11.4 0.8
HG12 A:VAL93 4.9 15.3 0.9
CZ3 A:TRP63 5.0 10.7 1.0
HD2 A:HIS143 5.0 13.0 1.0

Copper binding site 2 out of 5 in 9kws

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Copper binding site 2 out of 5 in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:9.2
occ:0.98
 NE2 A:HIS100 2.0 8.9 1.0
NE2 A:HIS134 2.0 9.1 1.0
CL A:CL408 2.3 13.3 0.7
CD2 A:HIS134 2.9 8.6 1.0
CE1 A:HIS100 2.9 8.3 1.0
CE1 A:HIS134 3.0 8.7 1.0
CD2 A:HIS100 3.0 8.5 1.0
HD2 A:HIS134 3.1 10.3 1.0
HE1 A:HIS100 3.1 10.0 1.0
HD2 A:HIS100 3.3 10.2 1.0
HE1 A:HIS134 3.3 10.4 0.9
HD22 A:ASN98 3.6 14.2 1.0
ND2 A:ASN98 3.8 11.8 1.0
ND1 A:HIS100 4.1 8.2 1.0
CG A:HIS134 4.1 8.3 1.0
HD21 A:ASN98 4.1 14.2 0.9
ND1 A:HIS134 4.1 8.8 1.0
CG A:HIS100 4.2 8.2 1.0
CG A:ASN98 4.3 10.4 1.0
OD1 A:ASN98 4.4 11.1 1.0
O A:HOH657 4.7 12.4 1.0
HE2 A:MET132 4.8 10.0 1.0
H1 A:HOH657 4.8 14.9 1.0
O A:HOH771 4.8 23.2 0.8
HB3 A:SER274 4.8 10.0 0.8
HG2 A:MET132 4.8 9.5 1.0
HD13 A:ILE144 4.8 12.1 1.0
HD1 A:HIS100 4.8 9.8 1.0
HB3 A:ASN98 4.9 11.6 0.9
HD1 A:HIS134 4.9 10.5 0.7
HB2 A:SER274 5.0 10.0 1.0
HB3 A:MET132 5.0 9.4 1.0
SD A:MET132 5.0 8.0 1.0

Copper binding site 3 out of 5 in 9kws

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Copper binding site 3 out of 5 in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu405

b:13.3
occ:0.80
 ND1 A:HIS83 1.9 13.3 1.0
O A:HOH801 2.0 15.4 0.2
NE2 A:HIS42 2.0 12.8 1.0
O A:HOH801 2.4 16.3 0.8
CE1 A:HIS83 2.8 13.6 1.0
H2 A:HOH801 2.9 19.6 0.8
HE1 A:HIS83 2.9 16.4 0.7
CE1 A:HIS42 3.0 13.2 1.0
H1 A:HOH801 3.0 19.6 0.8
CD2 A:HIS42 3.0 11.9 1.0
CG A:HIS83 3.0 11.8 1.0
HE1 A:HIS42 3.2 15.9 1.0
HD2 A:HIS42 3.2 14.3 0.9
HB3 A:HIS83 3.3 13.6 1.0
HB2 A:HIS83 3.4 13.6 0.8
CB A:HIS83 3.5 11.3 1.0
HG22 A:VAL36 3.6 14.8 0.9
NE2 A:HIS83 3.9 13.3 1.0
CD2 A:HIS83 4.1 13.6 1.0
ND1 A:HIS42 4.1 12.7 1.0
CG A:HIS42 4.1 11.4 1.0
O A:HOH755 4.2 22.9 1.0
O A:HOH825 4.3 16.5 1.0
CG2 A:VAL36 4.6 12.3 1.0
O A:HOH847 4.6 17.4 1.0
O A:HOH872 4.6 37.8 1.0
HG23 A:THR122 4.7 14.9 0.2
HE2 A:HIS83 4.7 16.0 0.4
HG13 A:VAL36 4.8 15.9 1.0
HD1 A:HIS42 4.9 15.2 1.0
HG23 A:VAL36 4.9 14.8 1.0
HD2 A:HIS83 4.9 16.3 1.0
CA A:HIS83 5.0 10.5 1.0

Copper binding site 4 out of 5 in 9kws

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Copper binding site 4 out of 5 in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu406

b:29.2
occ:0.50
 NE2 A:HIS39 1.9 17.9 1.0
O A:HOH772 2.0 47.4 0.9
O A:HOH746 2.1 52.9 0.8
O A:HOH697 2.2 47.3 0.7
CE1 A:HIS39 2.9 17.4 1.0
CD2 A:HIS39 3.0 16.3 1.0
HE1 A:HIS39 3.1 20.9 1.0
HD2 A:HIS39 3.2 19.6 1.0
HB2 A:PRO38 3.9 16.1 0.6
O A:HOH853 3.9 38.1 0.7
ND1 A:HIS39 4.0 15.8 1.0
CG A:HIS39 4.1 14.7 1.0
HB2 A:PRO38 4.1 15.4 0.4
HB3 A:PRO38 4.6 15.4 0.4
O A:HOH766 4.8 43.5 0.7
HD1 A:HIS39 4.8 18.9 0.9
CB A:PRO38 4.8 13.4 0.6
CB A:PRO38 4.8 12.8 0.4
HG2 A:PRO38 4.9 15.8 0.6

Copper binding site 5 out of 5 in 9kws

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Copper binding site 5 out of 5 in the D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of D98N Mutant of A Copper-Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:19.8
occ:0.28
 O A:HOH520 2.0 36.1 1.0
OD2 A:ASP167 2.1 15.1 1.0
O A:HOH830 2.2 39.6 0.5
O A:HOH501 2.3 38.7 1.0
O A:HOH656 2.6 32.0 1.0
CG A:ASP167 2.8 15.1 1.0
OD1 A:ASP167 2.9 17.8 1.0
O A:HOH830 3.4 39.9 0.5
H A:LYS227 3.4 13.7 1.0
HA A:GLU226 3.6 14.3 0.9
O A:GLY225 4.1 14.3 1.0
O A:GLU165 4.1 15.9 1.0
N A:LYS227 4.2 11.4 1.0
HB3 A:LYS227 4.3 16.1 1.0
CB A:ASP167 4.3 13.6 1.0
CA A:GLU226 4.5 11.9 1.0
HB2 A:ASP167 4.5 16.4 0.7
O A:HOH742 4.6 49.1 1.0
HB2 A:LYS227 4.6 16.1 1.0
HG2 A:GLU226 4.7 15.6 1.0
HB3 A:ASP167 4.7 16.4 0.7
C A:GLU226 4.8 11.4 1.0
CB A:LYS227 4.8 13.4 1.0

Reference:

Y.Fukuda, M.Lintuluoto, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada. Structural Basis of Cuproenzyme Nitrite Reduction at the Level of A Single Hydrogen Atom. J.Biol.Chem. 10290 2025.
ISSN: ESSN 1083-351X
PubMed: 40436316
DOI: 10.1016/J.JBC.2025.110290
Page generated: Mon Jul 14 10:04:03 2025

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