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Copper in PDB 6l46: High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans

Enzymatic activity of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans

All present enzymatic activity of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans:
1.7.2.1;

Protein crystallography data

The structure of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 6l46 was solved by Y.Fukuda, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 114.212, 114.212, 83.688, 90.00, 90.00, 120.00
R / Rfree (%) 14.2 / 15.9

Other elements in 6l46:

The structure of High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans also contains other interesting chemical elements:

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

Copper Binding Sites:

The binding sites of Copper atom in the High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans (pdb code 6l46). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans, PDB code: 6l46:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 6l46

Go back to Copper Binding Sites List in 6l46
Copper binding site 1 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of 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 High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:8.9
occ:0.98
 ND1 A:HIS143 1.9 8.9 1.0
ND1 A:HIS95 2.0 8.5 1.0
SG A:CYS135 2.2 8.5 1.0
SD A:MET148 2.6 9.3 1.0
HB3 A:HIS143 2.8 11.5 1.0
CE1 A:HIS143 2.9 9.0 1.0
CE1 A:HIS95 2.9 9.1 1.0
CG A:HIS143 3.0 8.3 1.0
CG A:HIS95 3.0 8.1 1.0
HE1 A:HIS143 3.0 10.2 1.0
HB3 A:HIS95 3.1 8.7 1.0
HA A:HIS95 3.1 9.4 1.0
HE1 A:HIS95 3.1 9.7 1.0
CB A:CYS135 3.2 8.2 1.0
HB2 A:CYS135 3.2 7.7 1.0
HB3 A:CYS135 3.3 9.7 1.0
HE3 A:MET148 3.3 12.2 1.0
CB A:HIS95 3.4 8.2 1.0
CB A:HIS143 3.4 8.7 1.0
CE A:MET148 3.5 10.7 1.0
HB A:THR137 3.5 10.9 1.0
CA A:HIS95 3.7 8.5 1.0
HE1 A:MET148 3.7 12.7 1.0
HE3 A:TRP63 3.7 10.8 1.0
H A:SER96 3.8 11.7 1.0
NE2 A:HIS143 4.0 10.0 1.0
O A:PRO94 4.0 9.6 1.0
CG A:MET148 4.0 8.8 1.0
NE2 A:HIS95 4.1 9.7 1.0
HB2 A:HIS143 4.1 9.9 1.0
CD2 A:HIS143 4.1 8.8 1.0
CD2 A:HIS95 4.1 8.3 1.0
HA A:HIS143 4.2 9.7 1.0
HG3 A:MET148 4.2 12.0 1.0
HB2 A:MET148 4.2 10.3 1.0
OG1 A:THR137 4.3 9.2 1.0
HB2 A:HIS95 4.3 11.4 1.0
CB A:THR137 4.3 9.6 1.0
HE2 A:MET148 4.3 15.4 1.0
D A:THR137 4.4 7.8 0.1
H A:THR137 4.4 10.8 0.9
HB3 A:MET148 4.4 7.6 1.0
CA A:HIS143 4.4 8.4 1.0
N A:SER96 4.5 9.0 1.0
CB A:MET148 4.5 8.4 1.0
CE3 A:TRP63 4.5 8.7 1.0
HZ3 A:TRP63 4.5 10.4 1.0
CA A:CYS135 4.6 7.8 1.0
C A:HIS95 4.7 9.0 1.0
N A:HIS95 4.7 9.2 1.0
HB3 A:TRP63 4.7 10.7 1.0
DE2 A:HIS143 4.8 13.9 1.0
HG2 A:MET148 4.8 9.8 1.0
C A:PRO94 4.8 9.6 1.0
HA A:CYS135 4.8 8.5 1.0
HG22 A:THR137 4.8 6.4 1.0
DE2 A:HIS95 4.8 15.8 1.0
CZ3 A:TRP63 4.9 9.5 1.0
HD2 A:HIS143 5.0 8.5 1.0
HG11 A:VAL93 5.0 14.1 1.0
HD2 A:HIS95 5.0 8.4 1.0
DG A:SER96 5.0 10.9 1.0

Copper binding site 2 out of 4 in 6l46

Go back to Copper Binding Sites List in 6l46
Copper binding site 2 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of 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 High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:8.6
occ:0.96
 NE2 A:HIS100 2.0 7.6 1.0
O A:DOD520 2.0 15.1 1.0
NE2 A:HIS134 2.1 8.3 1.0
CL A:CL406 2.2 7.3 0.3
O A:DOD781 2.2 19.9 0.7
D2 A:DOD781 2.4 24.6 0.7
D1 A:DOD520 2.5 19.6 1.0
D1 A:DOD781 2.9 15.5 0.7
CE1 A:HIS100 3.0 7.2 1.0
CD2 A:HIS100 3.0 7.3 1.0
CD2 A:HIS134 3.0 7.8 1.0
CE1 A:HIS134 3.1 8.0 1.0
NA A:NA405 3.1 6.0 0.2
HE1 A:HIS100 3.2 9.1 1.0
HD2 A:HIS134 3.2 9.0 1.0
HD2 A:HIS100 3.2 8.5 1.0
HE1 A:HIS134 3.3 8.7 1.0
CU A:CU404 3.6 6.3 0.1
OD2 A:ASP98 3.8 12.3 1.0
ND1 A:HIS100 4.1 7.3 1.0
CG A:HIS100 4.2 6.8 1.0
ND1 A:HIS134 4.2 7.9 1.0
CG A:HIS134 4.2 7.6 1.0
O A:DOD807 4.3 27.9 0.9
CG A:ASP98 4.3 9.7 1.0
OD1 A:ASP98 4.5 10.4 1.0
D1 A:DOD640 4.5 14.7 0.9
O A:DOD640 4.7 11.0 0.9
D2 A:DOD526 4.7 25.5 0.7
D1 A:DOD807 4.7 33.0 0.9
D2 A:DOD807 4.8 23.7 0.9
HE1 A:MET132 4.9 7.7 1.0
DD1 A:HIS100 4.9 11.8 1.0
HB3 A:SER274 4.9 8.2 1.0
HD1 A:HIS134 4.9 9.0 0.7
HD11 A:ILE144 4.9 10.7 1.0
DD1 A:HIS134 5.0 2.7 0.3
HB3 A:ASP98 5.0 11.5 1.0

Copper binding site 3 out of 4 in 6l46

Go back to Copper Binding Sites List in 6l46
Copper binding site 3 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of 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 High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu403

b:8.8
occ:0.92
 NE2 A:HIS42 2.0 9.3 1.0
ND1 A:HIS83 2.0 9.2 1.0
O A:DOD771 2.2 11.8 1.0
D2 A:DOD771 2.8 14.9 1.0
CE1 A:HIS83 2.8 8.6 1.0
D1 A:DOD771 2.9 17.8 1.0
CE1 A:HIS42 2.9 9.8 1.0
HE1 A:HIS83 2.9 11.3 1.0
CD2 A:HIS42 3.0 8.8 1.0
HE1 A:HIS42 3.1 10.0 1.0
CG A:HIS83 3.1 9.7 1.0
HD2 A:HIS42 3.2 10.7 1.0
HB3 A:HIS83 3.4 12.1 1.0
HB2 A:HIS83 3.4 12.9 1.0
CB A:HIS83 3.5 9.4 1.0
HG23 A:VAL36 3.6 10.7 1.0
D1 A:DOD725 3.6 33.7 1.0
NE2 A:HIS83 4.0 10.6 1.0
ND1 A:HIS42 4.0 10.1 1.0
O A:DOD725 4.1 23.7 1.0
CG A:HIS42 4.1 9.2 1.0
CD2 A:HIS83 4.2 11.8 1.0
O A:DOD818 4.3 16.4 1.0
D2 A:DOD725 4.3 22.4 1.0
O A:DOD922 4.5 23.6 1.0
CG2 A:VAL36 4.6 9.8 1.0
D2 A:DOD818 4.6 18.2 1.0
HG12 A:VAL36 4.7 12.4 1.0
DE2 A:HIS83 4.8 17.1 1.0
DD1 A:HIS42 4.8 12.7 1.0
HG21 A:VAL36 4.9 10.7 1.0
HG22 A:VAL36 4.9 8.6 1.0
HG22 A:THR122 5.0 14.5 0.1

Copper binding site 4 out of 4 in 6l46

Go back to Copper Binding Sites List in 6l46
Copper binding site 4 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of 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 High-Resolution Neutron and X-Ray Joint Refined Structure of Copper- Containing Nitrite Reductase From Geobacillus Thermodenitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:6.3
occ:0.10
 O A:DOD640 1.6 11.0 0.9
D1 A:DOD640 2.0 14.7 0.9
O A:DOD520 2.0 15.1 1.0
D2 A:DOD640 2.2 11.5 0.9
D1 A:DOD520 2.4 19.6 1.0
HD2 A:HIS100 2.8 8.5 1.0
CD2 A:HIS100 2.9 7.3 1.0
NE2 A:HIS100 3.2 7.6 1.0
HA A:HIS100 3.4 10.2 1.0
OD1 A:ASP98 3.6 10.4 1.0
CU A:CU402 3.6 8.6 1.0
CG A:HIS100 3.7 6.8 1.0
O A:DOD663 3.7 10.2 0.8
D2 A:DOD663 3.7 22.4 0.2
OD2 A:ASP98 3.8 12.3 1.0
D2 A:DOD663 3.9 16.6 0.8
NA A:NA405 4.0 6.0 0.2
O A:DOD663 4.0 17.3 0.2
CE1 A:HIS100 4.0 7.2 1.0
CG A:ASP98 4.1 9.7 1.0
ND1 A:HIS100 4.2 7.3 1.0
CA A:HIS100 4.3 7.3 1.0
CL A:CL406 4.3 7.3 0.3
O A:DOD781 4.3 19.9 0.7
HE2 A:PHE110 4.4 12.4 1.0
CB A:HIS100 4.4 7.0 1.0
D1 A:DOD663 4.5 13.7 0.8
HB3 A:HIS100 4.6 8.5 1.0
HE1 A:HIS100 4.6 9.1 1.0
D1 A:DOD781 4.7 15.5 0.7
D1 A:DOD663 4.8 14.1 0.2
N A:HIS100 4.9 7.1 1.0
DD1 A:HIS100 4.9 11.8 1.0

Reference:

Y.Fukuda, Y.Hirano, K.Kusaka, T.Inoue, T.Tamada. High-Resolution Neutron Crystallography Visualizes An Oh-Bound Resting State of A Copper-Containing Nitrite Reductase Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1918125117
Page generated: Sun Dec 13 11:23:59 2020

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