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Copper in PDB 2dv6: Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans

Enzymatic activity of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans

All present enzymatic activity of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans, PDB code: 2dv6 was solved by M.Nojiri, Y.Xie, T.Yamamoto, T.Inoue, S.Suzuki, Y.Kai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 162.551, 162.551, 148.970, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 16.5

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans (pdb code 2dv6). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 18 binding sites of Copper where determined in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans, PDB code: 2dv6:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16; 17; 18;

Copper binding site 1 out of 18 in 2dv6

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Copper binding site 1 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu500

b:24.1
occ:1.00
ND1 A:HIS268 2.1 21.8 1.0
SG A:CYS260 2.1 21.8 1.0
ND1 A:HIS219 2.1 20.1 1.0
SD A:MET273 2.6 21.2 1.0
CE1 A:HIS268 3.0 20.8 1.0
CB A:CYS260 3.1 21.9 1.0
CG A:HIS219 3.1 20.4 1.0
CG A:HIS268 3.1 21.0 1.0
CE1 A:HIS219 3.2 21.3 1.0
CB A:HIS219 3.3 21.7 1.0
CB A:HIS268 3.5 20.6 1.0
CE A:MET273 3.5 20.1 1.0
CA A:HIS219 3.6 23.2 1.0
CG A:MET273 4.1 18.9 1.0
O A:VAL218 4.1 24.3 1.0
NE2 A:HIS268 4.1 23.3 1.0
CD2 A:HIS268 4.2 20.9 1.0
CD2 A:HIS219 4.2 20.6 1.0
NE2 A:HIS219 4.3 20.6 1.0
N A:SER220 4.4 23.2 1.0
CA A:CYS260 4.5 21.0 1.0
CB A:MET273 4.6 19.0 1.0
CB A:THR262 4.6 20.7 1.0
C A:HIS219 4.6 24.1 1.0
CA A:HIS268 4.6 20.2 1.0
OG1 A:THR262 4.7 21.1 1.0
CE3 A:TRP186 4.7 18.3 1.0
N A:HIS219 4.7 22.8 1.0
C A:VAL218 4.8 23.6 1.0
O A:SER220 5.0 23.8 1.0

Copper binding site 2 out of 18 in 2dv6

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Copper binding site 2 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:28.9
occ:1.00
NE2 A:HIS259 2.0 19.1 1.0
NE2 A:HIS224 2.1 23.5 1.0
NE2 C:HIS416 2.1 24.2 1.0
O A:HOH2521 2.5 36.5 0.5
CD2 C:HIS416 3.0 20.9 1.0
CE1 A:HIS259 3.0 20.0 1.0
CE1 A:HIS224 3.1 23.3 1.0
CD2 A:HIS224 3.1 23.4 1.0
CD2 A:HIS259 3.1 18.7 1.0
CE1 C:HIS416 3.2 20.7 1.0
OD1 A:ASP222 3.7 34.5 1.0
NE2 C:HIS365 3.9 23.6 1.0
CD2 C:HIS365 4.1 22.7 1.0
ND1 A:HIS259 4.1 21.1 1.0
CG C:HIS416 4.2 22.4 1.0
ND1 A:HIS224 4.2 24.6 1.0
CG A:HIS259 4.2 18.4 1.0
CG A:ASP222 4.2 32.9 1.0
CG A:HIS224 4.2 23.6 1.0
ND1 C:HIS416 4.2 21.5 1.0
O A:HOH2521 4.4 43.3 0.5
OD2 A:ASP222 4.5 34.8 1.0
CE1 C:HIS365 4.8 24.1 1.0
CD2 C:LEU418 4.9 24.2 1.0
O A:HOH2544 4.9 37.4 1.0

Copper binding site 3 out of 18 in 2dv6

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Copper binding site 3 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:25.1
occ:1.00
ND1 A:HIS119 2.1 21.7 1.0
ND1 A:HIS77 2.1 20.4 1.0
SG A:CYS114 2.2 21.6 1.0
SD A:MET124 2.9 26.6 1.0
CG A:HIS119 3.0 22.3 1.0
CE1 A:HIS77 3.1 19.3 1.0
CE1 A:HIS119 3.1 22.5 1.0
CG A:HIS77 3.2 20.2 1.0
CB A:CYS114 3.2 21.7 1.0
CB A:HIS119 3.3 21.3 1.0
O A:GLN76 3.3 26.0 1.0
CB A:HIS77 3.5 20.4 1.0
CA A:HIS77 3.6 22.7 1.0
CE A:MET124 3.8 25.7 1.0
CB A:ILE116 4.2 24.2 1.0
CD2 A:HIS119 4.2 23.0 1.0
NE2 A:HIS77 4.2 20.1 1.0
NE2 A:HIS119 4.2 23.7 1.0
C A:GLN76 4.2 25.7 1.0
CD2 A:HIS77 4.3 18.8 1.0
CG1 A:ILE116 4.3 23.9 1.0
N A:HIS77 4.4 23.3 1.0
CG A:MET124 4.4 24.8 1.0
N A:ASP78 4.5 22.6 1.0
CA A:CYS114 4.6 23.8 1.0
C A:HIS77 4.6 22.8 1.0
CA A:HIS119 4.8 23.7 1.0
CB A:MET124 4.8 24.6 1.0
CG2 A:ILE116 4.9 24.2 1.0
SD A:MET40 4.9 41.7 1.0
O A:ASP78 5.0 24.5 1.0

Copper binding site 4 out of 18 in 2dv6

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Copper binding site 4 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu500

b:23.5
occ:1.00
ND1 B:HIS268 2.2 22.0 1.0
ND1 B:HIS219 2.2 19.7 1.0
SG B:CYS260 2.2 18.9 1.0
SD B:MET273 2.5 22.4 1.0
CE1 B:HIS268 3.1 22.9 1.0
CG B:HIS268 3.1 21.1 1.0
CG B:HIS219 3.1 20.8 1.0
CB B:CYS260 3.2 17.9 1.0
CE1 B:HIS219 3.2 21.4 1.0
CB B:HIS219 3.4 21.1 1.0
CB B:HIS268 3.5 19.3 1.0
CE B:MET273 3.5 18.9 1.0
CA B:HIS219 3.6 21.7 1.0
CG B:MET273 4.1 17.6 1.0
O B:VAL218 4.1 22.2 1.0
NE2 B:HIS268 4.1 23.5 1.0
CD2 B:HIS268 4.2 20.1 1.0
CD2 B:HIS219 4.3 21.5 1.0
NE2 B:HIS219 4.3 21.7 1.0
N B:SER220 4.3 22.7 1.0
CG2 B:THR262 4.5 22.9 1.0
C B:HIS219 4.6 23.6 1.0
CE3 B:TRP186 4.6 17.6 1.0
CA B:CYS260 4.6 20.2 1.0
CA B:HIS268 4.6 19.8 1.0
CB B:MET273 4.6 18.0 1.0
N B:HIS219 4.7 22.1 1.0
C B:VAL218 4.8 22.8 1.0

Copper binding site 5 out of 18 in 2dv6

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Copper binding site 5 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:29.1
occ:1.00
NE2 B:HIS224 2.0 27.0 1.0
NE2 B:HIS259 2.1 21.5 1.0
NE2 A:HIS416 2.2 26.2 1.0
O B:HOH3658 2.6 52.0 1.0
CD2 B:HIS259 3.0 19.7 1.0
CE1 B:HIS224 3.0 27.1 1.0
CD2 B:HIS224 3.1 25.7 1.0
CD2 A:HIS416 3.1 24.1 1.0
CE1 B:HIS259 3.2 20.9 1.0
CE1 A:HIS416 3.2 23.8 1.0
OD1 B:ASP222 3.7 33.8 1.0
NE2 A:HIS365 3.9 25.5 1.0
CD2 A:HIS365 4.1 24.7 1.0
ND1 B:HIS224 4.1 27.1 1.0
CG B:HIS259 4.2 19.5 1.0
CG B:HIS224 4.2 27.6 1.0
ND1 B:HIS259 4.2 21.3 1.0
CG A:HIS416 4.3 23.9 1.0
CG B:ASP222 4.3 33.3 1.0
ND1 A:HIS416 4.3 24.5 1.0
OD2 B:ASP222 4.6 34.1 1.0
CE1 A:HIS365 4.7 26.1 1.0
CD2 A:LEU418 4.8 21.6 1.0
O B:HOH3615 4.8 43.1 1.0
O B:HOH3554 4.9 33.9 1.0
CG A:HIS365 4.9 24.1 1.0

Copper binding site 6 out of 18 in 2dv6

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Copper binding site 6 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:27.1
occ:1.00
ND1 B:HIS119 2.1 24.9 1.0
ND1 B:HIS77 2.1 26.4 1.0
SG B:CYS114 2.2 22.6 1.0
SD B:MET124 2.9 27.1 1.0
CG B:HIS119 3.0 24.9 1.0
CE1 B:HIS77 3.1 28.1 1.0
CG B:HIS77 3.1 26.4 1.0
CE1 B:HIS119 3.1 23.9 1.0
CB B:CYS114 3.2 22.3 1.0
CB B:HIS119 3.3 24.8 1.0
O B:GLN76 3.3 29.0 1.0
CB B:HIS77 3.4 25.9 1.0
CA B:HIS77 3.5 25.7 1.0
CE B:MET124 3.7 25.2 1.0
CD2 B:HIS119 4.2 25.6 1.0
C B:GLN76 4.2 28.4 1.0
NE2 B:HIS77 4.2 28.6 1.0
NE2 B:HIS119 4.2 24.6 1.0
CD2 B:HIS77 4.2 26.7 1.0
CB B:ILE116 4.2 25.1 1.0
N B:HIS77 4.3 26.3 1.0
CG B:MET124 4.4 26.4 1.0
CG1 B:ILE116 4.4 25.2 1.0
N B:ASP78 4.5 24.9 1.0
C B:HIS77 4.6 25.8 1.0
CA B:CYS114 4.6 25.1 1.0
CA B:HIS119 4.8 26.0 1.0
CB B:MET124 4.8 24.8 1.0
SD B:MET40 5.0 44.7 1.0
N B:ILE116 5.0 24.7 1.0
O B:ASP78 5.0 25.0 1.0

Copper binding site 7 out of 18 in 2dv6

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Copper binding site 7 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu500

b:27.6
occ:1.00
ND1 C:HIS219 2.0 27.6 1.0
ND1 C:HIS268 2.1 23.3 1.0
SG C:CYS260 2.2 24.3 1.0
SD C:MET273 2.5 25.6 1.0
CE1 C:HIS219 3.0 28.1 1.0
CE1 C:HIS268 3.0 24.5 1.0
CG C:HIS219 3.1 28.2 1.0
CB C:CYS260 3.1 22.8 1.0
CG C:HIS268 3.2 23.4 1.0
CE C:MET273 3.4 22.5 1.0
CB C:HIS219 3.5 27.7 1.0
CB C:HIS268 3.6 20.5 1.0
CA C:HIS219 3.7 30.1 1.0
CG C:MET273 4.1 22.9 1.0
NE2 C:HIS219 4.1 29.5 1.0
O C:VAL218 4.1 30.8 1.0
NE2 C:HIS268 4.1 25.8 1.0
CD2 C:HIS219 4.2 28.3 1.0
CD2 C:HIS268 4.2 23.1 1.0
N C:SER220 4.4 29.4 1.0
CG2 C:THR262 4.4 28.1 1.0
CA C:CYS260 4.6 23.9 1.0
CE3 C:TRP186 4.6 21.4 1.0
CB C:MET273 4.6 20.1 1.0
C C:HIS219 4.6 30.3 1.0
CA C:HIS268 4.7 20.8 1.0
N C:HIS219 4.8 30.6 1.0
C C:VAL218 4.9 31.3 1.0

Copper binding site 8 out of 18 in 2dv6

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Copper binding site 8 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:31.6
occ:1.00
NE2 C:HIS259 2.0 24.3 1.0
NE2 C:HIS224 2.1 30.9 1.0
NE2 B:HIS416 2.2 23.1 1.0
CE1 C:HIS259 3.0 24.4 1.0
CD2 C:HIS259 3.0 22.6 1.0
CE1 B:HIS416 3.1 21.3 1.0
CE1 C:HIS224 3.1 31.1 1.0
CD2 C:HIS224 3.1 30.1 1.0
CD2 B:HIS416 3.2 22.5 1.0
OD1 C:ASP222 3.8 37.7 1.0
NE2 B:HIS365 4.0 29.3 1.0
ND1 C:HIS259 4.1 24.9 1.0
CG C:HIS259 4.2 23.0 1.0
ND1 C:HIS224 4.2 29.8 1.0
ND1 B:HIS416 4.2 22.3 1.0
CD2 B:HIS365 4.3 27.7 1.0
CG C:HIS224 4.3 30.7 1.0
CG B:HIS416 4.3 22.2 1.0
CG C:ASP222 4.3 35.0 1.0
CE1 B:HIS365 4.6 29.2 1.0
OD2 C:ASP222 4.6 35.2 1.0
CD2 B:LEU418 4.8 21.9 1.0
O C:HOH4698 4.8 51.0 1.0
O C:HOH4592 4.9 38.6 1.0
CG1 B:ILE367 4.9 26.8 1.0

Copper binding site 9 out of 18 in 2dv6

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Copper binding site 9 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:27.3
occ:1.00
ND1 C:HIS77 2.1 27.4 1.0
ND1 C:HIS119 2.1 20.9 1.0
SG C:CYS114 2.3 26.9 1.0
SD C:MET124 2.9 24.9 1.0
CE1 C:HIS77 3.0 26.6 1.0
CG C:HIS119 3.0 21.8 1.0
O C:GLN76 3.1 25.7 1.0
CG C:HIS77 3.2 26.7 1.0
CE1 C:HIS119 3.2 22.1 1.0
CB C:CYS114 3.2 25.8 1.0
CB C:HIS119 3.3 22.0 1.0
CA C:HIS77 3.5 25.7 1.0
CB C:HIS77 3.5 25.4 1.0
CE C:MET124 3.9 21.9 1.0
C C:GLN76 4.1 26.4 1.0
NE2 C:HIS77 4.2 27.6 1.0
CD2 C:HIS119 4.2 21.4 1.0
NE2 C:HIS119 4.2 22.9 1.0
CD2 C:HIS77 4.3 27.2 1.0
CB C:ILE116 4.3 25.7 1.0
N C:HIS77 4.3 25.7 1.0
CG1 C:ILE116 4.3 26.4 1.0
CG C:MET124 4.4 22.4 1.0
N C:ASP78 4.6 26.0 1.0
C C:HIS77 4.6 26.6 1.0
CA C:CYS114 4.7 26.5 1.0
CA C:HIS119 4.7 24.3 1.0
CB C:MET124 4.9 23.1 1.0
SD C:MET40 4.9 39.7 1.0

Copper binding site 10 out of 18 in 2dv6

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Copper binding site 10 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu500

b:23.8
occ:1.00
ND1 D:HIS219 2.2 23.3 1.0
SG D:CYS260 2.2 20.6 1.0
ND1 D:HIS268 2.2 21.6 1.0
SD D:MET273 2.5 20.4 1.0
CE1 D:HIS219 3.1 21.7 1.0
CG D:HIS219 3.1 23.4 1.0
CE1 D:HIS268 3.1 21.2 1.0
CG D:HIS268 3.1 21.2 1.0
CB D:CYS260 3.2 20.7 1.0
CE D:MET273 3.3 20.2 1.0
CB D:HIS219 3.4 23.7 1.0
CB D:HIS268 3.5 19.3 1.0
CA D:HIS219 3.6 23.8 1.0
O D:VAL218 4.1 23.7 1.0
CG D:MET273 4.1 18.5 1.0
NE2 D:HIS219 4.2 23.2 1.0
NE2 D:HIS268 4.2 21.2 1.0
CD2 D:HIS268 4.3 19.6 1.0
CD2 D:HIS219 4.3 23.7 1.0
N D:SER220 4.4 24.3 1.0
CA D:CYS260 4.6 20.7 1.0
CB D:MET273 4.6 17.7 1.0
CE3 D:TRP186 4.6 19.6 1.0
CA D:HIS268 4.6 20.0 1.0
C D:HIS219 4.6 24.5 1.0
N D:HIS219 4.6 23.9 1.0
C D:VAL218 4.8 24.2 1.0
CB D:THR262 4.8 24.2 1.0
OG1 D:THR262 4.8 25.0 1.0

Copper binding site 11 out of 18 in 2dv6

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Copper binding site 11 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 11 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu501

b:29.9
occ:1.00
NE2 D:HIS259 2.0 21.5 1.0
NE2 D:HIS224 2.1 29.2 1.0
NE2 F:HIS416 2.2 23.2 1.0
O D:HOH5633 2.6 38.6 1.0
CD2 D:HIS259 3.0 20.5 1.0
CE1 D:HIS224 3.0 27.3 1.0
CE1 D:HIS259 3.0 20.0 1.0
CD2 D:HIS224 3.1 27.1 1.0
CD2 F:HIS416 3.1 22.6 1.0
CE1 F:HIS416 3.2 21.6 1.0
OD1 D:ASP222 3.7 33.9 1.0
NE2 F:HIS365 3.9 25.6 1.0
ND1 D:HIS224 4.1 27.8 1.0
CG D:HIS259 4.1 19.3 1.0
ND1 D:HIS259 4.1 20.1 1.0
CD2 F:HIS365 4.1 23.9 1.0
CG D:HIS224 4.2 27.7 1.0
CG D:ASP222 4.3 30.6 1.0
ND1 F:HIS416 4.3 21.8 1.0
CG F:HIS416 4.3 22.7 1.0
OD2 D:ASP222 4.5 31.8 1.0
CE1 F:HIS365 4.7 24.3 1.0
CD2 F:LEU418 4.8 20.3 1.0
O D:HOH5605 4.8 33.4 1.0
O D:HOH5652 5.0 42.2 1.0
CG F:HIS365 5.0 23.5 1.0

Copper binding site 12 out of 18 in 2dv6

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Copper binding site 12 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 12 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu502

b:25.7
occ:1.00
ND1 D:HIS77 2.0 21.7 1.0
ND1 D:HIS119 2.1 23.3 1.0
SG D:CYS114 2.3 24.1 1.0
SD D:MET124 2.9 23.9 1.0
CE1 D:HIS77 3.0 22.5 1.0
CG D:HIS119 3.0 22.8 1.0
CG D:HIS77 3.1 23.4 1.0
CE1 D:HIS119 3.1 22.8 1.0
O D:GLN76 3.2 23.6 1.0
CB D:CYS114 3.2 21.0 1.0
CB D:HIS119 3.3 22.3 1.0
CB D:HIS77 3.4 22.5 1.0
CA D:HIS77 3.5 23.5 1.0
CE D:MET124 3.7 21.4 1.0
NE2 D:HIS77 4.1 23.1 1.0
C D:GLN76 4.1 24.5 1.0
CD2 D:HIS77 4.2 23.1 1.0
CD2 D:HIS119 4.2 23.4 1.0
NE2 D:HIS119 4.2 24.2 1.0
CB D:ILE116 4.2 23.0 1.0
N D:HIS77 4.3 23.6 1.0
CG1 D:ILE116 4.4 23.7 1.0
CG D:MET124 4.5 21.3 1.0
N D:ASP78 4.5 23.5 1.0
C D:HIS77 4.6 23.6 1.0
CA D:CYS114 4.6 22.3 1.0
CA D:HIS119 4.8 23.6 1.0
CB D:MET124 4.9 21.0 1.0
SD D:MET40 4.9 41.0 1.0
CG2 D:ILE116 5.0 23.9 1.0
O D:ASP78 5.0 23.2 1.0

Copper binding site 13 out of 18 in 2dv6

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Copper binding site 13 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


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A full contact list of Copper with other atoms in the Cu binding site number 13 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu500

b:22.0
occ:1.00
ND1 E:HIS268 2.0 19.7 1.0
ND1 E:HIS219 2.1 21.2 1.0
SG E:CYS260 2.1 20.6 1.0
SD E:MET273 2.6 21.4 1.0
CE1 E:HIS268 2.9 19.4 1.0
CG E:HIS219 3.0 20.8 1.0
CE1 E:HIS219 3.1 22.0 1.0
CG E:HIS268 3.1 20.4 1.0
CB E:CYS260 3.2 20.6 1.0
CB E:HIS219 3.4 22.5 1.0
CE E:MET273 3.4 20.9 1.0
CB E:HIS268 3.6 18.6 1.0
CA E:HIS219 3.6 24.4 1.0
O E:VAL218 4.0 24.0 1.0
NE2 E:HIS268 4.0 20.8 1.0
CD2 E:HIS268 4.2 20.0 1.0
NE2 E:HIS219 4.2 20.6 1.0
CG E:MET273 4.2 20.2 1.0
CD2 E:HIS219 4.2 20.6 1.0
N E:SER220 4.4 25.3 1.0
CE3 E:TRP186 4.5 17.6 1.0
C E:HIS219 4.6 25.5 1.0
CA E:CYS260 4.6 21.6 1.0
N E:HIS219 4.6 23.9 1.0
CA E:HIS268 4.7 19.4 1.0
CB E:THR262 4.7 22.1 1.0
CB E:MET273 4.7 19.8 1.0
OG1 E:THR262 4.7 23.9 1.0
C E:VAL218 4.7 24.8 1.0

Copper binding site 14 out of 18 in 2dv6

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Copper binding site 14 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 14 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:28.6
occ:1.00
NE2 E:HIS259 2.0 20.9 1.0
NE2 E:HIS224 2.1 25.8 1.0
NE2 D:HIS416 2.2 24.9 1.0
O E:HOH6643 2.5 54.0 0.5
CD2 E:HIS259 3.0 20.9 1.0
CE1 E:HIS259 3.0 21.0 1.0
CE1 E:HIS224 3.0 25.1 1.0
CD2 E:HIS224 3.1 24.2 1.0
CE1 D:HIS416 3.1 24.7 1.0
CD2 D:HIS416 3.2 22.8 1.0
OD1 E:ASP222 3.8 35.0 1.0
NE2 D:HIS365 3.9 26.3 1.0
CD2 D:HIS365 4.0 25.4 1.0
ND1 E:HIS259 4.1 22.0 1.0
CG E:HIS259 4.2 21.0 1.0
ND1 E:HIS224 4.2 25.9 1.0
CG E:HIS224 4.3 25.9 1.0
ND1 D:HIS416 4.3 24.6 1.0
CG E:ASP222 4.3 31.9 1.0
CG D:HIS416 4.3 22.8 1.0
OD2 E:ASP222 4.5 33.3 1.0
O E:HOH6643 4.5 34.6 0.5
CD2 D:LEU418 4.8 26.7 1.0
CE1 D:HIS365 4.8 25.8 1.0
CG D:HIS365 5.0 24.7 1.0

Copper binding site 15 out of 18 in 2dv6

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Copper binding site 15 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 15 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:26.3
occ:1.00
ND1 E:HIS77 2.1 26.1 1.0
ND1 E:HIS119 2.1 22.6 1.0
SG E:CYS114 2.2 22.5 1.0
SD E:MET124 3.0 25.4 1.0
CE1 E:HIS77 3.0 25.5 1.0
CG E:HIS119 3.0 22.9 1.0
CG E:HIS77 3.1 25.1 1.0
CE1 E:HIS119 3.2 22.8 1.0
CB E:HIS119 3.2 22.8 1.0
CB E:CYS114 3.2 23.2 1.0
O E:GLN76 3.3 25.7 1.0
CB E:HIS77 3.5 23.4 1.0
CA E:HIS77 3.5 24.1 1.0
CE E:MET124 3.9 24.8 1.0
CB E:ILE116 4.2 24.6 1.0
NE2 E:HIS77 4.2 25.4 1.0
C E:GLN76 4.2 25.4 1.0
CD2 E:HIS119 4.2 21.9 1.0
CD2 E:HIS77 4.2 25.6 1.0
NE2 E:HIS119 4.3 22.2 1.0
N E:HIS77 4.3 23.8 1.0
CG1 E:ILE116 4.4 24.4 1.0
CG E:MET124 4.4 25.4 1.0
N E:ASP78 4.5 23.6 1.0
C E:HIS77 4.6 24.1 1.0
CA E:CYS114 4.7 24.4 1.0
CA E:HIS119 4.8 24.9 1.0
CB E:MET124 4.8 24.9 1.0
CG2 E:ILE116 4.9 22.7 1.0
SD E:MET40 4.9 41.7 1.0
N E:ILE116 5.0 25.4 1.0

Copper binding site 16 out of 18 in 2dv6

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Copper binding site 16 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 16 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu500

b:23.2
occ:1.00
ND1 F:HIS268 2.1 18.6 1.0
ND1 F:HIS219 2.2 20.8 1.0
SG F:CYS260 2.2 21.4 1.0
SD F:MET273 2.5 19.2 1.0
CE1 F:HIS268 3.0 18.2 1.0
CG F:HIS268 3.0 19.1 1.0
CG F:HIS219 3.1 21.5 1.0
CE1 F:HIS219 3.1 19.8 1.0
CB F:CYS260 3.2 19.0 1.0
CE F:MET273 3.4 18.1 1.0
CB F:HIS268 3.4 17.3 1.0
CB F:HIS219 3.4 20.2 1.0
CA F:HIS219 3.7 21.9 1.0
NE2 F:HIS268 4.0 20.0 1.0
CD2 F:HIS268 4.1 18.7 1.0
O F:VAL218 4.1 22.3 1.0
CG F:MET273 4.1 18.2 1.0
NE2 F:HIS219 4.3 21.9 1.0
CD2 F:HIS219 4.3 21.9 1.0
N F:SER220 4.4 22.8 1.0
CE3 F:TRP186 4.5 18.2 1.0
CA F:HIS268 4.6 17.3 1.0
CA F:CYS260 4.6 20.7 1.0
C F:HIS219 4.6 22.5 1.0
CB F:MET273 4.6 18.0 1.0
CB F:THR262 4.7 21.8 1.0
N F:HIS219 4.7 22.1 1.0
C F:VAL218 4.8 22.8 1.0
OG1 F:THR262 4.9 22.0 1.0

Copper binding site 17 out of 18 in 2dv6

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Copper binding site 17 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 17 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu501

b:28.7
occ:1.00
NE2 F:HIS259 2.1 20.3 1.0
NE2 F:HIS224 2.1 21.1 1.0
NE2 E:HIS416 2.1 23.6 1.0
O F:HOH7701 2.6 50.7 0.5
CD2 F:HIS259 3.0 18.7 1.0
CE1 F:HIS224 3.0 22.8 1.0
CD2 E:HIS416 3.1 22.0 1.0
CD2 F:HIS224 3.1 21.8 1.0
CE1 F:HIS259 3.1 19.0 1.0
CE1 E:HIS416 3.2 22.2 1.0
OD1 F:ASP222 3.7 33.3 1.0
NE2 E:HIS365 3.9 23.1 1.0
CD2 E:HIS365 4.1 22.0 1.0
ND1 F:HIS224 4.2 23.4 1.0
CG F:HIS259 4.2 19.7 1.0
ND1 F:HIS259 4.2 19.1 1.0
CG F:HIS224 4.2 22.2 1.0
CG E:HIS416 4.2 21.5 1.0
ND1 E:HIS416 4.3 21.6 1.0
CG F:ASP222 4.3 30.1 1.0
OD2 F:ASP222 4.5 29.7 1.0
CE1 E:HIS365 4.7 22.7 1.0
O F:HOH7701 4.7 36.5 0.5
CD2 E:LEU418 4.8 18.2 1.0
O F:HOH7539 4.9 29.5 1.0
CG E:HIS365 5.0 22.1 1.0

Copper binding site 18 out of 18 in 2dv6

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Copper binding site 18 out of 18 in the Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 18 of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cu502

b:26.9
occ:1.00
ND1 F:HIS119 2.1 22.5 1.0
ND1 F:HIS77 2.1 25.0 1.0
SG F:CYS114 2.2 24.2 1.0
SD F:MET124 2.9 27.1 1.0
CG F:HIS119 3.0 23.5 1.0
CE1 F:HIS77 3.0 25.6 1.0
CG F:HIS77 3.2 25.7 1.0
CE1 F:HIS119 3.2 23.7 1.0
O F:GLN76 3.2 26.3 1.0
CB F:HIS119 3.2 24.4 1.0
CB F:CYS114 3.3 24.6 1.0
CA F:HIS77 3.5 24.3 1.0
CB F:HIS77 3.5 23.0 1.0
CE F:MET124 4.0 22.7 1.0
C F:GLN76 4.1 25.2 1.0
NE2 F:HIS77 4.1 27.3 1.0
CD2 F:HIS119 4.2 23.4 1.0
CB F:ILE116 4.2 25.7 1.0
NE2 F:HIS119 4.2 24.1 1.0
CD2 F:HIS77 4.2 25.1 1.0
N F:HIS77 4.3 23.7 1.0
CG1 F:ILE116 4.3 25.0 1.0
CG F:MET124 4.3 23.8 1.0
N F:ASP78 4.6 24.5 1.0
C F:HIS77 4.6 24.7 1.0
CA F:CYS114 4.7 24.7 1.0
CA F:HIS119 4.7 26.2 1.0
CB F:MET124 4.8 25.0 1.0
SD F:MET40 4.9 43.2 1.0

Reference:

M.Nojiri, Y.Xie, T.Inoue, T.Yamamoto, H.Matsumura, K.Kataoka, Deligeer, K.Yamaguchi, Y.Kai, S.Suzuki. Structure and Function of A Hexameric Copper-Containing Nitrite Reductase. Proc.Natl.Acad.Sci.Usa V. 104 4315 2007.
ISSN: ISSN 0027-8424
PubMed: 17360521
DOI: 10.1073/PNAS.0609195104
Page generated: Thu Sep 3 16:34:33 2020
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