Copper in PDB 2dv6: 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;

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

The structure of Crystal Structure of Nitrite Reductase From Hyphomicrobium Denitrificans also contains other interesting chemical elements:

Potassium

(K)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

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;

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 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 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 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 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 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 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 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 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 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

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