Copper in PDB 4kns: Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5

The structure of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5, PDB code: 4kns was solved by A.C.Rosenzweig, T.L.Lawton, L.A.Sayavedra-Soto, D.J.Arp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.01 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.438, 138.069, 120.688, 90.00, 101.64, 90.00
R / Rfree (%)	18.5 / 22.9

The structure of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 (pdb code 4kns). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5, PDB code: 4kns:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu401 b:26.8 occ:1.00 ND1 A:HIS83 2.1 22.8 1.0 ND1 A:HIS131 2.3 20.9 1.0 SG A:CYS123 2.3 21.4 1.0 SD A:MET136 2.4 20.4 1.0 CE1 A:HIS131 3.0 21.1 1.0 CE1 A:HIS83 3.1 22.4 1.0 CG A:HIS83 3.1 23.0 1.0 CB A:CYS123 3.3 21.4 1.0 CG A:HIS131 3.3 21.1 1.0 CE A:MET136 3.5 20.2 1.0 CB A:HIS83 3.5 23.2 1.0 CA A:HIS83 3.8 23.6 1.0 CB A:HIS131 3.8 21.3 1.0 CG A:MET136 3.9 20.3 1.0 O A:SER82 4.1 23.9 1.0 NE2 A:HIS131 4.1 20.8 1.0 NE2 A:HIS83 4.2 22.6 1.0 CD2 A:HIS83 4.3 22.7 1.0 CD2 A:HIS131 4.3 21.1 1.0 CB A:SER125 4.4 26.3 1.0 CB A:MET136 4.5 19.8 1.0 N A:SER84 4.5 24.0 1.0 OG A:SER125 4.5 26.2 1.0 CE3 A:TRP50 4.6 20.7 1.0 C A:HIS83 4.7 23.7 1.0 CA A:CYS123 4.7 21.5 1.0 N A:HIS83 4.7 23.7 1.0 CA A:HIS131 4.8 21.5 1.0 C A:SER82 4.8 23.9 1.0

Copper binding site 2 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu402 b:27.7 occ:1.00 NE2 A:HIS122 2.1 19.0 1.0 NE2 A:HIS88 2.1 22.4 1.0 NE2 F:HIS277 2.1 21.4 1.0 CD2 A:HIS122 2.9 19.3 1.0 CE1 F:HIS277 3.0 21.6 1.0 CE1 A:HIS88 3.0 22.4 1.0 CD2 A:HIS88 3.1 22.3 1.0 CE1 A:HIS122 3.1 19.1 1.0 CD2 F:HIS277 3.2 21.5 1.0 CD2 A:PHE120 3.9 18.6 1.0 OD2 A:ASP86 3.9 24.2 1.0 NE2 F:HIS227 4.0 21.7 1.0 CD2 F:HIS227 4.1 21.8 1.0 CG A:HIS122 4.1 19.3 1.0 CE2 A:PHE120 4.1 18.5 1.0 ND1 F:HIS277 4.2 21.7 1.0 ND1 A:HIS88 4.2 22.4 1.0 ND1 A:HIS122 4.2 19.2 1.0 CG A:HIS88 4.3 22.4 1.0 CG F:HIS277 4.3 21.7 1.0 CG A:ASP86 4.4 24.1 1.0 O F:HOH611 4.6 22.7 1.0 OD1 A:ASP86 4.6 24.3 1.0 CE1 F:HIS227 4.7 21.6 1.0 CG A:PHE120 4.9 18.4 1.0 CG F:HIS227 4.9 21.9 1.0

Copper binding site 3 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu401 b:24.6 occ:1.00 ND1 B:HIS83 2.2 19.5 1.0 SG B:CYS123 2.2 19.4 1.0 ND1 B:HIS131 2.2 19.4 1.0 SD B:MET136 2.5 19.5 1.0 CE1 B:HIS131 3.0 19.4 1.0 CE1 B:HIS83 3.1 19.7 1.0 CB B:CYS123 3.2 20.1 1.0 CG B:HIS131 3.2 19.5 1.0 CG B:HIS83 3.2 19.7 1.0 CB B:HIS83 3.5 19.8 1.0 CE B:MET136 3.5 19.4 1.0 CB B:HIS131 3.6 19.5 1.0 CA B:HIS83 3.8 20.1 1.0 O B:SER82 4.0 21.0 1.0 CG B:MET136 4.1 19.0 1.0 NE2 B:HIS131 4.2 19.3 1.0 CD2 B:HIS131 4.2 19.5 1.0 NE2 B:HIS83 4.3 19.6 1.0 CB B:SER125 4.3 24.3 1.0 CD2 B:HIS83 4.3 19.6 1.0 OG B:SER125 4.4 24.1 1.0 N B:SER84 4.5 20.0 1.0 CB B:MET136 4.6 18.8 1.0 CA B:CYS123 4.6 20.3 1.0 CA B:HIS131 4.6 19.6 1.0 CE3 B:TRP50 4.7 19.6 1.0 C B:HIS83 4.7 20.1 1.0 N B:HIS83 4.8 20.5 1.0 C B:SER82 4.8 21.1 1.0

Copper binding site 4 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu402 b:24.1 occ:1.00 NE2 A:HIS277 2.0 19.9 1.0 NE2 B:HIS88 2.1 20.1 1.0 NE2 B:HIS122 2.2 19.1 1.0 CE1 A:HIS277 3.0 19.8 1.0 CD2 A:HIS277 3.0 19.8 1.0 CD2 B:HIS122 3.1 19.0 1.0 CE1 B:HIS88 3.1 20.0 1.0 CD2 B:HIS88 3.2 20.0 1.0 CE1 B:HIS122 3.2 19.1 1.0 NE2 A:HIS227 3.8 18.8 1.0 OD2 B:ASP86 3.9 20.7 1.0 CD2 A:HIS227 3.9 18.7 1.0 CD2 B:PHE120 4.0 17.6 1.0 ND1 A:HIS277 4.1 19.7 1.0 CE2 B:PHE120 4.1 17.7 1.0 CG A:HIS277 4.2 19.7 1.0 ND1 B:HIS88 4.2 20.0 1.0 CG B:HIS122 4.3 19.1 1.0 ND1 B:HIS122 4.3 19.2 1.0 CG B:HIS88 4.3 20.1 1.0 CG B:ASP86 4.4 20.7 1.0 CE1 A:HIS227 4.5 18.6 1.0 OD1 B:ASP86 4.6 20.8 1.0 O A:HOH644 4.7 17.9 1.0 CG A:HIS227 4.7 18.7 1.0 CG B:PHE120 5.0 17.6 1.0

Copper binding site 5 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu401 b:27.7 occ:1.00 ND1 C:HIS131 2.2 21.4 1.0 ND1 C:HIS83 2.2 22.2 1.0 SG C:CYS123 2.3 19.5 1.0 SD C:MET136 2.4 20.2 1.0 CE1 C:HIS131 3.0 21.4 1.0 CE1 C:HIS83 3.1 21.9 1.0 CG C:HIS131 3.2 21.4 1.0 CG C:HIS83 3.2 22.4 1.0 CB C:CYS123 3.2 19.7 1.0 CE C:MET136 3.3 20.4 1.0 CB C:HIS83 3.6 22.3 1.0 CB C:HIS131 3.6 21.2 1.0 CA C:HIS83 3.9 22.7 1.0 CG C:MET136 3.9 20.1 1.0 O C:SER82 4.1 23.8 1.0 NE2 C:HIS131 4.2 21.3 1.0 NE2 C:HIS83 4.3 22.1 1.0 CD2 C:HIS131 4.3 21.3 1.0 CD2 C:HIS83 4.3 22.2 1.0 CB C:MET136 4.4 19.5 1.0 CB C:SER125 4.5 24.6 1.0 CA C:HIS131 4.6 21.4 1.0 N C:SER84 4.6 22.5 1.0 OG C:SER125 4.6 24.4 1.0 CE3 C:TRP50 4.7 22.4 1.0 CA C:CYS123 4.7 19.7 1.0 C C:HIS83 4.8 22.5 1.0 N C:HIS83 4.8 23.1 1.0 C C:SER82 4.9 23.6 1.0

Copper binding site 6 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu402 b:23.8 occ:1.00 NE2 C:HIS122 2.0 18.8 1.0 NE2 E:HIS277 2.0 18.3 1.0 NE2 C:HIS88 2.1 19.0 1.0 CE1 E:HIS277 2.9 18.3 1.0 CD2 C:HIS122 2.9 18.7 1.0 CE1 C:HIS88 3.1 19.2 1.0 CE1 C:HIS122 3.1 18.8 1.0 CD2 E:HIS277 3.1 18.2 1.0 CD2 C:HIS88 3.1 19.1 1.0 CD2 C:PHE120 3.8 17.7 1.0 CE2 C:PHE120 4.0 17.8 1.0 OD2 C:ASP86 4.0 22.1 1.0 NE2 E:HIS227 4.1 18.7 1.0 ND1 E:HIS277 4.1 18.3 1.0 CG C:HIS122 4.1 18.7 1.0 ND1 C:HIS122 4.1 18.9 1.0 CD2 E:HIS227 4.2 18.7 1.0 ND1 C:HIS88 4.2 19.2 1.0 CG E:HIS277 4.2 18.3 1.0 CG C:HIS88 4.3 19.3 1.0 CG C:ASP86 4.3 21.8 1.0 OD1 C:ASP86 4.5 21.9 1.0 O E:HOH654 4.7 16.6 1.0 CG C:PHE120 4.8 17.8 1.0 CE1 E:HIS227 4.8 18.6 1.0 CG E:HIS227 5.0 18.7 1.0

Copper binding site 7 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu401 b:32.1 occ:1.00 ND1 D:HIS83 2.2 29.2 1.0 ND1 D:HIS131 2.3 27.1 1.0 SG D:CYS123 2.3 26.2 1.0 SD D:MET136 2.5 27.6 1.0 CE1 D:HIS131 3.0 27.4 1.0 CG D:HIS83 3.1 29.3 1.0 CE1 D:HIS83 3.2 28.8 1.0 CB D:CYS123 3.2 26.4 1.0 CG D:HIS131 3.3 27.0 1.0 CB D:HIS83 3.4 29.5 1.0 CE D:MET136 3.5 26.8 1.0 CA D:HIS83 3.6 29.8 1.0 CB D:HIS131 3.8 26.6 1.0 CG D:MET136 4.0 26.8 1.0 O D:SER82 4.0 30.8 1.0 NE2 D:HIS131 4.2 27.2 1.0 CD2 D:HIS83 4.3 29.3 1.0 CB D:SER125 4.3 32.4 1.0 CD2 D:HIS131 4.4 27.3 1.0 NE2 D:HIS83 4.4 29.3 1.0 OG D:SER125 4.4 32.3 1.0 N D:SER84 4.4 29.4 1.0 CB D:MET136 4.5 26.1 1.0 C D:HIS83 4.6 29.7 1.0 N D:HIS83 4.6 30.1 1.0 CE3 D:TRP50 4.7 30.9 1.0 CA D:CYS123 4.7 26.3 1.0 C D:SER82 4.7 30.5 1.0 CA D:HIS131 4.8 26.6 1.0

Copper binding site 8 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu402 b:28.2 occ:1.00 NE2 D:HIS122 2.0 24.7 1.0 NE2 D:HIS88 2.2 22.6 1.0 NE2 C:HIS277 2.2 20.7 1.0 CD2 D:HIS122 3.0 24.6 1.0 CE1 D:HIS122 3.1 24.7 1.0 CE1 C:HIS277 3.1 20.7 1.0 CE1 D:HIS88 3.1 22.7 1.0 CD2 C:HIS277 3.2 20.8 1.0 CD2 D:HIS88 3.2 22.9 1.0 OD2 D:ASP86 3.7 28.6 1.0 NE2 C:HIS227 3.9 21.2 1.0 CD2 C:HIS227 4.0 21.1 1.0 CD2 D:PHE120 4.1 23.0 1.0 CG D:HIS122 4.2 24.7 1.0 ND1 D:HIS122 4.2 24.5 1.0 ND1 C:HIS277 4.2 20.8 1.0 CE2 D:PHE120 4.3 23.1 1.0 ND1 D:HIS88 4.3 23.0 1.0 CG C:HIS277 4.3 20.8 1.0 CG D:ASP86 4.3 28.5 1.0 CG D:HIS88 4.3 23.2 1.0 OD1 D:ASP86 4.6 28.9 1.0 CE1 C:HIS227 4.7 21.2 1.0 O C:HOH668 4.7 24.5 1.0 CG C:HIS227 4.8 21.4 1.0

Copper binding site 9 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu401 b:28.8 occ:1.00 ND1 E:HIS131 2.1 22.0 1.0 ND1 E:HIS83 2.2 21.1 1.0 SG E:CYS123 2.3 18.9 1.0 SD E:MET136 2.5 20.7 1.0 CE1 E:HIS131 2.9 22.3 1.0 CG E:HIS131 3.1 22.1 1.0 CE1 E:HIS83 3.1 21.2 1.0 CG E:HIS83 3.2 21.3 1.0 CB E:CYS123 3.2 19.3 1.0 CE E:MET136 3.5 20.2 1.0 CB E:HIS131 3.5 21.7 1.0 CB E:HIS83 3.6 21.3 1.0 CA E:HIS83 3.8 21.7 1.0 CG E:MET136 4.0 20.2 1.0 O E:SER82 4.0 22.1 1.0 NE2 E:HIS131 4.1 22.4 1.0 CD2 E:HIS131 4.1 22.3 1.0 NE2 E:HIS83 4.3 21.3 1.0 CB E:SER125 4.3 23.9 1.0 CD2 E:HIS83 4.3 21.2 1.0 OG E:SER125 4.4 23.7 1.0 CB E:MET136 4.5 19.6 1.0 CA E:HIS131 4.5 21.6 1.0 N E:SER84 4.6 22.3 1.0 CE3 E:TRP50 4.6 20.9 1.0 CA E:CYS123 4.7 19.4 1.0 C E:HIS83 4.8 22.0 1.0 N E:HIS83 4.8 21.8 1.0 C E:SER82 4.8 22.0 1.0

Copper binding site 10 out of 12 in the Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Reduced Crystal Structure of the Nitrosomonas Europaea Copper Nitrite Reductase at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu402 b:24.6 occ:1.00 NE2 D:HIS277 2.0 21.1 1.0 NE2 E:HIS88 2.1 20.9 1.0 NE2 E:HIS122 2.1 18.4 1.0 CE1 D:HIS277 2.9 21.1 1.0 CE1 E:HIS88 3.0 21.0 1.0 CD2 E:HIS122 3.0 18.5 1.0 CD2 D:HIS277 3.0 21.2 1.0 CD2 E:HIS88 3.2 20.9 1.0 CE1 E:HIS122 3.2 18.5 1.0 CD2 E:PHE120 4.0 19.5 1.0 ND1 D:HIS277 4.0 21.2 1.0 CD2 D:HIS227 4.1 20.4 1.0 NE2 D:HIS227 4.1 20.4 1.0 CG D:HIS277 4.1 21.3 1.0 OD2 E:ASP86 4.1 24.1 1.0 ND1 E:HIS88 4.1 21.2 1.0 CE2 E:PHE120 4.2 19.4 1.0 CG E:HIS122 4.2 18.4 1.0 ND1 E:HIS122 4.2 18.4 1.0 CG E:HIS88 4.3 21.1 1.0 CG E:ASP86 4.5 24.1 1.0 OD1 E:ASP86 4.7 24.4 1.0 CE1 D:HIS227 4.8 20.2 1.0 CG D:HIS227 4.8 20.4 1.0 O E:HOH501 4.8 19.1 1.0 CG E:PHE120 5.0 19.3 1.0

T.J.Lawton, K.E.Bowen, L.A.Sayavedra-Soto, D.J.Arp, A.C.Rosenzweig. Characterization of A Nitrite Reductase Involved in Nitrifier Denitrification. J.Biol.Chem. V. 288 25575 2013.
ISSN: ISSN 0021-9258
PubMed: 23857587
DOI: 10.1074/JBC.M113.484543