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Copper in PDB 4knu: Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5

Protein crystallography data

The structure of Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5, PDB code: 4knu 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) 29.80 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.087, 136.940, 121.486, 90.00, 101.18, 90.00
R / Rfree (%) 17.1 / 20.9

Other elements in 4knu:

The structure of Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Copper Binding Sites:

Pages:

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

Binding sites:

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

Copper binding site 1 out of 12 in 4knu

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Copper binding site 1 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:10.5
occ:1.00
ND1 A:HIS131 2.1 8.8 1.0
ND1 A:HIS83 2.1 9.3 1.0
SG A:CYS123 2.2 8.8 1.0
SD A:MET136 2.5 8.6 1.0
CE1 A:HIS131 2.9 9.0 1.0
CE1 A:HIS83 3.1 9.3 1.0
CG A:HIS131 3.1 9.0 1.0
CG A:HIS83 3.1 9.4 1.0
CB A:CYS123 3.1 8.8 1.0
CE A:MET136 3.3 8.6 1.0
CB A:HIS83 3.5 9.5 1.0
CB A:HIS131 3.5 8.9 1.0
CA A:HIS83 3.7 9.4 1.0
NE2 A:HIS131 4.0 8.8 1.0
O A:SER82 4.1 10.4 1.0
CG A:MET136 4.1 8.4 1.0
CD2 A:HIS131 4.1 9.0 1.0
CB A:SER125 4.2 12.6 1.0
NE2 A:HIS83 4.2 9.5 1.0
CD2 A:HIS83 4.3 9.3 1.0
OG A:SER125 4.3 12.1 1.0
N A:SER84 4.5 9.1 1.0
CB A:MET136 4.6 8.3 1.0
CA A:CYS123 4.6 8.9 1.0
CA A:HIS131 4.6 8.9 1.0
CE3 A:TRP50 4.6 8.9 1.0
C A:HIS83 4.7 9.5 1.0
N A:HIS83 4.7 9.8 1.0
C A:SER82 4.8 10.3 1.0
N A:SER125 5.0 11.9 1.0

Copper binding site 2 out of 12 in 4knu

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Copper binding site 2 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:10.2
occ:1.00
NE2 A:HIS88 2.0 7.9 1.0
NE2 F:HIS277 2.0 8.9 1.0
NE2 A:HIS122 2.2 7.9 1.0
O A:HOH748 2.5 13.7 1.0
CE1 A:HIS88 2.9 7.9 1.0
CD2 A:HIS122 3.0 8.0 1.0
CD2 A:HIS88 3.0 8.0 1.0
CE1 F:HIS277 3.0 9.0 1.0
CD2 F:HIS277 3.0 9.1 1.0
CE1 A:HIS122 3.2 8.0 1.0
NE2 F:HIS227 4.0 8.4 1.0
CD2 A:PHE120 4.0 7.4 1.0
CD2 F:HIS227 4.0 8.5 1.0
ND1 A:HIS88 4.1 7.8 1.0
OD2 A:ASP86 4.1 10.8 1.0
CG A:HIS88 4.1 7.9 1.0
ND1 F:HIS277 4.2 9.2 1.0
CE2 A:PHE120 4.2 7.4 1.0
CG F:HIS277 4.2 9.1 1.0
CG A:HIS122 4.2 8.0 1.0
ND1 A:HIS122 4.3 7.9 1.0
CG A:ASP86 4.4 9.8 1.0
OD1 A:ASP86 4.5 9.9 1.0
O F:HOH782 4.7 10.5 1.0
CE1 F:HIS227 4.7 8.4 1.0
CG F:HIS227 4.8 8.4 1.0
CG A:PHE120 4.9 7.4 1.0

Copper binding site 3 out of 12 in 4knu

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Copper binding site 3 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:9.5
occ:1.00
ND1 B:HIS83 2.1 8.5 1.0
ND1 B:HIS131 2.2 8.6 1.0
SG B:CYS123 2.3 8.4 1.0
SD B:MET136 2.4 9.0 1.0
CE1 B:HIS131 3.0 8.6 1.0
CE1 B:HIS83 3.0 8.4 1.0
CG B:HIS131 3.2 8.6 1.0
CB B:CYS123 3.2 8.3 1.0
CG B:HIS83 3.2 8.3 1.0
CE B:MET136 3.3 8.6 1.0
CB B:HIS83 3.6 8.4 1.0
CB B:HIS131 3.6 8.4 1.0
CA B:HIS83 3.8 8.4 1.0
CG B:MET136 4.0 8.7 1.0
O B:SER82 4.1 8.5 1.0
NE2 B:HIS131 4.1 8.7 1.0
NE2 B:HIS83 4.2 8.2 1.0
CD2 B:HIS131 4.2 8.7 1.0
CB B:SER125 4.3 12.2 1.0
CD2 B:HIS83 4.3 8.4 1.0
CB B:MET136 4.4 8.0 1.0
N B:SER84 4.5 7.9 1.0
CE3 B:TRP50 4.6 8.4 1.0
OG B:SER125 4.6 11.5 1.0
CA B:HIS131 4.6 8.0 1.0
CA B:CYS123 4.6 8.3 1.0
C B:HIS83 4.7 8.2 1.0
N B:HIS83 4.8 8.5 1.0
C B:SER82 4.9 8.8 1.0

Copper binding site 4 out of 12 in 4knu

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Copper binding site 4 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:8.8
occ:1.00
NE2 B:HIS88 2.0 6.9 1.0
NE2 A:HIS277 2.0 7.2 1.0
NE2 B:HIS122 2.0 6.9 1.0
O B:HOH784 2.4 18.9 1.0
CD2 B:HIS122 2.9 7.0 1.0
CE1 B:HIS88 3.0 6.8 1.0
CE1 A:HIS277 3.0 7.3 1.0
CD2 A:HIS277 3.0 7.3 1.0
CD2 B:HIS88 3.0 6.8 1.0
CE1 B:HIS122 3.1 7.1 1.0
NE2 A:HIS227 3.9 6.9 1.0
CD2 B:PHE120 3.9 6.5 1.0
CD2 A:HIS227 4.0 6.8 1.0
OD2 B:ASP86 4.0 8.9 1.0
ND1 B:HIS88 4.1 6.8 1.0
CE2 B:PHE120 4.1 6.5 1.0
CG B:HIS122 4.1 6.9 1.0
ND1 A:HIS277 4.2 7.4 1.0
CG B:HIS88 4.2 6.7 1.0
ND1 B:HIS122 4.2 7.0 1.0
CG A:HIS277 4.2 7.3 1.0
CG B:ASP86 4.4 8.3 1.0
OD1 B:ASP86 4.5 8.5 1.0
CE1 A:HIS227 4.8 6.8 1.0
O A:HOH754 4.8 8.8 1.0
CG A:HIS227 4.8 6.7 1.0
CG B:PHE120 4.9 6.5 1.0

Copper binding site 5 out of 12 in 4knu

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Copper binding site 5 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:11.4
occ:1.00
ND1 C:HIS131 2.1 10.5 1.0
ND1 C:HIS83 2.1 10.5 1.0
SG C:CYS123 2.2 9.1 1.0
SD C:MET136 2.5 11.1 1.0
CE1 C:HIS131 2.9 10.7 1.0
CE1 C:HIS83 3.0 10.6 1.0
CG C:HIS131 3.1 10.5 1.0
CG C:HIS83 3.1 10.4 1.0
CB C:CYS123 3.2 9.1 1.0
CE C:MET136 3.3 10.9 1.0
CB C:HIS83 3.5 10.0 1.0
CB C:HIS131 3.6 10.3 1.0
CA C:HIS83 3.8 10.2 1.0
CG C:MET136 4.0 10.7 1.0
NE2 C:HIS131 4.0 11.0 1.0
O C:SER82 4.1 10.2 1.0
CD2 C:HIS131 4.1 10.8 1.0
NE2 C:HIS83 4.2 10.8 1.0
CB C:SER125 4.3 13.5 1.0
CD2 C:HIS83 4.3 10.6 1.0
CB C:MET136 4.4 10.1 1.0
N C:SER84 4.5 9.7 1.0
OG C:SER125 4.5 13.0 1.0
CE3 C:TRP50 4.6 10.8 1.0
CA C:HIS131 4.6 10.0 1.0
CA C:CYS123 4.6 9.3 1.0
C C:HIS83 4.7 9.9 1.0
N C:HIS83 4.8 10.2 1.0
C C:SER82 4.9 10.7 1.0

Copper binding site 6 out of 12 in 4knu

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Copper binding site 6 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu402

b:9.8
occ:1.00
NE2 C:HIS88 2.0 6.7 1.0
NE2 C:HIS122 2.0 8.6 1.0
NE2 E:HIS277 2.1 8.3 1.0
O C:HOH750 2.4 17.0 1.0
CE1 C:HIS88 2.9 6.9 1.0
CD2 C:HIS122 3.0 8.3 1.0
CE1 C:HIS122 3.0 8.5 1.0
CD2 C:HIS88 3.0 6.7 1.0
CE1 E:HIS277 3.1 8.3 1.0
CD2 E:HIS277 3.1 8.3 1.0
CD2 C:PHE120 3.9 7.8 1.0
OD2 C:ASP86 4.0 10.9 1.0
CD2 E:HIS227 4.0 7.0 1.0
NE2 E:HIS227 4.0 7.1 1.0
ND1 C:HIS88 4.1 6.7 1.0
CE2 C:PHE120 4.1 8.2 1.0
ND1 C:HIS122 4.1 8.5 1.0
CG C:HIS122 4.1 8.2 1.0
CG C:HIS88 4.2 6.7 1.0
ND1 E:HIS277 4.2 8.2 1.0
CG E:HIS277 4.2 8.2 1.0
CG C:ASP86 4.4 9.7 1.0
OD1 C:ASP86 4.4 9.7 1.0
O E:HOH784 4.7 8.4 1.0
CE1 E:HIS227 4.8 7.1 1.0
CG E:HIS227 4.8 7.2 1.0
CG C:PHE120 4.9 7.7 1.0

Copper binding site 7 out of 12 in 4knu

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Copper binding site 7 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu401

b:13.4
occ:1.00
ND1 D:HIS131 2.1 11.4 1.0
ND1 D:HIS83 2.1 11.6 1.0
SG D:CYS123 2.2 10.8 1.0
SD D:MET136 2.5 13.1 1.0
CE1 D:HIS131 2.9 11.7 1.0
CE1 D:HIS83 3.0 12.2 1.0
CG D:HIS131 3.1 11.2 1.0
CG D:HIS83 3.1 12.1 1.0
CB D:CYS123 3.2 10.7 1.0
CE D:MET136 3.3 12.6 1.0
CB D:HIS83 3.5 12.3 1.0
CB D:HIS131 3.6 10.8 1.0
CA D:HIS83 3.7 12.7 1.0
CG D:MET136 4.0 12.2 1.0
NE2 D:HIS131 4.1 11.6 1.0
O D:SER82 4.1 14.6 1.0
CD2 D:HIS131 4.2 11.7 1.0
NE2 D:HIS83 4.2 11.9 1.0
CD2 D:HIS83 4.3 11.8 1.0
CB D:SER125 4.3 14.2 1.0
CB D:MET136 4.5 11.9 1.0
OG D:SER125 4.5 13.5 1.0
N D:SER84 4.5 12.0 1.0
CA D:HIS131 4.6 10.6 1.0
CA D:CYS123 4.6 10.6 1.0
CE3 D:TRP50 4.6 12.4 1.0
C D:HIS83 4.7 12.5 1.0
N D:HIS83 4.8 13.4 1.0
C D:SER82 4.8 13.9 1.0

Copper binding site 8 out of 12 in 4knu

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Copper binding site 8 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu402

b:10.4
occ:1.00
NE2 D:HIS88 2.0 8.0 1.0
NE2 D:HIS122 2.0 10.1 1.0
NE2 C:HIS277 2.1 8.9 1.0
O D:HOH755 2.5 19.3 1.0
CE1 D:HIS88 2.9 8.0 1.0
CD2 D:HIS122 2.9 10.1 1.0
CE1 D:HIS122 3.0 10.3 1.0
CE1 C:HIS277 3.0 8.8 1.0
CD2 D:HIS88 3.1 8.4 1.0
CD2 C:HIS277 3.1 8.7 1.0
CD2 D:PHE120 3.9 8.9 1.0
OD2 D:ASP86 4.0 12.2 1.0
NE2 C:HIS227 4.1 7.1 1.0
CD2 C:HIS227 4.1 7.0 1.0
CE2 D:PHE120 4.1 9.3 1.0
ND1 D:HIS88 4.1 8.1 1.0
CG D:HIS122 4.1 9.9 1.0
ND1 D:HIS122 4.1 10.0 1.0
CG D:HIS88 4.2 8.0 1.0
ND1 C:HIS277 4.2 8.5 1.0
CG C:HIS277 4.3 8.6 1.0
CG D:ASP86 4.4 11.2 1.0
OD1 D:ASP86 4.6 11.0 1.0
CG D:PHE120 4.8 8.9 1.0
O C:HOH759 4.9 9.3 1.0
CE1 C:HIS227 4.9 7.2 1.0
CG C:HIS227 4.9 7.4 1.0

Copper binding site 9 out of 12 in 4knu

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Copper binding site 9 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu401

b:9.7
occ:1.00
ND1 E:HIS131 2.1 7.7 1.0
ND1 E:HIS83 2.2 8.1 1.0
SG E:CYS123 2.2 7.8 1.0
SD E:MET136 2.5 8.7 1.0
CE1 E:HIS131 2.9 7.8 1.0
CG E:HIS131 3.1 7.8 1.0
CE1 E:HIS83 3.1 8.4 1.0
CB E:CYS123 3.2 8.1 1.0
CG E:HIS83 3.2 8.1 1.0
CE E:MET136 3.4 8.4 1.0
CB E:HIS83 3.5 8.2 1.0
CB E:HIS131 3.6 7.8 1.0
CA E:HIS83 3.7 8.3 1.0
O E:SER82 4.1 8.8 1.0
CG E:MET136 4.1 8.1 1.0
NE2 E:HIS131 4.1 7.5 1.0
CB E:SER125 4.2 11.1 1.0
CD2 E:HIS131 4.2 7.8 1.0
NE2 E:HIS83 4.3 8.2 1.0
CD2 E:HIS83 4.3 8.3 1.0
OG E:SER125 4.4 10.9 1.0
N E:SER84 4.4 8.1 1.0
CB E:MET136 4.5 7.9 1.0
CA E:HIS131 4.6 7.9 1.0
CA E:CYS123 4.6 8.1 1.0
CE3 E:TRP50 4.6 8.7 1.0
C E:HIS83 4.6 8.2 1.0
N E:HIS83 4.7 8.5 1.0
C E:SER82 4.8 8.9 1.0
N E:SER125 5.0 10.9 1.0

Copper binding site 10 out of 12 in 4knu

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Copper binding site 10 out of 12 in the Copper Nitrite Reductase From Nitrosomonas Europaea 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 Copper Nitrite Reductase From Nitrosomonas Europaea at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu402

b:8.8
occ:1.00
NE2 E:HIS122 2.1 7.3 1.0
NE2 E:HIS88 2.1 7.3 1.0
NE2 D:HIS277 2.1 7.7 1.0
O E:HOH777 2.4 16.3 1.0
CD2 E:HIS122 3.0 7.3 1.0
CE1 E:HIS88 3.0 7.3 1.0
CE1 E:HIS122 3.0 7.4 1.0
CD2 D:HIS277 3.1 7.7 1.0
CD2 E:HIS88 3.1 7.4 1.0
CE1 D:HIS277 3.1 7.6 1.0
CD2 E:PHE120 4.0 6.9 1.0
NE2 D:HIS227 4.0 8.0 1.0
OD2 E:ASP86 4.0 9.4 1.0
CD2 D:HIS227 4.1 7.9 1.0
ND1 E:HIS122 4.1 7.3 1.0
CE2 E:PHE120 4.2 7.1 1.0
CG E:HIS122 4.2 7.2 1.0
ND1 E:HIS88 4.2 7.4 1.0
ND1 D:HIS277 4.2 7.6 1.0
CG E:HIS88 4.2 7.4 1.0
CG D:HIS277 4.3 7.7 1.0
CG E:ASP86 4.4 8.8 1.0
OD1 E:ASP86 4.5 8.9 1.0
CE1 D:HIS227 4.7 7.8 1.0
CG D:HIS227 4.8 8.0 1.0
O E:HOH501 4.8 9.4 1.0
CG E:PHE120 4.9 6.8 1.0

Reference:

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
Page generated: Sun Dec 13 11:15:04 2020

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