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Copper in PDB 4knt: Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5

Protein crystallography data

The structure of Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5, PDB code: 4knt 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) 34.11 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.868, 123.090, 88.431, 90.00, 97.23, 90.00
R / Rfree (%) 17 / 20

Copper Binding Sites:

The binding sites of Copper atom in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5 (pdb code 4knt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5, PDB code: 4knt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 4knt

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Copper binding site 1 out of 6 in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5


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 pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu407

b:21.3
occ:0.85
NE2 A:HIS88 2.0 14.1 1.0
NE2 A:HIS122 2.1 13.1 1.0
NE2 B:HIS277 2.1 14.9 1.0
O A:HOH658 2.2 24.7 1.0
CE1 A:HIS88 2.9 13.8 1.0
CD2 A:HIS122 3.0 13.0 1.0
CE1 B:HIS277 3.0 14.4 1.0
CD2 A:HIS88 3.1 13.9 1.0
CE1 A:HIS122 3.1 13.3 1.0
CD2 B:HIS277 3.1 15.4 1.0
CD2 A:PHE120 4.0 14.4 1.0
NE2 B:HIS227 4.0 14.1 1.0
OD2 A:ASP86 4.1 20.2 1.0
ND1 A:HIS88 4.1 13.8 1.0
CD2 B:HIS227 4.1 14.0 1.0
CG A:HIS122 4.1 13.0 1.0
ND1 B:HIS277 4.2 14.9 1.0
ND1 A:HIS122 4.2 13.2 1.0
CG A:HIS88 4.2 14.2 1.0
CE2 A:PHE120 4.2 14.9 1.0
CG B:HIS277 4.2 14.6 1.0
CG A:ASP86 4.4 18.8 1.0
OD1 A:ASP86 4.5 20.4 1.0
CE1 B:HIS227 4.7 14.0 1.0
O A:HOH550 4.8 15.5 1.0
CG B:HIS227 4.9 14.1 1.0
CG A:PHE120 4.9 14.2 1.0

Copper binding site 2 out of 6 in 4knt

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Copper binding site 2 out of 6 in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5


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 pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu408

b:21.4
occ:0.90
ND1 A:HIS83 2.1 14.9 1.0
ND1 A:HIS131 2.1 12.8 1.0
SG A:CYS123 2.2 14.0 1.0
SD A:MET136 2.5 14.5 1.0
CE1 A:HIS131 3.0 13.8 1.0
CE1 A:HIS83 3.1 15.0 1.0
CG A:HIS131 3.1 13.7 1.0
CG A:HIS83 3.1 15.0 1.0
CB A:CYS123 3.2 14.3 1.0
CE A:MET136 3.4 13.8 1.0
CB A:HIS83 3.5 14.9 1.0
CB A:HIS131 3.5 13.7 1.0
CA A:HIS83 3.8 15.1 1.0
CG A:MET136 4.0 14.5 1.0
O A:SER82 4.1 15.3 1.0
NE2 A:HIS131 4.1 13.4 1.0
CD2 A:HIS131 4.2 13.9 1.0
CB A:SER125 4.2 16.7 1.0
NE2 A:HIS83 4.2 14.2 1.0
CD2 A:HIS83 4.3 14.6 1.0
OG A:SER125 4.4 17.0 1.0
N A:SER84 4.5 15.1 1.0
CB A:MET136 4.5 13.6 1.0
CA A:HIS131 4.6 13.7 1.0
CE3 A:TRP50 4.6 14.1 1.0
CA A:CYS123 4.6 14.2 1.0
C A:HIS83 4.7 15.1 1.0
N A:HIS83 4.8 15.1 1.0
C A:SER82 4.9 15.7 1.0

Copper binding site 3 out of 6 in 4knt

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Copper binding site 3 out of 6 in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5


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 pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:20.9
occ:0.90
NE2 B:HIS88 2.1 11.0 1.0
NE2 B:HIS122 2.1 11.8 1.0
NE2 C:HIS277 2.1 14.3 1.0
O B:HOH665 2.3 28.3 1.0
CE1 B:HIS88 3.0 11.6 1.0
CD2 B:HIS122 3.0 12.0 1.0
CD2 B:HIS88 3.1 11.6 1.0
CD2 C:HIS277 3.1 13.8 1.0
CE1 B:HIS122 3.1 12.2 1.0
CE1 C:HIS277 3.1 14.0 1.0
NE2 C:HIS227 3.9 13.8 1.0
CD2 B:PHE120 4.0 11.8 1.0
CD2 C:HIS227 4.0 13.2 1.0
ND1 B:HIS88 4.1 11.9 1.0
CG B:HIS122 4.2 11.7 1.0
ND1 B:HIS122 4.2 11.7 1.0
CG B:HIS88 4.2 11.6 1.0
CE2 B:PHE120 4.2 11.8 1.0
ND1 C:HIS277 4.2 13.5 1.0
OD2 B:ASP86 4.2 18.7 1.0
CG C:HIS277 4.2 13.3 1.0
CG B:ASP86 4.5 16.7 1.0
OD1 B:ASP86 4.5 18.4 1.0
CE1 C:HIS227 4.6 12.9 1.0
CG C:HIS227 4.8 12.6 1.0
O B:HOH591 4.8 12.4 1.0
CG B:PHE120 4.9 11.4 1.0

Copper binding site 4 out of 6 in 4knt

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Copper binding site 4 out of 6 in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5


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 pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu404

b:18.9
occ:0.90
ND1 B:HIS83 2.1 12.8 1.0
ND1 B:HIS131 2.2 10.8 1.0
SG B:CYS123 2.3 12.4 1.0
SD B:MET136 2.5 14.1 1.0
CE1 B:HIS131 3.0 11.4 1.0
CE1 B:HIS83 3.1 12.8 1.0
CG B:HIS83 3.2 13.1 1.0
CG B:HIS131 3.2 11.1 1.0
CB B:CYS123 3.2 13.0 1.0
CE B:MET136 3.3 12.8 1.0
CB B:HIS83 3.5 12.7 1.0
CB B:HIS131 3.6 11.3 1.0
CA B:HIS83 3.8 12.8 1.0
CG B:MET136 4.0 13.1 1.0
O B:SER82 4.1 13.0 1.0
NE2 B:HIS131 4.1 11.2 1.0
CB B:SER125 4.2 14.5 1.0
NE2 B:HIS83 4.2 12.9 1.0
CD2 B:HIS131 4.2 11.2 1.0
CD2 B:HIS83 4.3 12.4 1.0
OG B:SER125 4.4 15.0 1.0
N B:SER84 4.5 12.8 1.0
CB B:MET136 4.5 12.3 1.0
CE3 B:TRP50 4.5 12.3 1.0
CA B:HIS131 4.6 11.4 1.0
CA B:CYS123 4.7 13.0 1.0
C B:HIS83 4.7 12.7 1.0
N B:HIS83 4.8 13.0 1.0
C B:SER82 4.8 13.4 1.0

Copper binding site 5 out of 6 in 4knt

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Copper binding site 5 out of 6 in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5


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 pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu405

b:20.2
occ:0.85
NE2 C:HIS88 2.0 13.1 1.0
NE2 C:HIS122 2.1 12.8 1.0
NE2 A:HIS277 2.1 14.1 1.0
O C:HOH723 2.4 25.6 1.0
CE1 C:HIS88 2.9 13.4 1.0
CD2 C:HIS122 2.9 12.3 1.0
CD2 C:HIS88 3.0 12.9 1.0
CE1 A:HIS277 3.1 14.1 1.0
CD2 A:HIS277 3.1 14.3 1.0
CE1 C:HIS122 3.2 12.3 1.0
CD2 C:PHE120 4.0 14.0 1.0
NE2 A:HIS227 4.0 14.3 1.0
OD2 C:ASP86 4.0 19.5 1.0
ND1 C:HIS88 4.1 13.1 1.0
CD2 A:HIS227 4.1 13.7 1.0
CG C:HIS122 4.1 11.5 1.0
CG C:HIS88 4.2 13.2 1.0
ND1 A:HIS277 4.2 13.8 1.0
CE2 C:PHE120 4.2 14.2 1.0
ND1 C:HIS122 4.2 12.1 1.0
CG A:HIS277 4.3 14.1 1.0
CG C:ASP86 4.4 17.8 1.0
OD1 C:ASP86 4.5 19.2 1.0
CE1 A:HIS227 4.7 14.2 1.0
O C:HOH508 4.8 17.7 1.0
CG A:HIS227 4.9 13.8 1.0
CG C:PHE120 4.9 13.5 1.0

Copper binding site 6 out of 6 in 4knt

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Copper binding site 6 out of 6 in the Copper Nitrite Reductase From Nitrosomonas Europaea pH 8.5


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 pH 8.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu406

b:21.8
occ:0.95
ND1 C:HIS131 2.1 12.6 1.0
ND1 C:HIS83 2.1 13.4 1.0
SG C:CYS123 2.3 12.8 1.0
SD C:MET136 2.5 15.2 1.0
CE1 C:HIS131 2.9 12.9 1.0
CE1 C:HIS83 3.1 14.4 1.0
CG C:HIS131 3.1 12.7 1.0
CB C:CYS123 3.2 13.0 1.0
CG C:HIS83 3.2 14.6 1.0
CE C:MET136 3.4 14.6 1.0
CB C:HIS83 3.5 14.5 1.0
CB C:HIS131 3.5 12.1 1.0
CA C:HIS83 3.8 14.9 1.0
CG C:MET136 4.0 14.0 1.0
NE2 C:HIS131 4.0 13.1 1.0
CD2 C:HIS131 4.1 13.0 1.0
O C:SER82 4.2 15.6 1.0
CB C:SER125 4.2 15.4 1.0
NE2 C:HIS83 4.2 13.6 1.0
CD2 C:HIS83 4.3 13.6 1.0
OG C:SER125 4.3 15.7 1.0
CB C:MET136 4.5 13.0 1.0
N C:SER84 4.5 14.9 1.0
CA C:HIS131 4.5 12.1 1.0
CE3 C:TRP50 4.6 14.1 1.0
CA C:CYS123 4.6 13.0 1.0
C C:HIS83 4.7 14.8 1.0
N C:HIS83 4.8 15.1 1.0
C C:SER82 4.9 15.9 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 11:15:00 2020

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