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Copper in PDB 5zl1: Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1

Protein crystallography data

The structure of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1, PDB code: 5zl1 was solved by D.Hira, M.Matsumura, R.Kitamura, T.Fujii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.20
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 270.217, 270.217, 128.909, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 25.4

Other elements in 5zl1:

The structure of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 (pdb code 5zl1). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 9 binding sites of Copper where determined in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1, PDB code: 5zl1:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Copper binding site 1 out of 9 in 5zl1

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Copper binding site 1 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:49.1
occ:1.00
 ND1 A:HIS111 2.0 49.4 1.0
ND1 A:HIS157 2.0 44.3 1.0
SG A:CYS148 2.3 43.6 1.0
SD A:MET162 2.3 40.7 1.0
CE1 A:HIS111 2.7 49.0 1.0
CE1 A:HIS157 2.8 43.9 1.0
CG A:HIS157 3.1 43.0 1.0
CG A:HIS111 3.1 49.4 1.0
CE A:MET162 3.4 40.0 1.0
CE3 A:TRP69 3.6 38.3 1.0
CB A:HIS157 3.6 42.1 1.0
CB A:CYS148 3.6 44.1 1.0
CB A:HIS111 3.7 50.3 1.0
O A:PRO110 3.8 54.6 1.0
NE2 A:HIS111 3.8 48.8 1.0
NE2 A:HIS157 3.9 44.4 1.0
CG A:MET162 4.0 38.5 1.0
CZ3 A:TRP69 4.0 38.3 1.0
CD2 A:HIS157 4.0 44.0 1.0
CD2 A:HIS111 4.1 49.1 1.0
CA A:HIS111 4.1 51.2 1.0
CA A:HIS157 4.4 41.6 1.0
CD2 A:TRP69 4.5 38.3 1.0
C A:PRO110 4.7 54.1 1.0
CB A:MET162 4.7 37.5 1.0
CB A:ALA150 4.8 49.2 1.0
N A:HIS111 4.9 52.2 1.0
O A:HIS157 4.9 40.0 1.0
CB A:TRP69 4.9 38.5 1.0
CA A:CYS148 5.0 44.3 1.0

Copper binding site 2 out of 9 in 5zl1

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Copper binding site 2 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu402

b:57.1
occ:1.00
 NE2 A:HIS147 2.1 49.5 1.0
NE2 A:HIS116 2.1 52.7 1.0
CE1 A:HIS116 2.6 51.3 1.0
CE1 A:HIS147 3.0 48.2 1.0
CD2 A:HIS147 3.1 47.8 1.0
CD2 A:HIS116 3.3 51.4 1.0
ND1 A:HIS116 3.9 50.8 1.0
ND1 A:HIS147 4.1 47.2 1.0
CG A:HIS147 4.1 46.4 1.0
CG A:HIS116 4.2 50.7 1.0
OD2 A:ASP114 4.3 51.9 1.0
CG2 A:ILE145 4.5 37.1 1.0

Copper binding site 3 out of 9 in 5zl1

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Copper binding site 3 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:60.9
occ:1.00
 ND1 B:HIS111 2.0 61.7 1.0
ND1 B:HIS157 2.0 56.8 1.0
SG B:CYS148 2.3 54.4 1.0
SD B:MET162 2.3 52.2 1.0
CE1 B:HIS111 2.7 61.8 1.0
CE1 B:HIS157 2.8 56.7 1.0
CG B:HIS157 3.1 55.5 1.0
CG B:HIS111 3.1 61.7 1.0
CE B:MET162 3.4 51.4 1.0
CE3 B:TRP69 3.6 44.5 1.0
CB B:HIS157 3.6 53.9 1.0
CB B:CYS148 3.6 54.1 1.0
CB B:HIS111 3.7 62.0 1.0
O B:PRO110 3.8 63.3 1.0
NE2 B:HIS111 3.8 61.8 1.0
NE2 B:HIS157 3.9 57.7 1.0
CG B:MET162 4.0 49.4 1.0
CZ3 B:TRP69 4.0 44.8 1.0
CD2 B:HIS157 4.0 57.2 1.0
CD2 B:HIS111 4.0 61.8 1.0
CA B:HIS111 4.1 62.4 1.0
CA B:HIS157 4.4 52.8 1.0
CD2 B:TRP69 4.5 44.5 1.0
C B:PRO110 4.7 64.1 1.0
CB B:MET162 4.7 48.3 1.0
CB B:ALA150 4.9 58.5 1.0
N B:HIS111 4.9 63.3 1.0
CB B:TRP69 4.9 44.1 1.0
O B:HIS157 4.9 51.3 1.0
CA B:CYS148 5.0 53.6 1.0

Copper binding site 4 out of 9 in 5zl1

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Copper binding site 4 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu402

b:59.7
occ:1.00
 NE2 B:HIS147 2.1 53.9 1.0
NE2 B:HIS116 2.1 56.3 1.0
NE2 C:HIS310 2.1 50.9 1.0
CE1 B:HIS116 2.6 55.2 1.0
CE1 C:HIS310 2.9 49.3 1.0
CE1 B:HIS147 2.9 52.9 1.0
CD2 B:HIS147 3.1 52.4 1.0
CD2 C:HIS310 3.2 49.5 1.0
CD2 B:HIS116 3.3 55.2 1.0
ND1 B:HIS116 3.9 54.7 1.0
NE2 C:HIS261 4.0 50.2 1.0
ND1 B:HIS147 4.0 52.3 1.0
ND1 C:HIS310 4.1 49.0 1.0
CG B:HIS147 4.1 51.6 1.0
CG B:HIS116 4.2 54.8 1.0
CG C:HIS310 4.2 49.0 1.0
OD2 B:ASP114 4.3 58.1 1.0
CD2 C:HIS261 4.3 49.9 1.0
CG2 B:ILE145 4.5 45.5 1.0
CE1 C:HIS261 4.7 50.4 1.0
CG B:ASP114 5.0 57.5 1.0

Copper binding site 5 out of 9 in 5zl1

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Copper binding site 5 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:60.7
occ:1.00
 NE2 C:HIS214 2.1 61.7 1.0
NE2 B:HIS214 2.1 56.6 1.0
NE2 D:HIS214 2.1 59.6 1.0
CD2 C:HIS214 2.8 61.6 1.0
CD2 B:HIS214 2.8 55.7 1.0
CD2 D:HIS214 2.8 59.5 1.0
CE1 D:HIS214 3.1 59.0 1.0
CE1 C:HIS214 3.1 61.9 1.0
CE1 B:HIS214 3.2 55.8 1.0
CG C:HIS214 3.9 61.1 1.0
CG B:HIS214 4.0 54.5 1.0
CG D:HIS214 4.0 59.0 1.0
ND1 C:HIS214 4.1 61.8 1.0
ND1 D:HIS214 4.1 59.1 1.0
ND1 B:HIS214 4.1 55.2 1.0
O B:ALA212 4.4 48.5 1.0
O D:ALA212 4.5 54.0 1.0
O C:ALA212 4.5 61.3 1.0
O B:GLU213 4.9 48.3 1.0
O C:GLU213 4.9 57.9 1.0

Copper binding site 6 out of 9 in 5zl1

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Copper binding site 6 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:72.2
occ:1.00
 ND1 C:HIS157 2.0 67.9 1.0
ND1 C:HIS111 2.0 76.5 1.0
SD C:MET162 2.3 58.9 1.0
SG C:CYS148 2.3 68.0 1.0
CE1 C:HIS111 2.7 76.8 1.0
CE1 C:HIS157 2.7 68.2 1.0
CG C:HIS157 3.0 66.8 1.0
CG C:HIS111 3.2 76.9 1.0
CE C:MET162 3.4 57.9 1.0
CE3 C:TRP69 3.5 54.9 1.0
CB C:HIS157 3.6 65.4 1.0
CB C:CYS148 3.6 68.1 1.0
CB C:HIS111 3.8 76.9 1.0
O C:PRO110 3.8 80.5 1.0
NE2 C:HIS157 3.8 68.6 1.0
NE2 C:HIS111 3.8 76.8 1.0
CZ3 C:TRP69 3.9 55.2 1.0
CG C:MET162 4.0 58.1 1.0
CD2 C:HIS157 4.0 68.1 1.0
CD2 C:HIS111 4.1 77.1 1.0
CA C:HIS111 4.2 77.6 1.0
CA C:HIS157 4.3 64.3 1.0
CD2 C:TRP69 4.5 54.4 1.0
CB C:MET162 4.7 57.5 1.0
C C:PRO110 4.7 80.1 1.0
CB C:ALA150 4.9 74.8 1.0
CB C:TRP69 4.9 56.1 1.0
O C:HIS157 4.9 62.3 1.0
N C:HIS111 4.9 79.0 1.0
CA C:CYS148 5.0 67.2 1.0

Copper binding site 7 out of 9 in 5zl1

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Copper binding site 7 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu402

b:73.0
occ:1.00
 NE2 C:HIS147 2.1 67.3 1.0
NE2 C:HIS116 2.1 72.4 1.0
NE2 D:HIS310 2.1 62.5 1.0
CE1 C:HIS116 2.6 71.7 1.0
CE1 C:HIS147 2.9 66.2 1.0
CE1 D:HIS310 2.9 60.3 1.0
CD2 C:HIS147 3.1 65.8 1.0
CD2 D:HIS310 3.1 60.3 1.0
CD2 C:HIS116 3.3 72.1 1.0
ND1 C:HIS116 3.9 71.6 1.0
NE2 D:HIS261 3.9 59.0 1.0
ND1 C:HIS147 4.0 65.2 1.0
ND1 D:HIS310 4.1 59.6 1.0
CG C:HIS147 4.1 64.9 1.0
CG C:HIS116 4.2 71.8 1.0
CD2 D:HIS261 4.2 58.7 1.0
CG D:HIS310 4.2 59.5 1.0
OD2 C:ASP114 4.3 70.9 1.0
CG2 C:ILE145 4.5 56.5 1.0
CE1 D:HIS261 4.7 59.4 1.0
CG C:ASP114 5.0 70.3 1.0

Copper binding site 8 out of 9 in 5zl1

Go back to Copper Binding Sites List in 5zl1
Copper binding site 8 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu401

b:71.9
occ:1.00
 ND1 D:HIS111 2.0 72.7 1.0
ND1 D:HIS157 2.0 65.4 1.0
SG D:CYS148 2.3 61.2 1.0
SD D:MET162 2.3 64.0 1.0
CE1 D:HIS111 2.7 72.9 1.0
CE1 D:HIS157 2.8 64.4 1.0
CG D:HIS157 3.1 63.5 1.0
CG D:HIS111 3.1 72.1 1.0
CE D:MET162 3.4 63.3 1.0
CE3 D:TRP69 3.6 63.0 1.0
CB D:HIS157 3.6 62.3 1.0
CB D:CYS148 3.6 62.0 1.0
CB D:HIS111 3.7 71.4 1.0
O D:PRO110 3.8 73.0 1.0
NE2 D:HIS111 3.8 72.3 1.0
NE2 D:HIS157 3.8 64.7 1.0
CG D:MET162 4.0 61.9 1.0
CZ3 D:TRP69 4.0 63.1 1.0
CD2 D:HIS157 4.0 64.4 1.0
CD2 D:HIS111 4.0 72.2 1.0
CA D:HIS111 4.1 71.1 1.0
CA D:HIS157 4.4 61.8 1.0
CD2 D:TRP69 4.5 63.3 1.0
C D:PRO110 4.7 73.6 1.0
CB D:MET162 4.7 60.7 1.0
CB D:ALA150 4.9 67.9 1.0
N D:HIS111 4.9 72.1 1.0
CB D:TRP69 4.9 63.9 1.0
O D:HIS157 5.0 61.0 1.0
CA D:CYS148 5.0 61.7 1.0

Copper binding site 9 out of 9 in 5zl1

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Copper binding site 9 out of 9 in the Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu402

b:62.6
occ:1.00
 NE2 D:HIS116 2.1 60.6 1.0
NE2 D:HIS147 2.1 61.7 1.0
NE2 B:HIS310 2.1 53.3 1.0
CE1 D:HIS116 2.6 59.7 1.0
CE1 B:HIS310 2.9 51.5 1.0
CE1 D:HIS147 2.9 61.0 1.0
CD2 D:HIS147 3.1 61.2 1.0
CD2 B:HIS310 3.2 51.6 1.0
CD2 D:HIS116 3.3 60.1 1.0
ND1 D:HIS116 3.9 59.6 1.0
NE2 B:HIS261 4.0 42.6 1.0
ND1 D:HIS147 4.0 60.4 1.0
ND1 B:HIS310 4.1 50.8 1.0
CG D:HIS147 4.1 60.4 1.0
CG D:HIS116 4.2 59.7 1.0
CG B:HIS310 4.2 50.6 1.0
CD2 B:HIS261 4.3 42.5 1.0
OD2 D:ASP114 4.3 64.2 1.0
CG2 D:ILE145 4.5 55.5 1.0
CE1 B:HIS261 4.7 42.7 1.0

Reference:

D.Hira, M.Matsumura, R.Kitamura, T.Fujii. Hexameric Structure of Copper-Containing Nitrite Reductase of An Anammox Organism Ksu-1 To Be Published.
Page generated: Wed Jul 31 05:36:33 2024

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