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Copper in PDB 2avf: Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes

Enzymatic activity of Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes

All present enzymatic activity of Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes, PDB code: 2avf was solved by H.T.Li, T.Chang, W.C.Chang, C.J.Chen, M.Y.Liu, L.L.Gui, J.P.Zhang, X.M.An, W.R.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.783, 111.072, 122.884, 90.00, 101.67, 90.00
R / Rfree (%) 18.2 / 21.7

Other elements in 2avf:

The structure of Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Copper Binding Sites:

Pages:

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

Binding sites:

The binding sites of Copper atom in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes (pdb code 2avf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes, PDB code: 2avf:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in 2avf

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Copper binding site 1 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:16.3
occ:1.00
 NE2 B:HIS306 2.0 20.1 1.0
NE2 A:HIS100 2.1 21.0 1.0
NE2 A:HIS135 2.1 14.9 1.0
CL B:CL601 2.2 27.0 1.0
CE1 B:HIS306 2.9 21.3 1.0
CE1 A:HIS100 2.9 21.9 1.0
CE1 A:HIS135 3.0 16.6 1.0
CD2 B:HIS306 3.1 21.6 1.0
CD2 A:HIS135 3.1 16.0 1.0
CD2 A:HIS100 3.2 22.3 1.0
NE2 B:HIS255 4.0 17.5 1.0
ND1 B:HIS306 4.0 21.3 1.0
ND1 A:HIS100 4.1 21.5 1.0
ND1 A:HIS135 4.1 17.7 1.0
CD2 B:HIS255 4.1 17.6 1.0
CG B:HIS306 4.1 21.3 1.0
CG A:HIS135 4.2 16.8 1.0
CG A:HIS100 4.2 22.7 1.0
CE1 B:HIS255 4.5 19.4 1.0
OD1 A:ASP98 4.7 40.0 1.0
CG B:HIS255 4.8 19.2 1.0
CD2 B:LEU308 4.8 20.1 1.0
CG A:ASP98 4.9 39.3 1.0
ND1 B:HIS255 5.0 20.4 1.0

Copper binding site 2 out of 12 in 2avf

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Copper binding site 2 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:19.3
occ:1.00
 ND1 A:HIS145 2.1 23.1 1.0
ND1 A:HIS95 2.2 28.8 1.0
SG A:CYS136 2.3 14.5 1.0
SD A:MET150 2.4 24.9 1.0
CE1 A:HIS145 3.0 24.0 1.0
CE1 A:HIS95 3.1 28.4 1.0
CE A:MET150 3.1 27.4 1.0
CG A:HIS145 3.2 21.8 1.0
CG A:HIS95 3.2 27.2 1.0
CB A:CYS136 3.2 18.5 1.0
CB A:HIS95 3.5 27.3 1.0
CB A:HIS145 3.6 18.4 1.0
CG A:MET150 3.9 23.9 1.0
CA A:HIS95 4.0 28.3 1.0
NE2 A:HIS145 4.2 23.2 1.0
CB A:MET150 4.2 22.1 1.0
NE2 A:HIS95 4.2 27.8 1.0
CD2 A:HIS145 4.3 23.6 1.0
CD2 A:HIS95 4.3 27.4 1.0
O A:LEU94 4.5 32.4 1.0
CA A:CYS136 4.6 18.9 1.0
SD A:MET62 4.6 26.7 1.0
CD A:PRO138 4.7 28.2 1.0
CG A:PRO138 4.8 28.8 1.0
CA A:HIS145 4.8 20.6 1.0
N A:ASN96 4.8 29.7 1.0
CB A:MET62 4.9 26.2 1.0

Copper binding site 3 out of 12 in 2avf

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Copper binding site 3 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:14.3
occ:1.00
 NE2 B:HIS100 2.1 15.8 1.0
CL B:CL602 2.2 29.4 1.0
NE2 C:HIS306 2.2 17.4 1.0
NE2 B:HIS135 2.2 20.9 1.0
CE1 B:HIS100 2.9 15.4 1.0
CE1 C:HIS306 3.1 17.9 1.0
CD2 B:HIS135 3.2 20.6 1.0
CD2 B:HIS100 3.2 17.6 1.0
CE1 B:HIS135 3.2 19.9 1.0
CD2 C:HIS306 3.3 17.9 1.0
ND1 B:HIS100 4.1 16.2 1.0
NE2 C:HIS255 4.2 23.0 1.0
CG B:HIS100 4.3 18.1 1.0
ND1 C:HIS306 4.3 18.2 1.0
CG B:HIS135 4.3 20.4 1.0
ND1 B:HIS135 4.3 20.2 1.0
CD2 C:HIS255 4.3 21.8 1.0
CG C:HIS306 4.4 19.0 1.0
CE1 C:HIS255 4.5 22.1 1.0
CG C:HIS255 4.8 20.6 1.0
ND1 C:HIS255 4.9 22.0 1.0

Copper binding site 4 out of 12 in 2avf

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Copper binding site 4 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:25.4
occ:1.00
 ND1 B:HIS145 1.9 22.3 1.0
ND1 B:HIS95 2.2 34.5 1.0
SD B:MET150 2.3 29.3 1.0
SG B:CYS136 2.4 15.7 1.0
CE1 B:HIS145 2.8 21.8 1.0
CE1 B:HIS95 3.1 33.7 1.0
CG B:HIS145 3.1 23.3 1.0
CE B:MET150 3.1 26.8 1.0
CB B:CYS136 3.2 22.2 1.0
CG B:HIS95 3.3 32.0 1.0
CB B:HIS145 3.5 23.2 1.0
CB B:HIS95 3.7 31.1 1.0
CG B:MET150 3.8 27.1 1.0
NE2 B:HIS145 4.0 23.6 1.0
CA B:HIS95 4.1 31.8 1.0
CD2 B:HIS145 4.1 23.3 1.0
CB B:MET150 4.2 26.6 1.0
NE2 B:HIS95 4.2 34.6 1.0
O B:LEU94 4.3 33.8 1.0
CD2 B:HIS95 4.3 32.9 1.0
SD B:MET62 4.5 27.4 1.0
CA B:CYS136 4.7 22.4 1.0
CD B:PRO138 4.8 28.0 1.0
CA B:HIS145 4.8 24.7 1.0
CG B:PRO138 4.8 26.7 1.0
CB B:MET62 4.8 26.8 1.0
N B:ASN96 4.9 33.5 1.0

Copper binding site 5 out of 12 in 2avf

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Copper binding site 5 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:16.8
occ:1.00
 NE2 C:HIS135 2.0 13.5 1.0
NE2 C:HIS100 2.1 14.8 1.0
NE2 A:HIS306 2.1 12.0 1.0
CL C:CL603 2.2 26.7 1.0
CE1 C:HIS100 2.9 15.1 1.0
CD2 C:HIS135 2.9 12.2 1.0
CE1 A:HIS306 3.0 13.7 1.0
CE1 C:HIS135 3.1 13.3 1.0
CD2 C:HIS100 3.2 16.6 1.0
CD2 A:HIS306 3.2 13.7 1.0
NE2 A:HIS255 4.0 20.2 1.0
ND1 C:HIS100 4.1 15.8 1.0
CG C:HIS135 4.1 14.5 1.0
ND1 C:HIS135 4.2 14.1 1.0
ND1 A:HIS306 4.2 13.2 1.0
CG C:HIS100 4.2 16.7 1.0
CD2 A:HIS255 4.3 20.6 1.0
CG A:HIS306 4.3 12.6 1.0
OD2 C:ASP98 4.3 34.7 1.0
CE1 A:HIS255 4.6 20.6 1.0
CG C:ASP98 4.6 33.5 1.0
OD1 C:ASP98 4.8 34.4 1.0
O A:HOH540 4.9 18.8 1.0
CG A:HIS255 4.9 21.4 1.0

Copper binding site 6 out of 12 in 2avf

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Copper binding site 6 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:32.8
occ:1.00
 ND1 C:HIS145 2.1 23.8 1.0
ND1 C:HIS95 2.3 31.0 1.0
SD C:MET150 2.3 25.9 1.0
SG C:CYS136 2.4 21.3 1.0
CE1 C:HIS145 3.0 24.8 1.0
CE1 C:HIS95 3.1 27.9 1.0
CG C:HIS145 3.1 23.1 1.0
CB C:CYS136 3.3 23.8 1.0
CG C:HIS95 3.4 29.2 1.0
CE C:MET150 3.4 27.8 1.0
CB C:HIS145 3.5 20.7 1.0
CB C:HIS95 3.8 29.4 1.0
CG C:MET150 3.8 25.8 1.0
CG C:PRO138 4.0 31.8 1.0
CA C:HIS95 4.1 29.5 1.0
NE2 C:HIS145 4.1 24.8 1.0
CB C:MET150 4.2 21.4 1.0
CD2 C:HIS145 4.2 24.8 1.0
NE2 C:HIS95 4.3 28.2 1.0
SD C:MET62 4.3 33.2 1.0
CD2 C:HIS95 4.4 28.8 1.0
O C:LEU94 4.5 29.7 1.0
CD C:PRO138 4.5 29.8 1.0
CA C:HIS145 4.7 21.6 1.0
CA C:CYS136 4.7 23.4 1.0
CB C:MET62 4.8 27.8 1.0
N C:ASN96 4.9 29.9 1.0

Copper binding site 7 out of 12 in 2avf

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Copper binding site 7 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu502

b:17.1
occ:1.00
 NE2 D:HIS135 2.0 25.3 1.0
NE2 E:HIS306 2.0 16.5 1.0
CL D:CL604 2.0 31.5 1.0
NE2 D:HIS100 2.2 27.5 1.0
CE1 D:HIS135 2.9 25.2 1.0
CE1 E:HIS306 2.9 14.1 1.0
CD2 D:HIS135 3.0 24.6 1.0
CE1 D:HIS100 3.1 26.9 1.0
CD2 E:HIS306 3.1 18.4 1.0
CD2 D:HIS100 3.3 26.9 1.0
ND1 D:HIS135 4.0 24.3 1.0
ND1 E:HIS306 4.1 16.7 1.0
CG D:HIS135 4.1 24.7 1.0
CG E:HIS306 4.2 17.5 1.0
ND1 D:HIS100 4.2 26.1 1.0
OD2 D:ASP98 4.3 48.2 1.0
CG D:HIS100 4.4 26.9 1.0
NE2 E:HIS255 4.4 27.6 1.0
CD2 E:HIS255 4.6 26.5 1.0
CE1 E:HIS255 4.7 28.4 1.0
CD2 E:LEU308 4.9 19.6 1.0
CD1 E:LEU308 4.9 21.5 1.0

Copper binding site 8 out of 12 in 2avf

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Copper binding site 8 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cu501

b:37.6
occ:1.00
 ND1 D:HIS95 2.2 44.6 1.0
SG D:CYS136 2.2 29.1 1.0
SD D:MET150 2.3 32.8 1.0
ND1 D:HIS145 2.4 37.0 1.0
CE1 D:HIS95 2.9 44.2 1.0
CE D:MET150 3.0 32.9 1.0
CB D:CYS136 3.1 31.6 1.0
CE1 D:HIS145 3.3 37.5 1.0
CG D:HIS95 3.3 44.2 1.0
CG D:HIS145 3.4 36.1 1.0
CB D:HIS145 3.7 34.0 1.0
CG D:MET150 3.8 31.5 1.0
CB D:HIS95 3.8 44.1 1.0
NE2 D:HIS95 4.1 45.2 1.0
CB D:MET150 4.1 30.3 1.0
CA D:HIS95 4.3 44.2 1.0
CD2 D:HIS95 4.3 44.3 1.0
NE2 D:HIS145 4.4 37.2 1.0
CD2 D:HIS145 4.5 38.1 1.0
CA D:CYS136 4.5 31.4 1.0
SD D:MET62 4.6 47.8 1.0
CG D:PRO138 4.6 37.9 1.0
CD D:PRO138 4.6 36.6 1.0
O D:LEU94 4.8 43.1 1.0
CB D:MET62 4.9 44.7 1.0
CA D:HIS145 4.9 33.6 1.0
N D:ASN96 4.9 44.2 1.0

Copper binding site 9 out of 12 in 2avf

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Copper binding site 9 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu502

b:16.3
occ:1.00
 NE2 E:HIS100 1.9 16.8 1.0
NE2 F:HIS306 2.0 13.0 1.0
CL F:CL605 2.1 22.1 1.0
NE2 E:HIS135 2.2 14.8 1.0
CE1 E:HIS100 2.7 14.9 1.0
CE1 F:HIS306 3.0 15.0 1.0
CD2 E:HIS100 3.0 15.8 1.0
CD2 F:HIS306 3.1 13.9 1.0
CE1 E:HIS135 3.1 16.2 1.0
CD2 E:HIS135 3.2 14.0 1.0
ND1 E:HIS100 3.8 15.3 1.0
CG E:HIS100 4.0 15.8 1.0
ND1 F:HIS306 4.1 16.5 1.0
NE2 F:HIS255 4.1 19.4 1.0
CG F:HIS306 4.2 16.1 1.0
ND1 E:HIS135 4.2 16.5 1.0
CD2 F:HIS255 4.3 17.6 1.0
CG E:HIS135 4.3 17.1 1.0
CE1 F:HIS255 4.6 16.9 1.0
OD1 E:ASP98 4.6 43.4 1.0
CG F:HIS255 4.8 17.7 1.0
CG E:ASP98 4.9 42.8 1.0
ND1 F:HIS255 4.9 18.9 1.0
O F:HOH614 5.0 22.5 1.0

Copper binding site 10 out of 12 in 2avf

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Copper binding site 10 out of 12 in the Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes


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 C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cu501

b:29.7
occ:1.00
 ND1 E:HIS145 2.0 25.1 1.0
ND1 E:HIS95 2.2 32.1 1.0
SD E:MET150 2.3 36.0 1.0
SG E:CYS136 2.4 27.3 1.0
CE1 E:HIS145 2.9 26.3 1.0
CE1 E:HIS95 3.0 30.1 1.0
CG E:HIS145 3.1 26.1 1.0
CB E:CYS136 3.2 24.2 1.0
CE E:MET150 3.3 35.0 1.0
CG E:HIS95 3.4 31.5 1.0
CB E:HIS145 3.5 25.9 1.0
CB E:HIS95 3.8 33.4 1.0
CG E:MET150 3.9 33.0 1.0
NE2 E:HIS145 4.0 25.4 1.0
CD2 E:HIS145 4.1 26.6 1.0
CA E:HIS95 4.1 34.2 1.0
NE2 E:HIS95 4.2 30.7 1.0
CB E:MET150 4.2 29.5 1.0
O E:LEU94 4.3 30.4 1.0
SD E:MET62 4.4 30.2 1.0
CD2 E:HIS95 4.4 30.3 1.0
CA E:CYS136 4.7 22.9 1.0
CG E:PRO138 4.7 27.6 1.0
CA E:HIS145 4.7 26.2 1.0
CD E:PRO138 4.7 26.8 1.0
CB E:MET62 4.8 31.9 1.0
N E:ASN96 4.9 37.1 1.0

Reference:

H.T.Li, T.Chang, W.C.Chang, C.J.Chen, M.Y.Liu, L.L.Gui, J.P.Zhang, X.M.An, W.R.Chang. Crystal Structure of C-Terminal Desundecapeptide Nitrite Reductase From Achromobacter Cycloclastes Biochem.Biophys.Res.Commun. V. 338 1935 2005.
ISSN: ISSN 0006-291X
PubMed: 16293231
DOI: 10.1016/J.BBRC.2005.09.199
Page generated: Mon Jul 14 00:45:39 2025

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