Copper in PDB 2zon: Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
Enzymatic activity of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
All present enzymatic activity of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C:
1.7.2.1;
Protein crystallography data
The structure of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C, PDB code: 2zon
was solved by
M.Nojiri,
H.Koteishi,
K.Yamaguchi,
S.Suzuki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
63.345,
103.942,
163.144,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.2 /
19.5
|
Other elements in 2zon:
The structure of Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
(pdb code 2zon). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C, PDB code: 2zon:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 2zon
Go back to
Copper Binding Sites List in 2zon
Copper binding site 1 out
of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
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 Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu400
b:17.8
occ:1.00
|
ND1
|
A:HIS89
|
2.1
|
14.9
|
1.0
|
ND1
|
A:HIS139
|
2.1
|
14.3
|
1.0
|
SG
|
A:CYS130
|
2.2
|
14.9
|
1.0
|
SD
|
A:MET144
|
2.6
|
17.5
|
1.0
|
CE1
|
A:HIS139
|
3.0
|
14.8
|
1.0
|
CE1
|
A:HIS89
|
3.0
|
17.1
|
1.0
|
CG
|
A:HIS89
|
3.1
|
14.2
|
1.0
|
CG
|
A:HIS139
|
3.1
|
13.9
|
1.0
|
CB
|
A:CYS130
|
3.1
|
14.4
|
1.0
|
CE
|
A:MET144
|
3.3
|
17.6
|
1.0
|
CB
|
A:HIS89
|
3.5
|
14.7
|
1.0
|
CB
|
A:HIS139
|
3.5
|
13.4
|
1.0
|
CA
|
A:HIS89
|
3.9
|
15.0
|
1.0
|
CG
|
A:PRO132
|
4.0
|
14.3
|
1.0
|
CG
|
A:MET144
|
4.1
|
15.7
|
1.0
|
NE2
|
A:HIS139
|
4.2
|
16.0
|
1.0
|
NE2
|
A:HIS89
|
4.2
|
16.3
|
1.0
|
O
|
A:PRO88
|
4.2
|
16.0
|
1.0
|
CD2
|
A:HIS139
|
4.2
|
14.8
|
1.0
|
CD2
|
A:HIS89
|
4.2
|
15.3
|
1.0
|
SD
|
A:MET56
|
4.3
|
17.7
|
1.0
|
CD
|
A:PRO132
|
4.4
|
14.9
|
1.0
|
CA
|
A:CYS130
|
4.6
|
13.3
|
1.0
|
CB
|
A:MET144
|
4.6
|
14.0
|
1.0
|
CA
|
A:HIS139
|
4.7
|
13.0
|
1.0
|
N
|
A:ASN90
|
4.7
|
13.5
|
1.0
|
N
|
A:HIS89
|
4.9
|
15.3
|
1.0
|
C
|
A:HIS89
|
4.9
|
14.5
|
1.0
|
C
|
A:PRO88
|
4.9
|
15.8
|
1.0
|
|
Copper binding site 2 out
of 6 in 2zon
Go back to
Copper Binding Sites List in 2zon
Copper binding site 2 out
of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
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 Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu401
b:15.2
occ:1.00
|
NE2
|
B:HIS300
|
2.0
|
13.4
|
1.0
|
NE2
|
A:HIS129
|
2.0
|
14.4
|
1.0
|
NE2
|
A:HIS94
|
2.1
|
9.9
|
1.0
|
O
|
A:HOH622
|
2.1
|
29.3
|
1.0
|
CD2
|
A:HIS129
|
2.9
|
12.9
|
1.0
|
CE1
|
A:HIS94
|
2.9
|
10.7
|
1.0
|
CE1
|
B:HIS300
|
3.0
|
10.1
|
1.0
|
CD2
|
B:HIS300
|
3.0
|
10.6
|
1.0
|
CE1
|
A:HIS129
|
3.1
|
14.2
|
1.0
|
CD2
|
A:HIS94
|
3.2
|
12.4
|
1.0
|
OD2
|
A:ASP92
|
3.8
|
23.2
|
1.0
|
NE2
|
B:HIS249
|
3.9
|
20.4
|
1.0
|
ND1
|
B:HIS300
|
4.1
|
10.3
|
1.0
|
ND1
|
A:HIS94
|
4.1
|
10.9
|
1.0
|
CG
|
A:HIS129
|
4.1
|
13.3
|
1.0
|
CG
|
B:HIS300
|
4.1
|
11.0
|
1.0
|
ND1
|
A:HIS129
|
4.2
|
13.6
|
1.0
|
CG
|
A:HIS94
|
4.3
|
11.0
|
1.0
|
CE1
|
B:HIS249
|
4.3
|
18.3
|
1.0
|
CD2
|
B:HIS249
|
4.3
|
16.3
|
1.0
|
O
|
A:HOH695
|
4.4
|
37.5
|
1.0
|
CG
|
A:ASP92
|
4.4
|
19.4
|
1.0
|
OD1
|
A:ASP92
|
4.7
|
20.4
|
1.0
|
ND1
|
B:HIS249
|
4.9
|
15.9
|
1.0
|
CG
|
B:HIS249
|
5.0
|
12.4
|
1.0
|
|
Copper binding site 3 out
of 6 in 2zon
Go back to
Copper Binding Sites List in 2zon
Copper binding site 3 out
of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
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 Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu400
b:17.5
occ:1.00
|
ND1
|
B:HIS139
|
2.1
|
15.7
|
1.0
|
ND1
|
B:HIS89
|
2.1
|
12.9
|
1.0
|
SG
|
B:CYS130
|
2.2
|
13.8
|
1.0
|
SD
|
B:MET144
|
2.6
|
16.6
|
1.0
|
CE1
|
B:HIS139
|
3.0
|
16.2
|
1.0
|
CE1
|
B:HIS89
|
3.0
|
15.7
|
1.0
|
CG
|
B:HIS139
|
3.1
|
14.5
|
1.0
|
CB
|
B:CYS130
|
3.1
|
14.1
|
1.0
|
CG
|
B:HIS89
|
3.1
|
13.2
|
1.0
|
CE
|
B:MET144
|
3.4
|
16.0
|
1.0
|
CB
|
B:HIS139
|
3.5
|
12.7
|
1.0
|
CB
|
B:HIS89
|
3.5
|
13.7
|
1.0
|
CA
|
B:HIS89
|
3.8
|
13.8
|
1.0
|
CG
|
B:PRO132
|
3.9
|
15.3
|
1.0
|
O
|
B:PRO88
|
4.1
|
14.7
|
1.0
|
NE2
|
B:HIS139
|
4.1
|
15.8
|
1.0
|
CG
|
B:MET144
|
4.1
|
14.4
|
1.0
|
NE2
|
B:HIS89
|
4.2
|
12.9
|
1.0
|
CD2
|
B:HIS139
|
4.2
|
14.7
|
1.0
|
CD2
|
B:HIS89
|
4.3
|
13.3
|
1.0
|
CD
|
B:PRO132
|
4.3
|
14.4
|
1.0
|
CA
|
B:CYS130
|
4.5
|
12.4
|
1.0
|
SD
|
B:MET56
|
4.6
|
17.0
|
1.0
|
CB
|
B:MET144
|
4.6
|
12.3
|
1.0
|
N
|
B:ASN90
|
4.7
|
12.7
|
1.0
|
CA
|
B:HIS139
|
4.7
|
12.7
|
1.0
|
N
|
B:HIS89
|
4.8
|
14.4
|
1.0
|
C
|
B:HIS89
|
4.8
|
13.4
|
1.0
|
C
|
B:PRO88
|
4.9
|
15.1
|
1.0
|
|
Copper binding site 4 out
of 6 in 2zon
Go back to
Copper Binding Sites List in 2zon
Copper binding site 4 out
of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
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 Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu401
b:14.8
occ:1.00
|
NE2
|
B:HIS129
|
2.0
|
13.7
|
1.0
|
NE2
|
B:HIS94
|
2.0
|
11.3
|
1.0
|
NE2
|
C:HIS300
|
2.1
|
11.8
|
1.0
|
O
|
B:HOH528
|
2.1
|
25.3
|
1.0
|
CE1
|
B:HIS94
|
2.9
|
10.8
|
1.0
|
CD2
|
B:HIS129
|
2.9
|
13.2
|
1.0
|
CE1
|
C:HIS300
|
3.0
|
10.5
|
1.0
|
CD2
|
C:HIS300
|
3.1
|
10.8
|
1.0
|
CE1
|
B:HIS129
|
3.1
|
13.1
|
1.0
|
CD2
|
B:HIS94
|
3.2
|
11.1
|
1.0
|
OD2
|
B:ASP92
|
3.7
|
21.4
|
1.0
|
NE2
|
C:HIS249
|
3.9
|
17.1
|
1.0
|
ND1
|
B:HIS94
|
4.1
|
9.9
|
1.0
|
CG
|
B:HIS129
|
4.1
|
12.7
|
1.0
|
ND1
|
C:HIS300
|
4.1
|
11.0
|
1.0
|
ND1
|
B:HIS129
|
4.2
|
13.5
|
1.0
|
CG
|
C:HIS300
|
4.2
|
8.5
|
1.0
|
CG
|
B:HIS94
|
4.2
|
10.0
|
1.0
|
CE1
|
C:HIS249
|
4.3
|
15.7
|
1.0
|
CD2
|
C:HIS249
|
4.4
|
15.3
|
1.0
|
CG
|
B:ASP92
|
4.4
|
17.5
|
1.0
|
OD1
|
B:ASP92
|
4.7
|
18.4
|
1.0
|
ND1
|
C:HIS249
|
4.9
|
14.5
|
1.0
|
CG
|
C:HIS249
|
5.0
|
12.3
|
1.0
|
O
|
B:HOH744
|
5.0
|
51.2
|
1.0
|
|
Copper binding site 5 out
of 6 in 2zon
Go back to
Copper Binding Sites List in 2zon
Copper binding site 5 out
of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
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 Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu400
b:21.0
occ:1.00
|
ND1
|
C:HIS139
|
2.1
|
18.2
|
1.0
|
SG
|
C:CYS130
|
2.2
|
17.3
|
1.0
|
ND1
|
C:HIS89
|
2.2
|
16.5
|
1.0
|
SD
|
C:MET144
|
2.6
|
19.1
|
1.0
|
CE1
|
C:HIS139
|
3.0
|
18.2
|
1.0
|
CE1
|
C:HIS89
|
3.1
|
18.2
|
1.0
|
CB
|
C:CYS130
|
3.2
|
16.5
|
1.0
|
CG
|
C:HIS139
|
3.2
|
16.6
|
1.0
|
CG
|
C:HIS89
|
3.2
|
16.1
|
1.0
|
CE
|
C:MET144
|
3.4
|
18.4
|
1.0
|
CB
|
C:HIS89
|
3.5
|
17.1
|
1.0
|
CB
|
C:HIS139
|
3.6
|
15.6
|
1.0
|
CA
|
C:HIS89
|
3.8
|
17.7
|
1.0
|
CG
|
C:PRO132
|
3.9
|
19.9
|
1.0
|
O
|
C:PRO88
|
4.1
|
19.2
|
1.0
|
CG
|
C:MET144
|
4.2
|
16.2
|
1.0
|
NE2
|
C:HIS139
|
4.2
|
19.9
|
1.0
|
NE2
|
C:HIS89
|
4.3
|
15.4
|
1.0
|
CD2
|
C:HIS139
|
4.3
|
19.6
|
1.0
|
CD2
|
C:HIS89
|
4.3
|
16.5
|
1.0
|
CD
|
C:PRO132
|
4.3
|
18.9
|
1.0
|
SD
|
C:MET56
|
4.5
|
22.5
|
1.0
|
CA
|
C:CYS130
|
4.6
|
15.7
|
1.0
|
CB
|
C:MET144
|
4.6
|
14.9
|
1.0
|
N
|
C:ASN90
|
4.7
|
17.2
|
1.0
|
CA
|
C:HIS139
|
4.8
|
15.4
|
1.0
|
N
|
C:HIS89
|
4.8
|
18.5
|
1.0
|
C
|
C:HIS89
|
4.9
|
18.1
|
1.0
|
C
|
C:PRO88
|
4.9
|
19.6
|
1.0
|
|
Copper binding site 6 out
of 6 in 2zon
Go back to
Copper Binding Sites List in 2zon
Copper binding site 6 out
of 6 in the Crystal Structure of Electron Transfer Complex of Nitrite Reductase with Cytochrome C
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 Electron Transfer Complex of Nitrite Reductase with Cytochrome C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu401
b:16.1
occ:1.00
|
NE2
|
C:HIS94
|
2.0
|
13.9
|
1.0
|
NE2
|
A:HIS300
|
2.0
|
11.0
|
1.0
|
NE2
|
C:HIS129
|
2.1
|
15.5
|
1.0
|
O
|
C:HOH819
|
2.1
|
28.3
|
1.0
|
CE1
|
C:HIS94
|
2.9
|
13.6
|
1.0
|
CD2
|
C:HIS129
|
2.9
|
13.6
|
1.0
|
CE1
|
A:HIS300
|
3.0
|
11.8
|
1.0
|
CD2
|
A:HIS300
|
3.1
|
12.5
|
1.0
|
CD2
|
C:HIS94
|
3.1
|
13.7
|
1.0
|
CE1
|
C:HIS129
|
3.1
|
16.0
|
1.0
|
OD2
|
C:ASP92
|
3.7
|
24.4
|
1.0
|
NE2
|
A:HIS249
|
4.1
|
19.4
|
1.0
|
ND1
|
C:HIS94
|
4.1
|
12.4
|
1.0
|
ND1
|
A:HIS300
|
4.1
|
11.8
|
1.0
|
CG
|
C:HIS129
|
4.1
|
13.7
|
1.0
|
CG
|
A:HIS300
|
4.2
|
11.0
|
1.0
|
ND1
|
C:HIS129
|
4.2
|
15.6
|
1.0
|
CG
|
C:HIS94
|
4.2
|
12.9
|
1.0
|
CE1
|
A:HIS249
|
4.3
|
17.5
|
1.0
|
CG
|
C:ASP92
|
4.4
|
20.1
|
1.0
|
O
|
C:HOH1003
|
4.4
|
38.3
|
1.0
|
CD2
|
A:HIS249
|
4.5
|
19.1
|
1.0
|
OD1
|
C:ASP92
|
4.7
|
19.8
|
1.0
|
ND1
|
A:HIS249
|
4.9
|
15.8
|
1.0
|
|
Reference:
M.Nojiri,
H.Koteishi,
T.Nakagami,
K.Kobayashi,
T.Inoue,
K.Yamaguchi,
S.Suzuki.
Structural Basis of Inter-Protein Electron Transfer For Nitrite Reduction in Denitrification Nature V. 462 117 2009.
ISSN: ISSN 0028-0836
PubMed: 19890332
DOI: 10.1038/NATURE08507
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