Copper in PDB 2vw6: Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3
Enzymatic activity of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3
All present enzymatic activity of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3:
1.7.2.1;
Protein crystallography data
The structure of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3, PDB code: 2vw6
was solved by
M.J.Ellis,
S.G.Buffey,
M.A.Hough,
S.S.Hasnain,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
96.23 /
1.90
|
Space group
|
H 3
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.099,
89.099,
288.395,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
16.2 /
19.4
|
Other elements in 2vw6:
The structure of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3 also contains other interesting chemical elements:
Copper Binding Sites:
The binding sites of Copper atom in the Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3
(pdb code 2vw6). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the
Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3, PDB code: 2vw6:
Jump to Copper binding site number:
1;
2;
3;
4;
Copper binding site 1 out
of 4 in 2vw6
Go back to
Copper Binding Sites List in 2vw6
Copper binding site 1 out
of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu501
b:23.0
occ:1.00
|
SG
|
A:CYS130
|
2.2
|
18.3
|
1.0
|
ND1
|
A:HIS139
|
2.2
|
16.8
|
1.0
|
ND1
|
A:HIS89
|
2.2
|
17.8
|
1.0
|
SD
|
A:MET144
|
2.5
|
14.7
|
0.8
|
CB
|
A:CYS130
|
3.1
|
16.8
|
1.0
|
CE1
|
A:HIS139
|
3.1
|
15.9
|
1.0
|
CG
|
A:HIS89
|
3.2
|
19.0
|
1.0
|
CE1
|
A:HIS89
|
3.2
|
18.7
|
1.0
|
CG
|
A:HIS139
|
3.2
|
15.0
|
1.0
|
CE
|
A:MET144
|
3.2
|
17.0
|
0.1
|
CE
|
A:MET144
|
3.4
|
17.0
|
0.8
|
CB
|
A:HIS89
|
3.4
|
19.4
|
1.0
|
CB
|
A:HIS139
|
3.5
|
14.0
|
1.0
|
CA
|
A:HIS89
|
3.8
|
20.1
|
1.0
|
CG
|
A:PRO132
|
3.9
|
19.7
|
1.0
|
CG
|
A:MET144
|
4.0
|
16.4
|
1.0
|
O
|
A:PRO88
|
4.1
|
20.6
|
1.0
|
SD
|
A:MET144
|
4.1
|
16.8
|
0.1
|
NE2
|
A:HIS139
|
4.3
|
17.3
|
1.0
|
NE2
|
A:HIS89
|
4.3
|
17.2
|
1.0
|
CD2
|
A:HIS139
|
4.3
|
15.2
|
1.0
|
CD2
|
A:HIS89
|
4.3
|
17.8
|
1.0
|
CD
|
A:PRO132
|
4.3
|
18.1
|
1.0
|
SD
|
A:MET56
|
4.5
|
18.9
|
0.7
|
CA
|
A:CYS130
|
4.5
|
16.5
|
1.0
|
CB
|
A:MET144
|
4.6
|
14.1
|
1.0
|
SD
|
A:MET56
|
4.6
|
18.2
|
0.3
|
N
|
A:ASN90
|
4.7
|
18.8
|
1.0
|
CA
|
A:HIS139
|
4.7
|
13.8
|
1.0
|
N
|
A:HIS89
|
4.8
|
20.4
|
1.0
|
C
|
A:HIS89
|
4.8
|
20.1
|
1.0
|
C
|
A:PRO88
|
4.9
|
21.2
|
1.0
|
|
Copper binding site 2 out
of 4 in 2vw6
Go back to
Copper Binding Sites List in 2vw6
Copper binding site 2 out
of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu502
b:17.7
occ:1.00
|
O
|
A:HOH2135
|
1.9
|
19.8
|
1.0
|
NE2
|
A:HIS129
|
2.0
|
15.1
|
1.0
|
NE2
|
A:HIS94
|
2.1
|
15.2
|
1.0
|
CD2
|
A:HIS129
|
2.9
|
14.2
|
1.0
|
CE1
|
A:HIS94
|
3.0
|
16.0
|
1.0
|
CE1
|
A:HIS129
|
3.0
|
16.4
|
1.0
|
CD2
|
A:HIS94
|
3.1
|
15.3
|
1.0
|
OD2
|
A:ASP92
|
3.6
|
26.6
|
1.0
|
CG
|
A:HIS129
|
4.1
|
14.7
|
1.0
|
ND1
|
A:HIS129
|
4.1
|
13.2
|
1.0
|
ND1
|
A:HIS94
|
4.1
|
16.2
|
1.0
|
CG
|
A:HIS94
|
4.2
|
13.9
|
1.0
|
CG
|
A:ASP92
|
4.3
|
22.3
|
1.0
|
OD1
|
A:ASP92
|
4.6
|
22.0
|
1.0
|
O
|
A:HOH2136
|
4.9
|
23.1
|
1.0
|
|
Copper binding site 3 out
of 4 in 2vw6
Go back to
Copper Binding Sites List in 2vw6
Copper binding site 3 out
of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu501
b:23.1
occ:1.00
|
SG
|
B:CYS130
|
2.1
|
18.7
|
1.0
|
ND1
|
B:HIS89
|
2.2
|
17.4
|
1.0
|
ND1
|
B:HIS139
|
2.2
|
16.2
|
1.0
|
SD
|
B:MET144
|
2.5
|
16.8
|
0.8
|
CE1
|
B:HIS139
|
3.1
|
17.4
|
1.0
|
CE
|
B:MET144
|
3.1
|
18.3
|
0.1
|
CB
|
B:CYS130
|
3.1
|
17.7
|
1.0
|
CG
|
B:HIS89
|
3.1
|
20.1
|
1.0
|
CE1
|
B:HIS89
|
3.1
|
19.3
|
1.0
|
CG
|
B:HIS139
|
3.2
|
16.2
|
1.0
|
CE
|
B:MET144
|
3.3
|
17.6
|
0.8
|
CB
|
B:HIS89
|
3.4
|
20.4
|
1.0
|
CB
|
B:HIS139
|
3.6
|
15.2
|
1.0
|
CA
|
B:HIS89
|
3.8
|
20.4
|
1.0
|
CG
|
B:PRO132
|
3.9
|
20.7
|
1.0
|
CG
|
B:MET144
|
4.0
|
16.8
|
1.0
|
SD
|
B:MET144
|
4.1
|
18.8
|
0.1
|
O
|
B:PRO88
|
4.2
|
21.3
|
1.0
|
NE2
|
B:HIS139
|
4.2
|
17.4
|
1.0
|
NE2
|
B:HIS89
|
4.3
|
20.1
|
1.0
|
CD2
|
B:HIS89
|
4.3
|
18.7
|
1.0
|
CD2
|
B:HIS139
|
4.3
|
17.4
|
1.0
|
CD
|
B:PRO132
|
4.4
|
19.5
|
1.0
|
SD
|
B:MET56
|
4.4
|
18.6
|
0.7
|
CB
|
B:MET144
|
4.5
|
15.8
|
1.0
|
SD
|
B:MET56
|
4.5
|
18.8
|
0.3
|
CA
|
B:CYS130
|
4.6
|
17.8
|
1.0
|
N
|
B:ASN90
|
4.7
|
19.9
|
1.0
|
CA
|
B:HIS139
|
4.8
|
14.9
|
1.0
|
C
|
B:HIS89
|
4.9
|
20.7
|
1.0
|
N
|
B:HIS89
|
4.9
|
21.3
|
1.0
|
C
|
B:PRO88
|
4.9
|
21.8
|
1.0
|
|
Copper binding site 4 out
of 4 in 2vw6
Go back to
Copper Binding Sites List in 2vw6
Copper binding site 4 out
of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3
 Mono view
 Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Nitrite Reductase From Alcaligenes Xylosoxidans - 3 of 3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu502
b:18.7
occ:1.00
|
O
|
B:HOH2119
|
1.9
|
18.9
|
1.0
|
NE2
|
B:HIS129
|
2.0
|
15.8
|
1.0
|
NE2
|
B:HIS94
|
2.1
|
15.6
|
1.0
|
CE1
|
B:HIS94
|
3.0
|
16.7
|
1.0
|
CD2
|
B:HIS129
|
3.0
|
16.6
|
1.0
|
CE1
|
B:HIS129
|
3.1
|
15.8
|
1.0
|
CD2
|
B:HIS94
|
3.1
|
16.2
|
1.0
|
OD2
|
B:ASP92
|
3.6
|
29.4
|
1.0
|
ND1
|
B:HIS94
|
4.1
|
17.3
|
1.0
|
CG
|
B:HIS129
|
4.1
|
16.4
|
1.0
|
ND1
|
B:HIS129
|
4.1
|
14.6
|
1.0
|
CG
|
B:HIS94
|
4.2
|
16.3
|
1.0
|
CG
|
B:ASP92
|
4.3
|
23.3
|
1.0
|
OD1
|
B:ASP92
|
4.6
|
24.5
|
1.0
|
O
|
B:HOH2120
|
4.9
|
20.3
|
1.0
|
|
Reference:
M.J.Ellis,
S.G.Buffey,
M.A.Hough,
S.S.Hasnain.
On-Line Optical and X-Ray Spectroscopies with Crystallography: An Integrated Approach For Determining Metalloprotein Structures in Functionally Well Defined States. J.Synchrotron Radiat. V. 15 433 2008.
ISSN: ISSN 0909-0495
PubMed: 18728313
DOI: 10.1107/S0909049508014945
Page generated: Wed Jul 31 00:05:46 2024
|