Copper in PDB 1l9s: Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
Enzymatic activity of Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
All present enzymatic activity of Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6:
1.7.99.3;
Protein crystallography data
The structure of Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9s
was solved by
M.J.Boulanger,
M.E.P.Murphy,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.54 /
1.78
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.480,
102.030,
146.060,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.7 /
19.7
|
Copper Binding Sites:
The binding sites of Copper atom in the Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
(pdb code 1l9s). 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 the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6, PDB code: 1l9s:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 1l9s
Go back to
Copper Binding Sites List in 1l9s
Copper binding site 1 out
of 6 in the Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
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 the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu501
b:18.0
occ:1.00
|
ND1
|
A:HIS145
|
2.0
|
14.2
|
1.0
|
ND1
|
A:HIS95
|
2.1
|
14.7
|
1.0
|
SG
|
A:CYS136
|
2.2
|
13.4
|
1.0
|
SD
|
A:MET150
|
2.4
|
15.7
|
1.0
|
CE1
|
A:HIS145
|
2.9
|
13.1
|
1.0
|
CE1
|
A:HIS95
|
3.1
|
14.7
|
1.0
|
CG
|
A:HIS145
|
3.1
|
15.4
|
1.0
|
CB
|
A:CYS136
|
3.2
|
13.8
|
1.0
|
CG
|
A:HIS95
|
3.2
|
15.8
|
1.0
|
CE
|
A:MET150
|
3.3
|
14.3
|
1.0
|
CB
|
A:HIS145
|
3.5
|
12.4
|
1.0
|
CB
|
A:HIS95
|
3.5
|
13.3
|
1.0
|
CG
|
A:MET150
|
3.8
|
14.9
|
1.0
|
CA
|
A:HIS95
|
3.9
|
14.3
|
1.0
|
NE2
|
A:HIS145
|
4.1
|
15.7
|
1.0
|
CD2
|
A:HIS145
|
4.2
|
15.2
|
1.0
|
NE2
|
A:HIS95
|
4.2
|
14.9
|
1.0
|
CB
|
A:MET150
|
4.3
|
13.2
|
1.0
|
CD2
|
A:HIS95
|
4.3
|
14.3
|
1.0
|
SD
|
A:MET62
|
4.3
|
15.7
|
1.0
|
CG
|
A:PRO138
|
4.3
|
17.5
|
1.0
|
O
|
A:MET94
|
4.4
|
15.3
|
1.0
|
CA
|
A:CYS136
|
4.6
|
13.8
|
1.0
|
N
|
A:ASN96
|
4.7
|
15.6
|
1.0
|
CB
|
A:MET62
|
4.7
|
15.8
|
1.0
|
CD
|
A:PRO138
|
4.7
|
18.4
|
1.0
|
CA
|
A:HIS145
|
4.7
|
12.7
|
1.0
|
C
|
A:HIS95
|
4.8
|
15.4
|
1.0
|
N
|
A:HIS95
|
4.9
|
15.0
|
1.0
|
|
Copper binding site 2 out
of 6 in 1l9s
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Copper Binding Sites List in 1l9s
Copper binding site 2 out
of 6 in the Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
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 the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu502
b:17.5
occ:1.00
|
O1
|
B:NO2504
|
2.1
|
27.1
|
1.0
|
NE2
|
A:HIS100
|
2.1
|
15.3
|
1.0
|
O
|
A:HOH5294
|
2.1
|
17.4
|
1.0
|
NE2
|
B:HIS306
|
2.1
|
14.1
|
1.0
|
NE2
|
A:HIS135
|
2.2
|
15.3
|
1.0
|
CE1
|
A:HIS100
|
3.0
|
16.1
|
1.0
|
CE1
|
B:HIS306
|
3.1
|
12.9
|
1.0
|
N
|
B:NO2504
|
3.1
|
29.3
|
1.0
|
O2
|
B:NO2504
|
3.1
|
30.9
|
1.0
|
CD2
|
A:HIS135
|
3.1
|
13.6
|
1.0
|
CD2
|
B:HIS306
|
3.2
|
14.5
|
1.0
|
CE1
|
A:HIS135
|
3.2
|
14.9
|
1.0
|
CD2
|
A:HIS100
|
3.2
|
15.1
|
1.0
|
OD2
|
A:ASP98
|
3.7
|
19.5
|
1.0
|
NE2
|
B:HIS255
|
3.9
|
13.1
|
1.0
|
CD2
|
B:HIS255
|
4.1
|
14.8
|
1.0
|
ND1
|
A:HIS100
|
4.1
|
15.0
|
1.0
|
ND1
|
B:HIS306
|
4.2
|
14.3
|
1.0
|
CG
|
A:HIS100
|
4.3
|
12.0
|
1.0
|
ND1
|
A:HIS135
|
4.3
|
12.3
|
1.0
|
CG
|
A:HIS135
|
4.3
|
12.9
|
1.0
|
CG
|
B:HIS306
|
4.3
|
12.9
|
1.0
|
CE1
|
B:HIS255
|
4.3
|
15.0
|
1.0
|
CG
|
A:ASP98
|
4.4
|
17.9
|
1.0
|
CG
|
B:HIS255
|
4.6
|
15.3
|
1.0
|
OD1
|
A:ASP98
|
4.7
|
17.4
|
1.0
|
ND1
|
B:HIS255
|
4.7
|
17.2
|
1.0
|
O
|
B:HOH6001
|
4.8
|
14.2
|
1.0
|
CD2
|
B:LEU308
|
4.9
|
15.3
|
1.0
|
|
Copper binding site 3 out
of 6 in 1l9s
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Copper Binding Sites List in 1l9s
Copper binding site 3 out
of 6 in the Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
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 the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu501
b:19.9
occ:1.00
|
ND1
|
B:HIS95
|
2.1
|
14.8
|
1.0
|
ND1
|
B:HIS145
|
2.1
|
17.5
|
1.0
|
SG
|
B:CYS136
|
2.3
|
17.7
|
1.0
|
SD
|
B:MET150
|
2.5
|
17.1
|
1.0
|
CE1
|
B:HIS145
|
2.9
|
17.2
|
1.0
|
CE1
|
B:HIS95
|
3.0
|
15.6
|
1.0
|
CG
|
B:HIS95
|
3.1
|
17.2
|
1.0
|
CB
|
B:CYS136
|
3.2
|
16.6
|
1.0
|
CG
|
B:HIS145
|
3.2
|
17.9
|
1.0
|
CE
|
B:MET150
|
3.3
|
17.6
|
1.0
|
CB
|
B:HIS95
|
3.4
|
17.1
|
1.0
|
CB
|
B:HIS145
|
3.6
|
17.4
|
1.0
|
CA
|
B:HIS95
|
3.8
|
17.1
|
1.0
|
CG
|
B:MET150
|
3.9
|
17.5
|
1.0
|
NE2
|
B:HIS145
|
4.1
|
17.4
|
1.0
|
CG
|
B:PRO138
|
4.1
|
18.4
|
1.0
|
NE2
|
B:HIS95
|
4.1
|
15.6
|
1.0
|
CD2
|
B:HIS95
|
4.2
|
15.0
|
1.0
|
SD
|
B:MET62
|
4.2
|
18.5
|
1.0
|
CD2
|
B:HIS145
|
4.2
|
18.1
|
1.0
|
O
|
B:MET94
|
4.2
|
17.5
|
1.0
|
CB
|
B:MET150
|
4.4
|
15.6
|
1.0
|
CD
|
B:PRO138
|
4.6
|
17.0
|
1.0
|
CA
|
B:CYS136
|
4.6
|
17.5
|
1.0
|
N
|
B:ASN96
|
4.7
|
17.7
|
1.0
|
CB
|
B:MET62
|
4.8
|
18.3
|
1.0
|
CA
|
B:HIS145
|
4.8
|
17.4
|
1.0
|
N
|
B:HIS95
|
4.8
|
18.9
|
1.0
|
C
|
B:HIS95
|
4.9
|
18.1
|
1.0
|
C
|
B:MET94
|
5.0
|
18.9
|
1.0
|
|
Copper binding site 4 out
of 6 in 1l9s
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Copper Binding Sites List in 1l9s
Copper binding site 4 out
of 6 in the Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
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 the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu502
b:21.0
occ:1.00
|
NE2
|
C:HIS306
|
2.1
|
15.4
|
1.0
|
NE2
|
B:HIS100
|
2.1
|
15.3
|
1.0
|
NE2
|
B:HIS135
|
2.1
|
18.1
|
1.0
|
O
|
B:HOH5634
|
2.2
|
23.2
|
1.0
|
O1
|
C:NO2604
|
2.3
|
27.6
|
1.0
|
O2
|
C:NO2604
|
3.0
|
35.2
|
1.0
|
CE1
|
B:HIS100
|
3.0
|
14.6
|
1.0
|
CD2
|
C:HIS306
|
3.1
|
17.2
|
1.0
|
CE1
|
C:HIS306
|
3.1
|
15.8
|
1.0
|
CE1
|
B:HIS135
|
3.1
|
16.6
|
1.0
|
N
|
C:NO2604
|
3.1
|
33.5
|
1.0
|
CD2
|
B:HIS135
|
3.1
|
15.7
|
1.0
|
CD2
|
B:HIS100
|
3.2
|
15.2
|
1.0
|
OD2
|
B:ASP98
|
3.7
|
16.8
|
1.0
|
NE2
|
C:HIS255
|
3.9
|
15.2
|
1.0
|
CD2
|
C:HIS255
|
4.1
|
15.2
|
1.0
|
ND1
|
B:HIS100
|
4.2
|
15.2
|
1.0
|
ND1
|
C:HIS306
|
4.2
|
15.8
|
1.0
|
ND1
|
B:HIS135
|
4.2
|
16.2
|
1.0
|
CG
|
C:HIS306
|
4.2
|
16.6
|
1.0
|
CG
|
B:HIS100
|
4.3
|
13.5
|
1.0
|
CG
|
B:HIS135
|
4.3
|
16.3
|
1.0
|
CG
|
B:ASP98
|
4.3
|
17.1
|
1.0
|
CE1
|
C:HIS255
|
4.4
|
15.3
|
1.0
|
CG
|
C:HIS255
|
4.6
|
15.4
|
1.0
|
OD1
|
B:ASP98
|
4.7
|
15.1
|
1.0
|
ND1
|
C:HIS255
|
4.7
|
16.4
|
1.0
|
O
|
C:HOH6002
|
4.8
|
15.3
|
1.0
|
CD2
|
C:LEU308
|
5.0
|
17.8
|
1.0
|
|
Copper binding site 5 out
of 6 in 1l9s
Go back to
Copper Binding Sites List in 1l9s
Copper binding site 5 out
of 6 in the Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
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 the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu501
b:24.8
occ:1.00
|
ND1
|
C:HIS145
|
2.0
|
22.2
|
1.0
|
ND1
|
C:HIS95
|
2.2
|
22.6
|
1.0
|
SG
|
C:CYS136
|
2.2
|
22.2
|
1.0
|
SD
|
C:MET150
|
2.5
|
21.4
|
1.0
|
CE1
|
C:HIS145
|
2.8
|
23.1
|
1.0
|
CG
|
C:HIS145
|
3.1
|
22.3
|
1.0
|
CE1
|
C:HIS95
|
3.1
|
23.1
|
1.0
|
CB
|
C:CYS136
|
3.2
|
19.1
|
1.0
|
CG
|
C:HIS95
|
3.2
|
22.7
|
1.0
|
CE
|
C:MET150
|
3.2
|
20.2
|
1.0
|
CB
|
C:HIS145
|
3.5
|
20.3
|
1.0
|
CB
|
C:HIS95
|
3.5
|
22.7
|
1.0
|
CA
|
C:HIS95
|
3.8
|
22.1
|
1.0
|
CG
|
C:MET150
|
3.9
|
19.2
|
1.0
|
NE2
|
C:HIS145
|
4.0
|
21.6
|
1.0
|
CD2
|
C:HIS145
|
4.1
|
22.4
|
1.0
|
CG
|
C:PRO138
|
4.2
|
25.4
|
1.0
|
NE2
|
C:HIS95
|
4.2
|
20.3
|
1.0
|
O
|
C:MET94
|
4.3
|
24.1
|
1.0
|
CD2
|
C:HIS95
|
4.3
|
22.3
|
1.0
|
CB
|
C:MET150
|
4.3
|
19.5
|
1.0
|
SD
|
C:MET62
|
4.4
|
21.6
|
1.0
|
CA
|
C:CYS136
|
4.6
|
20.0
|
1.0
|
N
|
C:ASN96
|
4.6
|
22.1
|
1.0
|
CD
|
C:PRO138
|
4.7
|
22.2
|
1.0
|
CB
|
C:MET62
|
4.8
|
21.0
|
1.0
|
CA
|
C:HIS145
|
4.8
|
21.0
|
1.0
|
C
|
C:HIS95
|
4.8
|
22.0
|
1.0
|
N
|
C:HIS95
|
4.9
|
22.4
|
1.0
|
|
Copper binding site 6 out
of 6 in 1l9s
Go back to
Copper Binding Sites List in 1l9s
Copper binding site 6 out
of 6 in the Crystal Structure of the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6
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 the I257T Variant of the Copper- Containing Nitrite Reductase From Alcaligenes Faecalis S-6 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu502
b:22.1
occ:1.00
|
O1
|
A:NO2704
|
2.0
|
36.0
|
1.0
|
O
|
A:HOH5635
|
2.0
|
21.7
|
1.0
|
NE2
|
C:HIS100
|
2.1
|
18.2
|
1.0
|
NE2
|
A:HIS306
|
2.1
|
14.1
|
1.0
|
NE2
|
C:HIS135
|
2.2
|
18.1
|
1.0
|
N
|
A:NO2704
|
2.9
|
35.5
|
1.0
|
CE1
|
C:HIS100
|
3.0
|
17.6
|
1.0
|
O2
|
A:NO2704
|
3.0
|
35.3
|
1.0
|
CE1
|
A:HIS306
|
3.1
|
17.4
|
1.0
|
CD2
|
C:HIS135
|
3.1
|
19.8
|
1.0
|
CD2
|
A:HIS306
|
3.1
|
16.0
|
1.0
|
CD2
|
C:HIS100
|
3.2
|
17.3
|
1.0
|
CE1
|
C:HIS135
|
3.2
|
17.2
|
1.0
|
OD2
|
C:ASP98
|
3.8
|
23.5
|
1.0
|
NE2
|
A:HIS255
|
3.9
|
21.6
|
1.0
|
CD2
|
A:HIS255
|
3.9
|
20.7
|
1.0
|
ND1
|
C:HIS100
|
4.1
|
16.1
|
1.0
|
ND1
|
A:HIS306
|
4.2
|
16.4
|
1.0
|
CG
|
C:HIS100
|
4.3
|
16.7
|
1.0
|
CG
|
C:HIS135
|
4.3
|
17.5
|
1.0
|
CG
|
A:HIS306
|
4.3
|
14.5
|
1.0
|
ND1
|
C:HIS135
|
4.3
|
19.0
|
1.0
|
CG
|
C:ASP98
|
4.4
|
22.6
|
1.0
|
CE1
|
A:HIS255
|
4.5
|
21.0
|
1.0
|
CG
|
A:HIS255
|
4.6
|
19.8
|
1.0
|
OD1
|
C:ASP98
|
4.7
|
20.9
|
1.0
|
O
|
A:HOH5632
|
4.8
|
17.2
|
1.0
|
ND1
|
A:HIS255
|
4.9
|
20.4
|
1.0
|
OG1
|
A:THR257
|
5.0
|
21.6
|
1.0
|
|
Reference:
M.J.Boulanger,
M.E.P.Murphy.
Directing the Mode of Nitrite Binding to A Copper-Containing Nitrite Reductase From Alcaligenes Faecalis S-6: Characterization of An Active Site Isoleucine Protein Sci. V. 12 248 2003.
ISSN: ISSN 0961-8368
PubMed: 12538888
DOI: 10.1110/PS.0224503
Page generated: Tue Jul 30 22:14:47 2024
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