Copper in PDB 6kng: Cryoem Map and Model of Nitrite Reductase at pH 8.1
Enzymatic activity of Cryoem Map and Model of Nitrite Reductase at pH 8.1
All present enzymatic activity of Cryoem Map and Model of Nitrite Reductase at pH 8.1:
1.7.2.1;
Copper Binding Sites:
The binding sites of Copper atom in the Cryoem Map and Model of Nitrite Reductase at pH 8.1
(pdb code 6kng). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Cryoem Map and Model of Nitrite Reductase at pH 8.1, PDB code: 6kng:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 6kng
Go back to
Copper Binding Sites List in 6kng
Copper binding site 1 out
of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu500
b:74.0
occ:1.00
|
ND1
|
A:HIS95
|
2.2
|
57.6
|
1.0
|
ND1
|
A:HIS145
|
2.2
|
55.3
|
1.0
|
SG
|
A:CYS136
|
2.3
|
56.0
|
1.0
|
SD
|
A:MET150
|
2.4
|
53.4
|
1.0
|
CE1
|
A:HIS95
|
3.0
|
57.6
|
1.0
|
CE1
|
A:HIS145
|
3.0
|
55.3
|
1.0
|
CB
|
A:CYS136
|
3.2
|
56.0
|
1.0
|
CG
|
A:HIS145
|
3.3
|
55.3
|
1.0
|
CG
|
A:HIS95
|
3.3
|
57.6
|
1.0
|
CE
|
A:MET150
|
3.3
|
53.4
|
1.0
|
CB
|
A:HIS145
|
3.7
|
55.3
|
1.0
|
CB
|
A:HIS95
|
3.7
|
57.6
|
1.0
|
CG
|
A:MET150
|
4.0
|
53.4
|
1.0
|
CA
|
A:HIS95
|
4.1
|
57.6
|
1.0
|
NE2
|
A:HIS95
|
4.1
|
57.6
|
1.0
|
NE2
|
A:HIS145
|
4.2
|
55.3
|
1.0
|
CD2
|
A:HIS145
|
4.3
|
55.3
|
1.0
|
CD2
|
A:HIS95
|
4.3
|
57.6
|
1.0
|
CG
|
A:PRO138
|
4.3
|
59.2
|
1.0
|
O
|
A:LEU94
|
4.5
|
58.9
|
1.0
|
CB
|
A:MET150
|
4.5
|
53.4
|
1.0
|
SD
|
A:MET62
|
4.5
|
60.9
|
1.0
|
CA
|
A:CYS136
|
4.7
|
56.0
|
1.0
|
CD
|
A:PRO138
|
4.7
|
59.2
|
1.0
|
CA
|
A:HIS145
|
4.8
|
55.3
|
1.0
|
N
|
A:ASN96
|
4.9
|
56.9
|
1.0
|
|
Copper binding site 2 out
of 6 in 6kng
Go back to
Copper Binding Sites List in 6kng
Copper binding site 2 out
of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu501
b:74.2
occ:1.00
|
NE2
|
C:HIS306
|
2.1
|
53.6
|
1.0
|
NE2
|
A:HIS100
|
2.1
|
53.6
|
1.0
|
NE2
|
A:HIS135
|
2.2
|
52.0
|
1.0
|
CE1
|
A:HIS100
|
2.7
|
53.6
|
1.0
|
CE1
|
C:HIS306
|
3.0
|
53.6
|
1.0
|
CD2
|
A:HIS135
|
3.1
|
52.0
|
1.0
|
CE1
|
A:HIS135
|
3.2
|
52.0
|
1.0
|
CD2
|
C:HIS306
|
3.2
|
53.6
|
1.0
|
CD2
|
A:HIS100
|
3.4
|
53.6
|
1.0
|
ND1
|
A:HIS100
|
4.0
|
53.6
|
1.0
|
NE2
|
C:HIS255
|
4.1
|
52.6
|
1.0
|
ND1
|
C:HIS306
|
4.1
|
53.6
|
1.0
|
CD2
|
C:HIS255
|
4.2
|
52.6
|
1.0
|
CG
|
C:HIS306
|
4.3
|
53.6
|
1.0
|
ND1
|
A:HIS135
|
4.3
|
52.0
|
1.0
|
CG
|
A:HIS135
|
4.3
|
52.0
|
1.0
|
CG
|
A:HIS100
|
4.3
|
53.6
|
1.0
|
OD2
|
A:ASP98
|
4.8
|
57.2
|
1.0
|
CE1
|
C:HIS255
|
5.0
|
52.6
|
1.0
|
|
Copper binding site 3 out
of 6 in 6kng
Go back to
Copper Binding Sites List in 6kng
Copper binding site 3 out
of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu500
b:74.7
occ:1.00
|
ND1
|
B:HIS95
|
2.2
|
58.1
|
1.0
|
ND1
|
B:HIS145
|
2.2
|
56.2
|
1.0
|
SG
|
B:CYS136
|
2.3
|
56.2
|
1.0
|
SD
|
B:MET150
|
2.4
|
54.2
|
1.0
|
CE1
|
B:HIS95
|
3.0
|
58.1
|
1.0
|
CE1
|
B:HIS145
|
3.0
|
56.2
|
1.0
|
CB
|
B:CYS136
|
3.2
|
56.2
|
1.0
|
CG
|
B:HIS145
|
3.3
|
56.2
|
1.0
|
CG
|
B:HIS95
|
3.3
|
58.1
|
1.0
|
CE
|
B:MET150
|
3.3
|
54.2
|
1.0
|
CB
|
B:HIS145
|
3.7
|
56.2
|
1.0
|
CB
|
B:HIS95
|
3.7
|
58.1
|
1.0
|
CG
|
B:MET150
|
4.0
|
54.2
|
1.0
|
CA
|
B:HIS95
|
4.1
|
58.1
|
1.0
|
NE2
|
B:HIS95
|
4.1
|
58.1
|
1.0
|
NE2
|
B:HIS145
|
4.2
|
56.2
|
1.0
|
CD2
|
B:HIS145
|
4.3
|
56.2
|
1.0
|
CD2
|
B:HIS95
|
4.3
|
58.1
|
1.0
|
CG
|
B:PRO138
|
4.3
|
59.0
|
1.0
|
O
|
B:LEU94
|
4.5
|
59.6
|
1.0
|
CB
|
B:MET150
|
4.5
|
54.2
|
1.0
|
SD
|
B:MET62
|
4.5
|
60.4
|
1.0
|
CA
|
B:CYS136
|
4.7
|
56.2
|
1.0
|
CD
|
B:PRO138
|
4.7
|
59.0
|
1.0
|
CA
|
B:HIS145
|
4.8
|
56.2
|
1.0
|
N
|
B:ASN96
|
4.9
|
57.0
|
1.0
|
|
Copper binding site 4 out
of 6 in 6kng
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Copper Binding Sites List in 6kng
Copper binding site 4 out
of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cu501
b:78.0
occ:1.00
|
NE2
|
B:HIS100
|
2.1
|
54.0
|
1.0
|
NE2
|
A:HIS306
|
2.1
|
54.7
|
1.0
|
NE2
|
B:HIS135
|
2.2
|
52.3
|
1.0
|
CE1
|
B:HIS100
|
2.7
|
54.0
|
1.0
|
CE1
|
A:HIS306
|
3.0
|
54.7
|
1.0
|
CD2
|
B:HIS135
|
3.1
|
52.3
|
1.0
|
CE1
|
B:HIS135
|
3.2
|
52.3
|
1.0
|
CD2
|
A:HIS306
|
3.2
|
54.7
|
1.0
|
CD2
|
B:HIS100
|
3.4
|
54.0
|
1.0
|
ND1
|
B:HIS100
|
4.0
|
54.0
|
1.0
|
NE2
|
A:HIS255
|
4.1
|
52.7
|
1.0
|
ND1
|
A:HIS306
|
4.1
|
54.7
|
1.0
|
CD2
|
A:HIS255
|
4.2
|
52.7
|
1.0
|
ND1
|
B:HIS135
|
4.3
|
52.3
|
1.0
|
CG
|
A:HIS306
|
4.3
|
54.7
|
1.0
|
CG
|
B:HIS100
|
4.3
|
54.0
|
1.0
|
CG
|
B:HIS135
|
4.3
|
52.3
|
1.0
|
OD2
|
B:ASP98
|
4.8
|
57.6
|
1.0
|
CE1
|
A:HIS255
|
5.0
|
52.7
|
1.0
|
|
Copper binding site 5 out
of 6 in 6kng
Go back to
Copper Binding Sites List in 6kng
Copper binding site 5 out
of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu500
b:74.0
occ:1.00
|
ND1
|
C:HIS95
|
2.2
|
58.7
|
1.0
|
ND1
|
C:HIS145
|
2.2
|
55.7
|
1.0
|
SG
|
C:CYS136
|
2.3
|
56.8
|
1.0
|
SD
|
C:MET150
|
2.4
|
54.2
|
1.0
|
CE1
|
C:HIS95
|
3.0
|
58.7
|
1.0
|
CE1
|
C:HIS145
|
3.0
|
55.7
|
1.0
|
CB
|
C:CYS136
|
3.2
|
56.8
|
1.0
|
CG
|
C:HIS145
|
3.3
|
55.7
|
1.0
|
CG
|
C:HIS95
|
3.3
|
58.7
|
1.0
|
CE
|
C:MET150
|
3.3
|
54.2
|
1.0
|
CB
|
C:HIS145
|
3.7
|
55.7
|
1.0
|
CB
|
C:HIS95
|
3.7
|
58.7
|
1.0
|
CG
|
C:MET150
|
4.0
|
54.2
|
1.0
|
CA
|
C:HIS95
|
4.1
|
58.7
|
1.0
|
NE2
|
C:HIS95
|
4.1
|
58.7
|
1.0
|
NE2
|
C:HIS145
|
4.2
|
55.7
|
1.0
|
CD2
|
C:HIS145
|
4.3
|
55.7
|
1.0
|
CD2
|
C:HIS95
|
4.3
|
58.7
|
1.0
|
CG
|
C:PRO138
|
4.3
|
59.9
|
1.0
|
O
|
C:LEU94
|
4.5
|
61.9
|
1.0
|
CB
|
C:MET150
|
4.5
|
54.2
|
1.0
|
SD
|
C:MET62
|
4.5
|
59.9
|
1.0
|
CA
|
C:CYS136
|
4.7
|
56.8
|
1.0
|
CD
|
C:PRO138
|
4.7
|
59.9
|
1.0
|
CA
|
C:HIS145
|
4.8
|
55.7
|
1.0
|
N
|
C:ASN96
|
4.9
|
57.8
|
1.0
|
|
Copper binding site 6 out
of 6 in 6kng
Go back to
Copper Binding Sites List in 6kng
Copper binding site 6 out
of 6 in the Cryoem Map and Model of Nitrite Reductase at pH 8.1
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Cryoem Map and Model of Nitrite Reductase at pH 8.1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cu501
b:77.6
occ:1.00
|
NE2
|
C:HIS100
|
2.1
|
54.7
|
1.0
|
NE2
|
B:HIS306
|
2.1
|
53.7
|
1.0
|
NE2
|
C:HIS135
|
2.2
|
53.0
|
1.0
|
CE1
|
C:HIS100
|
2.7
|
54.7
|
1.0
|
CE1
|
B:HIS306
|
3.0
|
53.7
|
1.0
|
CD2
|
C:HIS135
|
3.1
|
53.0
|
1.0
|
CE1
|
C:HIS135
|
3.2
|
53.0
|
1.0
|
CD2
|
B:HIS306
|
3.2
|
53.7
|
1.0
|
CD2
|
C:HIS100
|
3.4
|
54.7
|
1.0
|
ND1
|
C:HIS100
|
4.0
|
54.7
|
1.0
|
NE2
|
B:HIS255
|
4.0
|
53.0
|
1.0
|
ND1
|
B:HIS306
|
4.1
|
53.7
|
1.0
|
CD2
|
B:HIS255
|
4.2
|
53.0
|
1.0
|
ND1
|
C:HIS135
|
4.3
|
53.0
|
1.0
|
CG
|
B:HIS306
|
4.3
|
53.7
|
1.0
|
CG
|
C:HIS135
|
4.3
|
53.0
|
1.0
|
CG
|
C:HIS100
|
4.3
|
54.7
|
1.0
|
OD2
|
C:ASP98
|
4.8
|
58.4
|
1.0
|
CE1
|
B:HIS255
|
4.9
|
53.0
|
1.0
|
|
Reference:
N.Adachi,
T.Yamaguchi,
T.Moriya,
M.Kawasaki,
K.Koiwai,
A.Shinoda,
Y.Yamada,
F.Yumoto,
T.Kohzuma,
T.Senda.
Cryoem Map and Model of Nitrite Reductase at pH 8.1 To Be Published.
Page generated: Wed Jul 31 06:27:56 2024
|