Copper in PDB 4e9r: Multicopper Oxidase Cueo (DATA4)
Protein crystallography data
The structure of Multicopper Oxidase Cueo (DATA4), PDB code: 4e9r
was solved by
H.Komori,
K.Kataoka,
T.Sakurai,
Y.Higuchi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
10.00 /
1.30
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
50.391,
90.756,
53.317,
90.00,
102.69,
90.00
|
|
R / Rfree (%)
|
13.7 /
n/a
|
Copper Binding Sites:
The binding sites of Copper atom in the Multicopper Oxidase Cueo (DATA4)
(pdb code 4e9r). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the
Multicopper Oxidase Cueo (DATA4), PDB code: 4e9r:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
Copper binding site 1 out
of 6 in 4e9r
Go back to
Copper Binding Sites List in 4e9r
Copper binding site 1 out
of 6 in the Multicopper Oxidase Cueo (DATA4)
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Multicopper Oxidase Cueo (DATA4) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1001
b:10.1
occ:1.00
|
ND1
|
A:HIS505
|
2.0
|
8.6
|
1.0
|
|
ND1
|
A:HIS443
|
2.0
|
9.5
|
1.0
|
|
SG
|
A:CYS500
|
2.2
|
9.4
|
1.0
|
|
CE1
|
A:HIS505
|
3.0
|
9.4
|
1.0
|
|
CE1
|
A:HIS443
|
3.0
|
9.8
|
1.0
|
|
CG
|
A:HIS505
|
3.0
|
9.0
|
1.0
|
|
CG
|
A:HIS443
|
3.0
|
10.2
|
1.0
|
|
CB
|
A:CYS500
|
3.2
|
9.8
|
1.0
|
|
SD
|
A:MET510
|
3.2
|
11.2
|
1.0
|
|
CB
|
A:HIS505
|
3.3
|
9.1
|
1.0
|
|
CB
|
A:HIS443
|
3.4
|
9.9
|
1.0
|
|
CA
|
A:HIS443
|
3.6
|
8.6
|
1.0
|
|
O
|
A:LEU442
|
3.6
|
11.5
|
1.0
|
|
CE
|
A:MET510
|
4.0
|
12.7
|
1.0
|
|
CB
|
A:LEU502
|
4.0
|
7.7
|
1.0
|
|
NE2
|
A:HIS505
|
4.1
|
9.5
|
1.0
|
|
NE2
|
A:HIS443
|
4.1
|
10.5
|
1.0
|
|
CD2
|
A:HIS505
|
4.2
|
9.7
|
1.0
|
|
CD2
|
A:HIS443
|
4.2
|
11.0
|
1.0
|
|
C
|
A:LEU442
|
4.4
|
9.7
|
1.0
|
|
N
|
A:HIS443
|
4.4
|
8.6
|
1.0
|
|
CA
|
A:CYS500
|
4.6
|
8.8
|
1.0
|
|
CD1
|
A:LEU502
|
4.7
|
9.3
|
1.0
|
|
CG
|
A:MET510
|
4.8
|
11.2
|
1.0
|
|
C
|
A:HIS443
|
4.9
|
8.7
|
1.0
|
|
CA
|
A:HIS505
|
4.9
|
9.2
|
1.0
|
|
CG
|
A:LEU502
|
4.9
|
7.5
|
1.0
|
|
O
|
A:LEU502
|
4.9
|
8.5
|
1.0
|
|
N
|
A:LEU502
|
5.0
|
8.4
|
1.0
|
|
Copper binding site 2 out
of 6 in 4e9r
Go back to
Copper Binding Sites List in 4e9r
Copper binding site 2 out
of 6 in the Multicopper Oxidase Cueo (DATA4)
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Multicopper Oxidase Cueo (DATA4) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1002
b:7.1
occ:0.35
|
CU
|
A:CU1002
|
0.0
|
7.1
|
0.3
|
|
CU
|
A:CU1002
|
1.0
|
9.4
|
0.6
|
|
O
|
A:HOH1101
|
1.8
|
10.7
|
0.4
|
|
NE2
|
A:HIS501
|
2.1
|
9.3
|
1.0
|
|
O
|
A:HOH1102
|
2.1
|
11.6
|
0.5
|
|
ND1
|
A:HIS103
|
2.1
|
8.6
|
1.0
|
|
O
|
A:HOH1101
|
2.2
|
10.8
|
0.5
|
|
NE2
|
A:HIS141
|
2.3
|
11.0
|
1.0
|
|
CD2
|
A:HIS501
|
2.9
|
9.1
|
1.0
|
|
CE1
|
A:HIS103
|
3.0
|
9.1
|
1.0
|
|
CE1
|
A:HIS141
|
3.1
|
11.8
|
1.0
|
|
CG
|
A:HIS103
|
3.2
|
7.4
|
1.0
|
|
CE1
|
A:HIS501
|
3.2
|
10.3
|
1.0
|
|
CU
|
A:CU1003
|
3.3
|
8.8
|
0.5
|
|
CD2
|
A:HIS141
|
3.5
|
10.3
|
1.0
|
|
CB
|
A:HIS103
|
3.7
|
8.0
|
1.0
|
|
CD2
|
A:HIS446
|
3.7
|
9.3
|
1.0
|
|
CU
|
A:CU1004
|
3.7
|
10.2
|
0.8
|
|
O
|
A:HOH1103
|
3.9
|
19.2
|
1.0
|
|
NE2
|
A:HIS446
|
3.9
|
11.2
|
1.0
|
|
CD2
|
A:HIS101
|
3.9
|
10.4
|
1.0
|
|
CU
|
A:CU1003
|
4.0
|
11.6
|
0.4
|
|
NE2
|
A:HIS103
|
4.1
|
8.2
|
1.0
|
|
CG
|
A:HIS501
|
4.2
|
7.6
|
1.0
|
|
CD2
|
A:HIS103
|
4.2
|
7.9
|
1.0
|
|
NE2
|
A:HIS101
|
4.3
|
11.3
|
1.0
|
|
ND1
|
A:HIS501
|
4.3
|
8.8
|
1.0
|
|
ND1
|
A:HIS141
|
4.3
|
10.3
|
1.0
|
|
CE1
|
A:HIS499
|
4.5
|
9.7
|
1.0
|
|
CZ2
|
A:TRP139
|
4.5
|
7.7
|
1.0
|
|
NE2
|
A:HIS499
|
4.5
|
10.0
|
1.0
|
|
CG
|
A:HIS141
|
4.6
|
9.4
|
1.0
|
|
CG
|
A:HIS446
|
4.6
|
8.8
|
1.0
|
|
NE2
|
A:HIS143
|
4.7
|
12.5
|
1.0
|
|
CA
|
A:HIS103
|
4.8
|
8.3
|
1.0
|
|
CE1
|
A:HIS446
|
4.8
|
10.9
|
1.0
|
|
CE2
|
A:TRP139
|
4.9
|
7.3
|
1.0
|
|
NE1
|
A:TRP139
|
4.9
|
7.6
|
1.0
|
|
NE2
|
A:HIS448
|
5.0
|
10.2
|
1.0
|
|
Copper binding site 3 out
of 6 in 4e9r
Go back to
Copper Binding Sites List in 4e9r
Copper binding site 3 out
of 6 in the Multicopper Oxidase Cueo (DATA4)
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Multicopper Oxidase Cueo (DATA4) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1002
b:9.4
occ:0.55
|
CU
|
A:CU1002
|
0.0
|
9.4
|
0.6
|
|
CU
|
A:CU1002
|
1.0
|
7.1
|
0.3
|
|
ND1
|
A:HIS103
|
1.9
|
8.6
|
1.0
|
|
NE2
|
A:HIS141
|
1.9
|
11.0
|
1.0
|
|
NE2
|
A:HIS501
|
2.1
|
9.3
|
1.0
|
|
O
|
A:HOH1101
|
2.6
|
10.7
|
0.4
|
|
CD2
|
A:HIS141
|
2.9
|
10.3
|
1.0
|
|
CE1
|
A:HIS103
|
2.9
|
9.1
|
1.0
|
|
O
|
A:HOH1102
|
2.9
|
11.6
|
0.5
|
|
CE1
|
A:HIS141
|
2.9
|
11.8
|
1.0
|
|
O
|
A:HOH1101
|
3.0
|
10.8
|
0.5
|
|
CG
|
A:HIS103
|
3.0
|
7.4
|
1.0
|
|
CE1
|
A:HIS501
|
3.0
|
10.3
|
1.0
|
|
CD2
|
A:HIS501
|
3.2
|
9.1
|
1.0
|
|
CB
|
A:HIS103
|
3.4
|
8.0
|
1.0
|
|
CZ2
|
A:TRP139
|
3.6
|
7.7
|
1.0
|
|
CE2
|
A:TRP139
|
3.9
|
7.3
|
1.0
|
|
CG
|
A:HIS141
|
4.0
|
9.4
|
1.0
|
|
NE2
|
A:HIS103
|
4.0
|
8.2
|
1.0
|
|
ND1
|
A:HIS141
|
4.0
|
10.3
|
1.0
|
|
CD2
|
A:HIS103
|
4.1
|
7.9
|
1.0
|
|
NE1
|
A:TRP139
|
4.1
|
7.6
|
1.0
|
|
ND1
|
A:HIS501
|
4.2
|
8.8
|
1.0
|
|
CU
|
A:CU1003
|
4.2
|
8.8
|
0.5
|
|
O
|
A:HOH1103
|
4.3
|
19.2
|
1.0
|
|
CG
|
A:HIS501
|
4.3
|
7.6
|
1.0
|
|
CD2
|
A:HIS101
|
4.3
|
10.4
|
1.0
|
|
CH2
|
A:TRP139
|
4.3
|
8.8
|
1.0
|
|
CU
|
A:CU1004
|
4.3
|
10.2
|
0.8
|
|
CD2
|
A:HIS446
|
4.5
|
9.3
|
1.0
|
|
NE2
|
A:HIS446
|
4.5
|
11.2
|
1.0
|
|
CA
|
A:HIS103
|
4.7
|
8.3
|
1.0
|
|
NE2
|
A:HIS101
|
4.7
|
11.3
|
1.0
|
|
CU
|
A:CU1003
|
4.9
|
11.6
|
0.4
|
|
CD2
|
A:TRP139
|
4.9
|
7.9
|
1.0
|
|
Copper binding site 4 out
of 6 in 4e9r
Go back to
Copper Binding Sites List in 4e9r
Copper binding site 4 out
of 6 in the Multicopper Oxidase Cueo (DATA4)
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Multicopper Oxidase Cueo (DATA4) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1003
b:8.8
occ:0.47
|
CU
|
A:CU1003
|
0.0
|
8.8
|
0.5
|
|
CU
|
A:CU1003
|
0.7
|
11.6
|
0.4
|
|
O
|
A:HOH1101
|
1.6
|
10.7
|
0.4
|
|
O
|
A:HOH1101
|
1.8
|
10.8
|
0.5
|
|
O
|
A:HOH1102
|
2.1
|
11.6
|
0.5
|
|
NE2
|
A:HIS448
|
2.1
|
10.2
|
1.0
|
|
NE2
|
A:HIS143
|
2.1
|
12.5
|
1.0
|
|
NE2
|
A:HIS499
|
2.2
|
10.0
|
1.0
|
|
CE1
|
A:HIS499
|
3.0
|
9.7
|
1.0
|
|
CE1
|
A:HIS448
|
3.1
|
11.5
|
1.0
|
|
CD2
|
A:HIS143
|
3.1
|
11.0
|
1.0
|
|
CE1
|
A:HIS143
|
3.2
|
11.5
|
1.0
|
|
CD2
|
A:HIS448
|
3.2
|
10.6
|
1.0
|
|
CD2
|
A:HIS499
|
3.3
|
10.5
|
1.0
|
|
CU
|
A:CU1002
|
3.3
|
7.1
|
0.3
|
|
CD2
|
A:HIS446
|
3.5
|
9.3
|
1.0
|
|
CU
|
A:CU1004
|
3.5
|
10.2
|
0.8
|
|
O
|
A:HOH1103
|
3.7
|
19.2
|
1.0
|
|
CD2
|
A:HIS101
|
3.7
|
10.4
|
1.0
|
|
NE2
|
A:HIS101
|
3.8
|
11.3
|
1.0
|
|
NE2
|
A:HIS446
|
3.9
|
11.2
|
1.0
|
|
ND1
|
A:HIS448
|
4.2
|
10.9
|
1.0
|
|
CU
|
A:CU1002
|
4.2
|
9.4
|
0.6
|
|
ND1
|
A:HIS499
|
4.2
|
9.9
|
1.0
|
|
ND1
|
A:HIS143
|
4.3
|
12.5
|
1.0
|
|
CG
|
A:HIS448
|
4.3
|
10.4
|
1.0
|
|
CG
|
A:HIS143
|
4.3
|
10.8
|
1.0
|
|
CG
|
A:HIS499
|
4.4
|
9.8
|
1.0
|
|
CE1
|
A:HIS141
|
4.4
|
11.8
|
1.0
|
|
NE2
|
A:HIS501
|
4.5
|
9.3
|
1.0
|
|
NE2
|
A:HIS141
|
4.6
|
11.0
|
1.0
|
|
CG
|
A:HIS101
|
4.6
|
10.5
|
1.0
|
|
CD2
|
A:HIS501
|
4.6
|
9.1
|
1.0
|
|
CE1
|
A:HIS101
|
4.7
|
10.1
|
1.0
|
|
CG
|
A:HIS446
|
4.7
|
8.8
|
1.0
|
|
OE2
|
A:GLU506
|
4.8
|
30.3
|
1.0
|
|
ND1
|
A:HIS103
|
5.0
|
8.6
|
1.0
|
|
Copper binding site 5 out
of 6 in 4e9r
Go back to
Copper Binding Sites List in 4e9r
Copper binding site 5 out
of 6 in the Multicopper Oxidase Cueo (DATA4)
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Multicopper Oxidase Cueo (DATA4) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1003
b:11.6
occ:0.43
|
CU
|
A:CU1003
|
0.0
|
11.6
|
0.4
|
|
CU
|
A:CU1003
|
0.7
|
8.8
|
0.5
|
|
NE2
|
A:HIS448
|
1.8
|
10.2
|
1.0
|
|
NE2
|
A:HIS499
|
1.9
|
10.0
|
1.0
|
|
NE2
|
A:HIS143
|
2.0
|
12.5
|
1.0
|
|
O
|
A:HOH1101
|
2.3
|
10.7
|
0.4
|
|
O
|
A:HOH1101
|
2.3
|
10.8
|
0.5
|
|
O
|
A:HOH1102
|
2.7
|
11.6
|
0.5
|
|
CE1
|
A:HIS448
|
2.8
|
11.5
|
1.0
|
|
CE1
|
A:HIS143
|
2.8
|
11.5
|
1.0
|
|
CD2
|
A:HIS499
|
2.8
|
10.5
|
1.0
|
|
CD2
|
A:HIS448
|
2.9
|
10.6
|
1.0
|
|
CE1
|
A:HIS499
|
3.0
|
9.7
|
1.0
|
|
CD2
|
A:HIS143
|
3.1
|
11.0
|
1.0
|
|
CD2
|
A:HIS446
|
3.8
|
9.3
|
1.0
|
|
O
|
A:HOH1103
|
3.9
|
19.2
|
1.0
|
|
ND1
|
A:HIS448
|
3.9
|
10.9
|
1.0
|
|
CU
|
A:CU1004
|
3.9
|
10.2
|
0.8
|
|
CG
|
A:HIS499
|
4.0
|
9.8
|
1.0
|
|
CU
|
A:CU1002
|
4.0
|
7.1
|
0.3
|
|
ND1
|
A:HIS143
|
4.0
|
12.5
|
1.0
|
|
ND1
|
A:HIS499
|
4.0
|
9.9
|
1.0
|
|
CG
|
A:HIS448
|
4.0
|
10.4
|
1.0
|
|
CG
|
A:HIS143
|
4.2
|
10.8
|
1.0
|
|
NE2
|
A:HIS101
|
4.2
|
11.3
|
1.0
|
|
CD2
|
A:HIS101
|
4.2
|
10.4
|
1.0
|
|
NE2
|
A:HIS446
|
4.3
|
11.2
|
1.0
|
|
CB
|
A:MET497
|
4.3
|
10.4
|
1.0
|
|
OE2
|
A:GLU506
|
4.6
|
30.3
|
1.0
|
|
CG
|
A:MET497
|
4.8
|
11.7
|
1.0
|
|
CE1
|
A:HIS101
|
4.9
|
10.1
|
1.0
|
|
CG
|
A:HIS101
|
4.9
|
10.5
|
1.0
|
|
CU
|
A:CU1002
|
4.9
|
9.4
|
0.6
|
|
CE1
|
A:HIS141
|
4.9
|
11.8
|
1.0
|
|
CG
|
A:HIS446
|
5.0
|
8.8
|
1.0
|
|
Copper binding site 6 out
of 6 in 4e9r
Go back to
Copper Binding Sites List in 4e9r
Copper binding site 6 out
of 6 in the Multicopper Oxidase Cueo (DATA4)
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Multicopper Oxidase Cueo (DATA4) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1004
b:10.2
occ:0.75
|
O
|
A:HOH1102
|
1.9
|
11.6
|
0.5
|
|
NE2
|
A:HIS446
|
1.9
|
11.2
|
1.0
|
|
NE2
|
A:HIS101
|
1.9
|
11.3
|
1.0
|
|
OXT
|
A:ACT1005
|
2.3
|
17.3
|
0.5
|
|
O
|
A:HOH1104
|
2.3
|
14.7
|
0.5
|
|
CE1
|
A:HIS101
|
2.9
|
10.1
|
1.0
|
|
CE1
|
A:HIS446
|
2.9
|
10.9
|
1.0
|
|
CD2
|
A:HIS446
|
2.9
|
9.3
|
1.0
|
|
CD2
|
A:HIS101
|
3.0
|
10.4
|
1.0
|
|
CD2
|
A:HIS448
|
3.2
|
10.6
|
1.0
|
|
C
|
A:ACT1005
|
3.2
|
16.9
|
0.5
|
|
NE2
|
A:HIS448
|
3.3
|
10.2
|
1.0
|
|
O
|
A:ACT1005
|
3.5
|
13.3
|
0.5
|
|
CU
|
A:CU1003
|
3.5
|
8.8
|
0.5
|
|
CA
|
A:HIS103
|
3.6
|
8.3
|
1.0
|
|
CG
|
A:HIS103
|
3.6
|
7.4
|
1.0
|
|
O
|
A:HOH1101
|
3.6
|
10.7
|
0.4
|
|
ND1
|
A:HIS103
|
3.7
|
8.6
|
1.0
|
|
CG
|
A:HIS448
|
3.7
|
10.4
|
1.0
|
|
CB
|
A:HIS103
|
3.7
|
8.0
|
1.0
|
|
CU
|
A:CU1002
|
3.7
|
7.1
|
0.3
|
|
CE1
|
A:HIS448
|
3.9
|
11.5
|
1.0
|
|
CU
|
A:CU1003
|
3.9
|
11.6
|
0.4
|
|
ND1
|
A:HIS101
|
4.0
|
10.6
|
1.0
|
|
ND1
|
A:HIS446
|
4.0
|
11.4
|
1.0
|
|
CG
|
A:HIS446
|
4.1
|
8.8
|
1.0
|
|
CG
|
A:HIS101
|
4.1
|
10.5
|
1.0
|
|
CD2
|
A:HIS103
|
4.1
|
7.9
|
1.0
|
|
ND1
|
A:HIS448
|
4.1
|
10.9
|
1.0
|
|
N
|
A:GLY104
|
4.2
|
9.0
|
1.0
|
|
CE1
|
A:HIS103
|
4.3
|
9.1
|
1.0
|
|
O
|
A:HOH1101
|
4.3
|
10.8
|
0.5
|
|
CU
|
A:CU1002
|
4.3
|
9.4
|
0.6
|
|
C
|
A:HIS103
|
4.5
|
8.2
|
1.0
|
|
NE2
|
A:HIS103
|
4.5
|
8.2
|
1.0
|
|
CA
|
A:HIS448
|
4.5
|
11.0
|
1.0
|
|
N
|
A:HIS103
|
4.5
|
7.6
|
1.0
|
|
CH3
|
A:ACT1005
|
4.5
|
18.5
|
0.5
|
|
CB
|
A:HIS448
|
4.6
|
10.4
|
1.0
|
|
O
|
A:HOH1105
|
4.6
|
12.9
|
0.5
|
|
O
|
A:HOH1106
|
4.6
|
10.2
|
0.5
|
|
O
|
A:TRP102
|
4.7
|
11.0
|
1.0
|
|
N
|
A:HIS448
|
4.9
|
11.3
|
1.0
|
|
C
|
A:TRP102
|
4.9
|
7.8
|
1.0
|
|
Reference:
K.Kataoka,
H.Komori,
Y.Ueki,
Y.Konno,
Y.Kamitaka,
S.Kurose,
S.Tsujimura,
Y.Higuchi,
K.Kano,
D.Seo,
T.Sakurai.
Structure and Function of the Engineered Multicopper Oxidase Cueo From Escherichia Coli--Deletion of the Methionine-Rich Helical Region Covering the Substrate-Binding Site. J.Mol.Biol. V. 373 141 2007.
ISSN: ISSN 0022-2836
PubMed: 17804014
DOI: 10.1016/J.JMB.2007.07.041
Page generated: Wed Jul 31 02:44:16 2024
|
