Copper in PDB 6rgh: Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
Enzymatic activity of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
All present enzymatic activity of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.:
1.10.3.2;
Protein crystallography data
The structure of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose., PDB code: 6rgh
was solved by
K.M.Polyakov,
S.Gavryushov,
T.V.Fedorova,
O.A.Glazunova,
A.N.Popov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
67.34 /
1.08
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.230,
84.129,
112.356,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
11.8 /
14
|
Copper Binding Sites:
The binding sites of Copper atom in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
(pdb code 6rgh). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 7 binding sites of Copper where determined in the
Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose., PDB code: 6rgh:
Jump to Copper binding site number:
1;
2;
3;
4;
5;
6;
7;
Copper binding site 1 out
of 7 in 6rgh
Go back to
Copper Binding Sites List in 6rgh
Copper binding site 1 out
of 7 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu501
b:6.7
occ:0.75
|
CU
|
A:CU501
|
0.0
|
6.7
|
0.8
|
|
CU
|
A:CU501
|
0.7
|
6.0
|
0.2
|
|
O
|
A:HOH821
|
1.8
|
9.0
|
1.0
|
|
NE2
|
A:HIS402
|
2.0
|
7.3
|
1.0
|
|
NE2
|
A:HIS452
|
2.1
|
8.6
|
1.0
|
|
NE2
|
A:HIS112
|
2.1
|
7.9
|
1.0
|
|
O
|
A:HOH626
|
2.3
|
7.2
|
0.8
|
|
HD2
|
A:HIS400
|
2.9
|
7.9
|
1.0
|
|
CE1
|
A:HIS402
|
2.9
|
8.2
|
1.0
|
|
CE1
|
A:HIS452
|
3.0
|
8.8
|
1.0
|
|
CD2
|
A:HIS402
|
3.1
|
7.5
|
1.0
|
|
HE1
|
A:HIS402
|
3.1
|
7.1
|
1.0
|
|
HE1
|
A:HIS452
|
3.1
|
8.6
|
1.0
|
|
CD2
|
A:HIS112
|
3.1
|
7.8
|
1.0
|
|
CE1
|
A:HIS112
|
3.2
|
8.6
|
1.0
|
|
HD2
|
A:HIS112
|
3.2
|
8.7
|
1.0
|
|
CU
|
A:CU502
|
3.2
|
6.9
|
0.8
|
|
CD2
|
A:HIS452
|
3.2
|
8.8
|
1.0
|
|
HD2
|
A:HIS402
|
3.3
|
7.1
|
1.0
|
|
HE1
|
A:HIS112
|
3.4
|
8.7
|
1.0
|
|
HD2
|
A:HIS452
|
3.5
|
8.6
|
1.0
|
|
HE1
|
A:HIS110
|
3.5
|
7.5
|
1.0
|
|
CD2
|
A:HIS400
|
3.7
|
8.2
|
1.0
|
|
CU
|
A:CU503
|
3.8
|
7.2
|
0.8
|
|
HD2
|
A:HIS65
|
3.9
|
7.8
|
1.0
|
|
O
|
A:HOH1217
|
3.9
|
11.1
|
1.0
|
|
CU
|
A:CU503
|
4.0
|
10.4
|
0.1
|
|
HD2
|
A:PHE450
|
4.0
|
8.6
|
1.0
|
|
CD2
|
A:HIS65
|
4.0
|
8.3
|
1.0
|
|
ND1
|
A:HIS402
|
4.1
|
7.2
|
1.0
|
|
NE2
|
A:HIS65
|
4.1
|
8.8
|
1.0
|
|
CG
|
A:HIS402
|
4.1
|
7.0
|
1.0
|
|
ND1
|
A:HIS452
|
4.2
|
8.6
|
1.0
|
|
NE2
|
A:HIS400
|
4.2
|
8.3
|
1.0
|
|
CU
|
A:CU502
|
4.2
|
11.1
|
0.2
|
|
CE1
|
A:HIS110
|
4.3
|
7.9
|
1.0
|
|
CG
|
A:HIS112
|
4.3
|
7.7
|
1.0
|
|
ND1
|
A:HIS112
|
4.3
|
8.5
|
1.0
|
|
CG
|
A:HIS452
|
4.3
|
8.2
|
1.0
|
|
HB3
|
A:PHE450
|
4.3
|
8.8
|
1.0
|
|
NE2
|
A:HIS454
|
4.4
|
7.5
|
1.0
|
|
HD2
|
A:HIS454
|
4.5
|
7.6
|
1.0
|
|
NE2
|
A:HIS110
|
4.5
|
8.2
|
1.0
|
|
HB3
|
A:PRO80
|
4.6
|
7.5
|
1.0
|
|
CD2
|
A:HIS454
|
4.7
|
7.7
|
1.0
|
|
CD2
|
A:PHE450
|
4.7
|
8.2
|
1.0
|
|
CG
|
A:HIS65
|
4.8
|
7.8
|
1.0
|
|
HD1
|
A:HIS402
|
4.8
|
7.1
|
1.0
|
|
CE1
|
A:HIS65
|
4.9
|
8.0
|
1.0
|
|
CG
|
A:HIS400
|
4.9
|
8.2
|
1.0
|
|
ND1
|
A:HIS67
|
4.9
|
7.6
|
1.0
|
|
HD1
|
A:HIS452
|
4.9
|
8.6
|
1.0
|
|
HD21
|
A:LEU459
|
4.9
|
9.7
|
1.0
|
|
Copper binding site 2 out
of 7 in 6rgh
Go back to
Copper Binding Sites List in 6rgh
Copper binding site 2 out
of 7 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu501
b:6.0
occ:0.20
|
CU
|
A:CU501
|
0.0
|
6.0
|
0.2
|
|
CU
|
A:CU501
|
0.7
|
6.7
|
0.8
|
|
NE2
|
A:HIS452
|
1.8
|
8.6
|
1.0
|
|
NE2
|
A:HIS112
|
1.9
|
7.9
|
1.0
|
|
NE2
|
A:HIS402
|
2.0
|
7.3
|
1.0
|
|
O
|
A:HOH821
|
2.2
|
9.0
|
1.0
|
|
CE1
|
A:HIS112
|
2.7
|
8.6
|
1.0
|
|
CE1
|
A:HIS452
|
2.8
|
8.8
|
1.0
|
|
CD2
|
A:HIS452
|
2.8
|
8.8
|
1.0
|
|
HE1
|
A:HIS112
|
2.8
|
8.7
|
1.0
|
|
CE1
|
A:HIS402
|
2.9
|
8.2
|
1.0
|
|
O
|
A:HOH626
|
3.0
|
7.2
|
0.8
|
|
HD2
|
A:HIS452
|
3.0
|
8.6
|
1.0
|
|
HE1
|
A:HIS452
|
3.0
|
8.6
|
1.0
|
|
HE1
|
A:HIS402
|
3.0
|
7.1
|
1.0
|
|
CD2
|
A:HIS112
|
3.1
|
7.8
|
1.0
|
|
CD2
|
A:HIS402
|
3.1
|
7.5
|
1.0
|
|
HD2
|
A:HIS400
|
3.2
|
7.9
|
1.0
|
|
HD2
|
A:HIS402
|
3.4
|
7.1
|
1.0
|
|
HD2
|
A:HIS112
|
3.4
|
8.7
|
1.0
|
|
HD2
|
A:PHE450
|
3.4
|
8.6
|
1.0
|
|
CU
|
A:CU502
|
3.8
|
6.9
|
0.8
|
|
HE1
|
A:HIS110
|
3.8
|
7.5
|
1.0
|
|
ND1
|
A:HIS452
|
3.9
|
8.6
|
1.0
|
|
CG
|
A:HIS452
|
3.9
|
8.2
|
1.0
|
|
O
|
A:HOH1217
|
3.9
|
11.1
|
1.0
|
|
HB3
|
A:PHE450
|
3.9
|
8.8
|
1.0
|
|
ND1
|
A:HIS112
|
4.0
|
8.5
|
1.0
|
|
CD2
|
A:HIS400
|
4.1
|
8.2
|
1.0
|
|
ND1
|
A:HIS402
|
4.1
|
7.2
|
1.0
|
|
CD2
|
A:PHE450
|
4.1
|
8.2
|
1.0
|
|
CG
|
A:HIS112
|
4.2
|
7.7
|
1.0
|
|
CG
|
A:HIS402
|
4.2
|
7.0
|
1.0
|
|
HB3
|
A:PRO80
|
4.3
|
7.5
|
1.0
|
|
CU
|
A:CU503
|
4.3
|
7.2
|
0.8
|
|
HD2
|
A:HIS65
|
4.4
|
7.8
|
1.0
|
|
HD21
|
A:LEU459
|
4.5
|
9.7
|
1.0
|
|
CU
|
A:CU503
|
4.5
|
10.4
|
0.1
|
|
CD2
|
A:HIS65
|
4.5
|
8.3
|
1.0
|
|
HD1
|
A:HIS452
|
4.6
|
8.6
|
1.0
|
|
CE1
|
A:HIS110
|
4.6
|
7.9
|
1.0
|
|
NE2
|
A:HIS65
|
4.6
|
8.8
|
1.0
|
|
NE2
|
A:HIS400
|
4.7
|
8.3
|
1.0
|
|
HD1
|
A:HIS112
|
4.7
|
8.7
|
1.0
|
|
CB
|
A:PHE450
|
4.7
|
8.3
|
1.0
|
|
HE2
|
A:PHE450
|
4.8
|
8.6
|
1.0
|
|
NE2
|
A:HIS454
|
4.8
|
7.5
|
1.0
|
|
CU
|
A:CU502
|
4.8
|
11.1
|
0.2
|
|
HD2
|
A:HIS454
|
4.8
|
7.6
|
1.0
|
|
HD1
|
A:HIS402
|
4.9
|
7.1
|
1.0
|
|
CG
|
A:PHE450
|
4.9
|
7.6
|
1.0
|
|
CE2
|
A:PHE450
|
4.9
|
9.4
|
1.0
|
|
HB2
|
A:PHE450
|
4.9
|
8.8
|
1.0
|
|
CD2
|
A:HIS454
|
5.0
|
7.7
|
1.0
|
|
NE2
|
A:HIS110
|
5.0
|
8.2
|
1.0
|
|
Copper binding site 3 out
of 7 in 6rgh
Go back to
Copper Binding Sites List in 6rgh
Copper binding site 3 out
of 7 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu502
b:6.9
occ:0.75
|
CU
|
A:CU502
|
0.0
|
6.9
|
0.8
|
|
CU
|
A:CU502
|
1.0
|
11.1
|
0.2
|
|
O
|
A:HOH821
|
1.9
|
9.0
|
1.0
|
|
NE2
|
A:HIS454
|
2.0
|
7.5
|
1.0
|
|
O
|
A:HOH626
|
2.0
|
7.2
|
0.8
|
|
ND1
|
A:HIS67
|
2.1
|
7.6
|
1.0
|
|
NE2
|
A:HIS110
|
2.3
|
8.2
|
1.0
|
|
CE1
|
A:HIS67
|
2.9
|
7.4
|
1.0
|
|
CD2
|
A:HIS454
|
3.0
|
7.7
|
1.0
|
|
HE1
|
A:HIS67
|
3.0
|
7.6
|
1.0
|
|
CE1
|
A:HIS110
|
3.0
|
7.9
|
1.0
|
|
CE1
|
A:HIS454
|
3.0
|
7.8
|
1.0
|
|
HE1
|
A:HIS110
|
3.1
|
7.5
|
1.0
|
|
HD2
|
A:HIS65
|
3.1
|
7.8
|
1.0
|
|
HD2
|
A:HIS454
|
3.1
|
7.6
|
1.0
|
|
CU
|
A:CU501
|
3.2
|
6.7
|
0.8
|
|
HE1
|
A:HIS454
|
3.3
|
7.6
|
1.0
|
|
CG
|
A:HIS67
|
3.3
|
7.3
|
1.0
|
|
HB2
|
A:HIS67
|
3.3
|
7.5
|
1.0
|
|
HD2
|
A:HIS400
|
3.3
|
7.9
|
1.0
|
|
CD2
|
A:HIS110
|
3.5
|
7.3
|
1.0
|
|
CU
|
A:CU503
|
3.6
|
7.2
|
0.8
|
|
CD2
|
A:HIS400
|
3.7
|
8.2
|
1.0
|
|
CU
|
A:CU503
|
3.7
|
10.4
|
0.1
|
|
HD2
|
A:HIS110
|
3.8
|
7.5
|
1.0
|
|
CD2
|
A:HIS65
|
3.8
|
8.3
|
1.0
|
|
CB
|
A:HIS67
|
3.8
|
7.6
|
1.0
|
|
CU
|
A:CU501
|
3.8
|
6.0
|
0.2
|
|
HE1
|
A:HIS452
|
3.9
|
8.6
|
1.0
|
|
NE2
|
A:HIS400
|
3.9
|
8.3
|
1.0
|
|
O
|
A:HOH1217
|
4.0
|
11.1
|
1.0
|
|
NE2
|
A:HIS67
|
4.1
|
8.1
|
1.0
|
|
CG
|
A:HIS454
|
4.1
|
7.2
|
1.0
|
|
ND1
|
A:HIS454
|
4.1
|
7.8
|
1.0
|
|
NE2
|
A:HIS65
|
4.1
|
8.8
|
1.0
|
|
HB2
|
A:ALA244
|
4.2
|
7.9
|
1.0
|
|
ND1
|
A:HIS110
|
4.3
|
7.6
|
1.0
|
|
CD2
|
A:HIS67
|
4.3
|
7.7
|
1.0
|
|
HZ2
|
A:TRP108
|
4.3
|
7.9
|
1.0
|
|
HD2
|
A:HIS112
|
4.4
|
8.7
|
1.0
|
|
NE2
|
A:HIS452
|
4.4
|
8.6
|
1.0
|
|
CE1
|
A:HIS452
|
4.5
|
8.8
|
1.0
|
|
HA
|
A:HIS67
|
4.5
|
6.8
|
1.0
|
|
HB3
|
A:HIS67
|
4.5
|
7.5
|
1.0
|
|
CG
|
A:HIS110
|
4.5
|
7.7
|
1.0
|
|
NE2
|
A:HIS112
|
4.6
|
7.9
|
1.0
|
|
CG
|
A:HIS400
|
4.6
|
8.2
|
1.0
|
|
HB1
|
A:ALA244
|
4.7
|
7.9
|
1.0
|
|
NE2
|
A:HIS402
|
4.7
|
7.3
|
1.0
|
|
CZ2
|
A:TRP108
|
4.7
|
7.2
|
1.0
|
|
CD2
|
A:HIS112
|
4.8
|
7.8
|
1.0
|
|
CA
|
A:HIS67
|
4.8
|
7.1
|
1.0
|
|
CE1
|
A:HIS400
|
4.8
|
7.9
|
1.0
|
|
HE2
|
A:HIS67
|
4.8
|
7.6
|
1.0
|
|
CB
|
A:ALA244
|
4.8
|
7.1
|
1.0
|
|
HE1
|
A:TRP108
|
4.9
|
7.9
|
1.0
|
|
HD1
|
A:HIS454
|
4.9
|
7.6
|
1.0
|
|
Copper binding site 4 out
of 7 in 6rgh
Go back to
Copper Binding Sites List in 6rgh
Copper binding site 4 out
of 7 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 4 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu502
b:11.1
occ:0.20
|
CU
|
A:CU502
|
0.0
|
11.1
|
0.2
|
|
CU
|
A:CU502
|
1.0
|
6.9
|
0.8
|
|
ND1
|
A:HIS67
|
1.7
|
7.6
|
1.0
|
|
NE2
|
A:HIS110
|
1.9
|
8.2
|
1.0
|
|
NE2
|
A:HIS454
|
2.1
|
7.5
|
1.0
|
|
HB2
|
A:HIS67
|
2.7
|
7.5
|
1.0
|
|
CE1
|
A:HIS67
|
2.8
|
7.4
|
1.0
|
|
CG
|
A:HIS67
|
2.8
|
7.3
|
1.0
|
|
CD2
|
A:HIS110
|
2.8
|
7.3
|
1.0
|
|
O
|
A:HOH626
|
2.8
|
7.2
|
0.8
|
|
O
|
A:HOH821
|
2.8
|
9.0
|
1.0
|
|
HD2
|
A:HIS110
|
2.9
|
7.5
|
1.0
|
|
CE1
|
A:HIS454
|
2.9
|
7.8
|
1.0
|
|
HE1
|
A:HIS454
|
3.0
|
7.6
|
1.0
|
|
HE1
|
A:HIS67
|
3.0
|
7.6
|
1.0
|
|
CE1
|
A:HIS110
|
3.0
|
7.9
|
1.0
|
|
CB
|
A:HIS67
|
3.2
|
7.6
|
1.0
|
|
HD2
|
A:HIS65
|
3.3
|
7.8
|
1.0
|
|
CD2
|
A:HIS454
|
3.3
|
7.7
|
1.0
|
|
HE1
|
A:HIS110
|
3.3
|
7.5
|
1.0
|
|
HZ2
|
A:TRP108
|
3.5
|
7.9
|
1.0
|
|
HD2
|
A:HIS454
|
3.6
|
7.6
|
1.0
|
|
HB2
|
A:ALA244
|
3.6
|
7.9
|
1.0
|
|
HB3
|
A:HIS67
|
3.7
|
7.5
|
1.0
|
|
CZ2
|
A:TRP108
|
3.8
|
7.2
|
1.0
|
|
NE2
|
A:HIS67
|
3.8
|
8.1
|
1.0
|
|
CD2
|
A:HIS67
|
3.9
|
7.7
|
1.0
|
|
CG
|
A:HIS110
|
4.0
|
7.7
|
1.0
|
|
CE2
|
A:TRP108
|
4.0
|
7.3
|
1.0
|
|
HE1
|
A:TRP108
|
4.0
|
7.9
|
1.0
|
|
CD2
|
A:HIS65
|
4.1
|
8.3
|
1.0
|
|
ND1
|
A:HIS110
|
4.1
|
7.6
|
1.0
|
|
ND1
|
A:HIS454
|
4.1
|
7.8
|
1.0
|
|
CU
|
A:CU503
|
4.2
|
7.2
|
0.8
|
|
NE1
|
A:TRP108
|
4.2
|
7.6
|
1.0
|
|
HD2
|
A:HIS400
|
4.2
|
7.9
|
1.0
|
|
CU
|
A:CU503
|
4.2
|
10.4
|
0.1
|
|
CU
|
A:CU501
|
4.2
|
6.7
|
0.8
|
|
HB1
|
A:ALA244
|
4.3
|
7.9
|
1.0
|
|
CG
|
A:HIS454
|
4.3
|
7.2
|
1.0
|
|
HA
|
A:HIS67
|
4.3
|
6.8
|
1.0
|
|
CB
|
A:ALA244
|
4.4
|
7.1
|
1.0
|
|
CD2
|
A:HIS400
|
4.4
|
8.2
|
1.0
|
|
NE2
|
A:HIS400
|
4.4
|
8.3
|
1.0
|
|
CA
|
A:HIS67
|
4.5
|
7.1
|
1.0
|
|
O
|
A:HOH1217
|
4.5
|
11.1
|
1.0
|
|
NE2
|
A:HIS65
|
4.5
|
8.8
|
1.0
|
|
CH2
|
A:TRP108
|
4.5
|
7.7
|
1.0
|
|
HE2
|
A:HIS67
|
4.6
|
7.6
|
1.0
|
|
HE1
|
A:HIS452
|
4.7
|
8.6
|
1.0
|
|
HH2
|
A:TRP108
|
4.7
|
7.9
|
1.0
|
|
HD2
|
A:HIS67
|
4.8
|
7.6
|
1.0
|
|
HB3
|
A:ALA244
|
4.8
|
7.9
|
1.0
|
|
CU
|
A:CU501
|
4.8
|
6.0
|
0.2
|
|
HD1
|
A:HIS454
|
4.8
|
7.6
|
1.0
|
|
HD1
|
A:HIS110
|
4.9
|
7.5
|
1.0
|
|
CD2
|
A:TRP108
|
4.9
|
7.6
|
1.0
|
|
HD2
|
A:HIS112
|
4.9
|
8.7
|
1.0
|
|
Copper binding site 5 out
of 7 in 6rgh
Go back to
Copper Binding Sites List in 6rgh
Copper binding site 5 out
of 7 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 5 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu503
b:7.2
occ:0.75
|
CU
|
A:CU503
|
0.0
|
7.2
|
0.8
|
|
CU
|
A:CU503
|
0.2
|
10.4
|
0.1
|
|
O
|
A:HOH626
|
1.9
|
7.2
|
0.8
|
|
NE2
|
A:HIS400
|
1.9
|
8.3
|
1.0
|
|
NE2
|
A:HIS65
|
1.9
|
8.8
|
1.0
|
|
O
|
A:HOH1120
|
2.0
|
6.2
|
0.8
|
|
O
|
A:HOH1120
|
2.4
|
3.7
|
0.2
|
|
HA
|
A:HIS67
|
2.9
|
6.8
|
1.0
|
|
CE1
|
A:HIS65
|
2.9
|
8.0
|
1.0
|
|
CD2
|
A:HIS400
|
2.9
|
8.2
|
1.0
|
|
CE1
|
A:HIS400
|
3.0
|
7.9
|
1.0
|
|
CD2
|
A:HIS65
|
3.0
|
8.3
|
1.0
|
|
HE1
|
A:HIS65
|
3.1
|
7.8
|
1.0
|
|
H
|
A:GLY68
|
3.1
|
6.8
|
1.0
|
|
HD2
|
A:HIS400
|
3.1
|
7.9
|
1.0
|
|
HE1
|
A:HIS400
|
3.2
|
7.9
|
1.0
|
|
HD2
|
A:HIS65
|
3.2
|
7.8
|
1.0
|
|
CD2
|
A:HIS402
|
3.3
|
7.5
|
1.0
|
|
NE2
|
A:HIS402
|
3.4
|
7.3
|
1.0
|
|
HD2
|
A:HIS402
|
3.5
|
7.1
|
1.0
|
|
ND1
|
A:HIS67
|
3.5
|
7.6
|
1.0
|
|
HA
|
A:HIS402
|
3.6
|
7.5
|
1.0
|
|
CU
|
A:CU502
|
3.6
|
6.9
|
0.8
|
|
CG
|
A:HIS402
|
3.7
|
7.0
|
1.0
|
|
CG
|
A:HIS67
|
3.7
|
7.3
|
1.0
|
|
CA
|
A:HIS67
|
3.8
|
7.1
|
1.0
|
|
CU
|
A:CU501
|
3.8
|
6.7
|
0.8
|
|
CE1
|
A:HIS402
|
3.9
|
8.2
|
1.0
|
|
N
|
A:GLY68
|
3.9
|
7.2
|
1.0
|
|
CE1
|
A:HIS67
|
3.9
|
7.4
|
1.0
|
|
ND1
|
A:HIS402
|
4.0
|
7.2
|
1.0
|
|
HB2
|
A:HIS67
|
4.0
|
7.5
|
1.0
|
|
ND1
|
A:HIS65
|
4.0
|
7.7
|
1.0
|
|
CB
|
A:HIS67
|
4.0
|
7.6
|
1.0
|
|
ND1
|
A:HIS400
|
4.1
|
8.0
|
1.0
|
|
CG
|
A:HIS400
|
4.1
|
8.2
|
1.0
|
|
CG
|
A:HIS65
|
4.1
|
7.8
|
1.0
|
|
CU
|
A:CU502
|
4.2
|
11.1
|
0.2
|
|
CD2
|
A:HIS67
|
4.2
|
7.7
|
1.0
|
|
HE1
|
A:HIS67
|
4.3
|
7.6
|
1.0
|
|
O
|
A:HOH821
|
4.3
|
9.0
|
1.0
|
|
CA
|
A:HIS402
|
4.3
|
7.1
|
1.0
|
|
CU
|
A:CU501
|
4.3
|
6.0
|
0.2
|
|
HE1
|
A:HIS402
|
4.3
|
7.1
|
1.0
|
|
NE2
|
A:HIS67
|
4.4
|
8.1
|
1.0
|
|
C
|
A:HIS67
|
4.4
|
6.9
|
1.0
|
|
CB
|
A:HIS402
|
4.5
|
7.6
|
1.0
|
|
O
|
A:HOH713
|
4.5
|
13.7
|
1.0
|
|
HD1
|
A:HIS402
|
4.5
|
7.1
|
1.0
|
|
O
|
A:HOH1042
|
4.6
|
13.2
|
1.0
|
|
HB3
|
A:HIS402
|
4.6
|
8.8
|
1.0
|
|
HA2
|
A:GLY68
|
4.7
|
7.7
|
1.0
|
|
N
|
A:HIS402
|
4.7
|
7.0
|
1.0
|
|
HD2
|
A:HIS67
|
4.8
|
7.6
|
1.0
|
|
HD1
|
A:HIS65
|
4.8
|
7.8
|
1.0
|
|
N
|
A:HIS67
|
4.8
|
7.1
|
1.0
|
|
O
|
A:TRP66
|
4.8
|
7.5
|
1.0
|
|
HD1
|
A:HIS400
|
4.8
|
7.9
|
1.0
|
|
O
|
A:LEU401
|
4.9
|
7.7
|
1.0
|
|
HE2
|
A:HIS67
|
4.9
|
7.6
|
1.0
|
|
CA
|
A:GLY68
|
4.9
|
7.4
|
1.0
|
|
HD2
|
A:HIS112
|
5.0
|
8.7
|
1.0
|
|
HB3
|
A:HIS67
|
5.0
|
7.5
|
1.0
|
|
Copper binding site 6 out
of 7 in 6rgh
Go back to
Copper Binding Sites List in 6rgh
Copper binding site 6 out
of 7 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 6 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu503
b:10.4
occ:0.08
|
CU
|
A:CU503
|
0.0
|
10.4
|
0.1
|
|
CU
|
A:CU503
|
0.2
|
7.2
|
0.8
|
|
O
|
A:HOH1120
|
1.8
|
6.2
|
0.8
|
|
NE2
|
A:HIS65
|
1.9
|
8.8
|
1.0
|
|
NE2
|
A:HIS400
|
2.0
|
8.3
|
1.0
|
|
O
|
A:HOH626
|
2.1
|
7.2
|
0.8
|
|
O
|
A:HOH1120
|
2.3
|
3.7
|
0.2
|
|
HA
|
A:HIS67
|
2.7
|
6.8
|
1.0
|
|
H
|
A:GLY68
|
2.9
|
6.8
|
1.0
|
|
CE1
|
A:HIS65
|
2.9
|
8.0
|
1.0
|
|
CE1
|
A:HIS400
|
2.9
|
7.9
|
1.0
|
|
CD2
|
A:HIS65
|
3.0
|
8.3
|
1.0
|
|
CD2
|
A:HIS400
|
3.0
|
8.2
|
1.0
|
|
HE1
|
A:HIS65
|
3.1
|
7.8
|
1.0
|
|
HE1
|
A:HIS400
|
3.1
|
7.9
|
1.0
|
|
HD2
|
A:HIS65
|
3.3
|
7.8
|
1.0
|
|
HD2
|
A:HIS400
|
3.3
|
7.9
|
1.0
|
|
CD2
|
A:HIS402
|
3.5
|
7.5
|
1.0
|
|
ND1
|
A:HIS67
|
3.5
|
7.6
|
1.0
|
|
HA
|
A:HIS402
|
3.6
|
7.5
|
1.0
|
|
CG
|
A:HIS67
|
3.6
|
7.3
|
1.0
|
|
CA
|
A:HIS67
|
3.6
|
7.1
|
1.0
|
|
HD2
|
A:HIS402
|
3.6
|
7.1
|
1.0
|
|
NE2
|
A:HIS402
|
3.6
|
7.3
|
1.0
|
|
N
|
A:GLY68
|
3.7
|
7.2
|
1.0
|
|
CU
|
A:CU502
|
3.7
|
6.9
|
0.8
|
|
CG
|
A:HIS402
|
3.8
|
7.0
|
1.0
|
|
HB2
|
A:HIS67
|
3.9
|
7.5
|
1.0
|
|
CE1
|
A:HIS67
|
3.9
|
7.4
|
1.0
|
|
CB
|
A:HIS67
|
3.9
|
7.6
|
1.0
|
|
CU
|
A:CU501
|
4.0
|
6.7
|
0.8
|
|
CE1
|
A:HIS402
|
4.0
|
8.2
|
1.0
|
|
ND1
|
A:HIS65
|
4.0
|
7.7
|
1.0
|
|
ND1
|
A:HIS400
|
4.1
|
8.0
|
1.0
|
|
ND1
|
A:HIS402
|
4.1
|
7.2
|
1.0
|
|
CD2
|
A:HIS67
|
4.1
|
7.7
|
1.0
|
|
CG
|
A:HIS65
|
4.2
|
7.8
|
1.0
|
|
CG
|
A:HIS400
|
4.2
|
8.2
|
1.0
|
|
C
|
A:HIS67
|
4.2
|
6.9
|
1.0
|
|
CU
|
A:CU502
|
4.2
|
11.1
|
0.2
|
|
NE2
|
A:HIS67
|
4.3
|
8.1
|
1.0
|
|
HE1
|
A:HIS67
|
4.3
|
7.6
|
1.0
|
|
CA
|
A:HIS402
|
4.4
|
7.1
|
1.0
|
|
O
|
A:HOH713
|
4.4
|
13.7
|
1.0
|
|
O
|
A:HOH1042
|
4.5
|
13.2
|
1.0
|
|
O
|
A:HOH821
|
4.5
|
9.0
|
1.0
|
|
HE1
|
A:HIS402
|
4.5
|
7.1
|
1.0
|
|
CB
|
A:HIS402
|
4.5
|
7.6
|
1.0
|
|
CU
|
A:CU501
|
4.5
|
6.0
|
0.2
|
|
HA2
|
A:GLY68
|
4.6
|
7.7
|
1.0
|
|
HD1
|
A:HIS402
|
4.6
|
7.1
|
1.0
|
|
HD2
|
A:HIS67
|
4.6
|
7.6
|
1.0
|
|
HB3
|
A:HIS402
|
4.7
|
8.8
|
1.0
|
|
N
|
A:HIS67
|
4.7
|
7.1
|
1.0
|
|
O
|
A:TRP66
|
4.7
|
7.5
|
1.0
|
|
CA
|
A:GLY68
|
4.8
|
7.4
|
1.0
|
|
HD1
|
A:HIS65
|
4.8
|
7.8
|
1.0
|
|
N
|
A:HIS402
|
4.8
|
7.0
|
1.0
|
|
HD1
|
A:HIS400
|
4.8
|
7.9
|
1.0
|
|
HE2
|
A:HIS67
|
4.8
|
7.6
|
1.0
|
|
HB3
|
A:HIS67
|
4.9
|
7.5
|
1.0
|
|
O
|
A:LEU401
|
4.9
|
7.7
|
1.0
|
|
Copper binding site 7 out
of 7 in 6rgh
Go back to
Copper Binding Sites List in 6rgh
Copper binding site 7 out
of 7 in the Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose.
 Mono view
 Stereo pair view
|
|
A full contact list of Copper with other atoms in the Cu binding
site number 7 of Single Crystal Serial Study of the X-Ray Induced Enzymatic Reduction of Molecular Oxygen to Water For Laccase From Steccherinum Murashkinskyi at Sub-Atomic Resolution. First Structure of the Series with 15 Kgy Dose. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu504
b:7.6
occ:0.78
|
ND1
|
A:HIS458
|
2.0
|
8.9
|
1.0
|
|
ND1
|
A:HIS397
|
2.0
|
9.2
|
1.0
|
|
SG
|
A:CYS453
|
2.1
|
9.3
|
1.0
|
|
HD11
|
A:ILE455
|
2.7
|
8.6
|
1.0
|
|
CE1
|
A:HIS397
|
2.9
|
9.5
|
1.0
|
|
CE1
|
A:HIS458
|
3.0
|
9.9
|
1.0
|
|
HD2
|
A:PHE463
|
3.0
|
11.3
|
1.0
|
|
CG
|
A:HIS458
|
3.0
|
8.8
|
1.0
|
|
CG
|
A:HIS397
|
3.0
|
9.4
|
1.0
|
|
HB
|
A:ILE455
|
3.1
|
8.6
|
1.0
|
|
HE1
|
A:HIS397
|
3.1
|
9.0
|
1.0
|
|
HB2
|
A:HIS458
|
3.1
|
8.6
|
1.0
|
|
HB3
|
A:HIS397
|
3.1
|
10.5
|
1.0
|
|
HE1
|
A:HIS458
|
3.1
|
9.4
|
1.0
|
|
HB3
|
A:HIS458
|
3.3
|
8.6
|
1.0
|
|
CB
|
A:CYS453
|
3.3
|
8.6
|
1.0
|
|
CB
|
A:HIS458
|
3.4
|
8.6
|
1.0
|
|
HA
|
A:HIS397
|
3.4
|
8.6
|
1.0
|
|
HB2
|
A:CYS453
|
3.4
|
8.3
|
1.0
|
|
HB3
|
A:CYS453
|
3.5
|
8.3
|
1.0
|
|
CB
|
A:HIS397
|
3.5
|
8.7
|
1.0
|
|
HE2
|
A:PHE463
|
3.5
|
11.3
|
1.0
|
|
CD1
|
A:ILE455
|
3.6
|
8.4
|
1.0
|
|
CD2
|
A:PHE463
|
3.8
|
8.9
|
1.0
|
|
HD2
|
A:PRO398
|
3.8
|
8.6
|
1.0
|
|
H
|
A:ILE455
|
3.9
|
8.6
|
1.0
|
|
CB
|
A:ILE455
|
4.0
|
8.3
|
1.0
|
|
CA
|
A:HIS397
|
4.0
|
8.2
|
1.0
|
|
CE2
|
A:PHE463
|
4.0
|
9.1
|
1.0
|
|
NE2
|
A:HIS397
|
4.1
|
9.5
|
1.0
|
|
HD12
|
A:ILE455
|
4.1
|
8.6
|
1.0
|
|
NE2
|
A:HIS458
|
4.1
|
9.9
|
1.0
|
|
HD13
|
A:ILE455
|
4.1
|
8.6
|
1.0
|
|
CG1
|
A:ILE455
|
4.1
|
8.8
|
1.0
|
|
CD2
|
A:HIS397
|
4.1
|
9.7
|
1.0
|
|
CD2
|
A:HIS458
|
4.2
|
9.3
|
1.0
|
|
HG13
|
A:ILE455
|
4.2
|
8.6
|
1.0
|
|
HB2
|
A:HIS397
|
4.4
|
10.5
|
1.0
|
|
HG21
|
A:ILE455
|
4.6
|
8.6
|
1.0
|
|
HZ
|
A:PHE341
|
4.6
|
19.6
|
1.0
|
|
O
|
A:GLY394
|
4.6
|
12.5
|
1.0
|
|
CA
|
A:CYS453
|
4.7
|
7.8
|
1.0
|
|
CD
|
A:PRO398
|
4.7
|
8.2
|
1.0
|
|
CG2
|
A:ILE455
|
4.7
|
8.9
|
1.0
|
|
HG22
|
A:ILE455
|
4.7
|
8.6
|
1.0
|
|
CZ
|
A:PHE341
|
4.7
|
10.9
|
1.0
|
|
HE1
|
A:PHE399
|
4.8
|
10.3
|
1.0
|
|
N
|
A:ILE455
|
4.8
|
8.1
|
1.0
|
|
HA
|
A:CYS453
|
4.8
|
7.6
|
1.0
|
|
HE2
|
A:HIS397
|
4.8
|
9.0
|
1.0
|
|
HE2
|
A:PHE341
|
4.9
|
19.6
|
1.0
|
|
HE2
|
A:HIS458
|
4.9
|
9.4
|
1.0
|
|
CE2
|
A:PHE341
|
4.9
|
10.9
|
1.0
|
|
HB3
|
A:PHE463
|
4.9
|
9.1
|
1.0
|
|
CA
|
A:HIS458
|
4.9
|
9.1
|
1.0
|
|
HD3
|
A:PRO398
|
4.9
|
8.6
|
1.0
|
|
CA
|
A:ILE455
|
4.9
|
8.2
|
1.0
|
|
O
|
A:ILE455
|
4.9
|
8.6
|
1.0
|
|
C
|
A:HIS397
|
5.0
|
7.7
|
1.0
|
|
CG
|
A:PHE463
|
5.0
|
8.3
|
1.0
|
|
N
|
A:HIS397
|
5.0
|
8.4
|
1.0
|
|
Reference:
K.M.Polyakov,
S.Gavryushov,
T.V.Fedorova,
O.A.Glazunova,
A.N.Popov.
The Subatomic Resolution Study of Laccase Inhibition By Chloride and Fluoride Anions Using Single-Crystal Serial Crystallography: Insights Into the Enzymatic Reaction Mechanism. Acta Crystallogr D Struct V. 75 804 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31478903
DOI: 10.1107/S2059798319010684
Page generated: Wed Jul 31 06:57:53 2024
|
