Copper in PDB 2yaf: X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose)
Enzymatic activity of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose)
All present enzymatic activity of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose):
1.10.3.2;
Protein crystallography data
The structure of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose), PDB code: 2yaf
was solved by
H.Serrano-Posada,
E.Rudino-Pinera,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.678 /
1.80
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.659,
110.324,
96.345,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.44 /
18.9
|
Copper Binding Sites:
The binding sites of Copper atom in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose)
(pdb code 2yaf). This binding sites where shown within
5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the
X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose), PDB code: 2yaf:
Jump to Copper binding site number:
1;
2;
3;
Copper binding site 1 out
of 3 in 2yaf
Go back to
Copper Binding Sites List in 2yaf
Copper binding site 1 out
of 3 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose)
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 1 of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1463
b:11.2
occ:1.00
|
ND1
|
A:HIS97
|
2.0
|
5.4
|
1.0
|
NE2
|
A:HIS135
|
2.0
|
8.0
|
1.0
|
NE2
|
A:HIS446
|
2.1
|
5.7
|
1.0
|
HO
|
A:OH1481
|
2.7
|
40.4
|
0.7
|
CE1
|
A:HIS97
|
2.9
|
10.2
|
1.0
|
CE1
|
A:HIS446
|
3.0
|
2.2
|
1.0
|
CE1
|
A:HIS135
|
3.0
|
8.4
|
1.0
|
CG
|
A:HIS97
|
3.0
|
6.1
|
1.0
|
CD2
|
A:HIS135
|
3.0
|
6.1
|
1.0
|
O
|
A:OH1481
|
3.1
|
33.7
|
0.7
|
CD2
|
A:HIS446
|
3.2
|
3.9
|
1.0
|
CB
|
A:HIS97
|
3.4
|
7.5
|
1.0
|
CZ2
|
A:TRP133
|
3.6
|
3.5
|
1.0
|
CD2
|
A:HIS95
|
3.7
|
9.7
|
1.0
|
CE2
|
A:TRP133
|
3.9
|
3.8
|
1.0
|
NE1
|
A:TRP133
|
4.0
|
5.9
|
1.0
|
NE2
|
A:HIS97
|
4.1
|
8.4
|
1.0
|
ND1
|
A:HIS446
|
4.1
|
3.8
|
1.0
|
ND1
|
A:HIS135
|
4.1
|
4.4
|
1.0
|
CD2
|
A:HIS97
|
4.1
|
8.0
|
1.0
|
CG
|
A:HIS135
|
4.2
|
3.0
|
1.0
|
NE2
|
A:HIS95
|
4.2
|
14.8
|
1.0
|
CG
|
A:HIS446
|
4.2
|
5.1
|
1.0
|
CH2
|
A:TRP133
|
4.3
|
4.0
|
1.0
|
NE2
|
A:HIS396
|
4.5
|
10.9
|
1.0
|
CD2
|
A:HIS396
|
4.5
|
7.3
|
1.0
|
CA
|
A:HIS97
|
4.7
|
4.7
|
1.0
|
CG
|
A:HIS95
|
4.8
|
8.0
|
1.0
|
CD2
|
A:TRP133
|
4.8
|
3.9
|
1.0
|
CU
|
A:CU1465
|
4.9
|
18.4
|
0.4
|
CD1
|
A:TRP133
|
5.0
|
4.5
|
1.0
|
|
Copper binding site 2 out
of 3 in 2yaf
Go back to
Copper Binding Sites List in 2yaf
Copper binding site 2 out
of 3 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose)
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 2 of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1464
b:10.6
occ:1.00
|
ND1
|
A:HIS450
|
2.1
|
5.1
|
1.0
|
ND1
|
A:HIS393
|
2.1
|
9.0
|
1.0
|
SG
|
A:CYS445
|
2.2
|
7.5
|
1.0
|
CE1
|
A:HIS393
|
3.0
|
12.2
|
1.0
|
CG
|
A:HIS450
|
3.1
|
4.3
|
1.0
|
CE1
|
A:HIS450
|
3.1
|
6.8
|
1.0
|
CG
|
A:HIS393
|
3.2
|
10.8
|
1.0
|
CB
|
A:CYS445
|
3.2
|
6.2
|
1.0
|
CB
|
A:HIS450
|
3.3
|
4.3
|
1.0
|
SD
|
A:MET455
|
3.6
|
14.1
|
1.0
|
CB
|
A:HIS393
|
3.6
|
7.7
|
1.0
|
CD1
|
A:ILE447
|
4.0
|
5.5
|
1.0
|
CB
|
A:ILE447
|
4.0
|
5.3
|
1.0
|
CA
|
A:HIS393
|
4.0
|
4.4
|
1.0
|
NE2
|
A:HIS393
|
4.2
|
8.0
|
1.0
|
NE2
|
A:HIS450
|
4.2
|
5.3
|
1.0
|
CD2
|
A:HIS450
|
4.2
|
6.8
|
1.0
|
CD2
|
A:HIS393
|
4.3
|
5.1
|
1.0
|
CG1
|
A:ILE447
|
4.4
|
2.3
|
1.0
|
O
|
A:ASP392
|
4.5
|
5.7
|
1.0
|
CE
|
A:MET455
|
4.5
|
11.7
|
1.0
|
CD
|
A:PRO394
|
4.6
|
1.7
|
0.7
|
CA
|
A:CYS445
|
4.6
|
3.6
|
1.0
|
CD
|
A:PRO394
|
4.6
|
4.2
|
0.3
|
O
|
A:ILE447
|
4.7
|
6.0
|
1.0
|
N
|
A:ILE447
|
4.8
|
2.6
|
1.0
|
CG2
|
A:ILE447
|
4.8
|
4.2
|
1.0
|
CA
|
A:ILE447
|
4.8
|
8.1
|
1.0
|
CA
|
A:HIS450
|
4.9
|
8.5
|
1.0
|
C
|
A:HIS393
|
5.0
|
5.0
|
1.0
|
N
|
A:PRO394
|
5.0
|
5.8
|
0.7
|
|
Copper binding site 3 out
of 3 in 2yaf
Go back to
Copper Binding Sites List in 2yaf
Copper binding site 3 out
of 3 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose)
Mono view
Stereo pair view
|
A full contact list of Copper with other atoms in the Cu binding
site number 3 of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (12.5-25.0 Percent Dose) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cu1465
b:18.4
occ:0.43
|
NE2
|
A:HIS398
|
1.8
|
6.0
|
1.0
|
NE2
|
A:HIS137
|
1.9
|
12.2
|
0.3
|
NE2
|
A:HIS444
|
1.9
|
6.4
|
1.0
|
HO
|
A:OH1481
|
2.3
|
40.4
|
0.7
|
CE1
|
A:HIS398
|
2.7
|
3.3
|
1.0
|
CD2
|
A:HIS137
|
2.8
|
11.1
|
0.3
|
O
|
A:OH1481
|
2.8
|
33.7
|
0.7
|
CD2
|
A:HIS398
|
2.8
|
6.2
|
1.0
|
CE1
|
A:HIS444
|
2.9
|
6.3
|
1.0
|
CD2
|
A:HIS444
|
2.9
|
6.6
|
1.0
|
CE1
|
A:HIS137
|
2.9
|
10.6
|
0.3
|
CD2
|
A:HIS137
|
3.0
|
11.3
|
0.7
|
NE2
|
A:HIS137
|
3.3
|
11.8
|
0.7
|
CD2
|
A:HIS95
|
3.5
|
9.7
|
1.0
|
CD2
|
A:HIS396
|
3.5
|
7.3
|
1.0
|
NE2
|
A:HIS95
|
3.6
|
14.8
|
1.0
|
ND1
|
A:HIS398
|
3.9
|
4.2
|
1.0
|
CG
|
A:HIS137
|
3.9
|
11.0
|
0.3
|
CG
|
A:HIS398
|
3.9
|
6.5
|
1.0
|
O
|
A:HOH2516
|
4.0
|
16.4
|
1.0
|
ND1
|
A:HIS137
|
4.0
|
10.8
|
0.3
|
ND1
|
A:HIS444
|
4.0
|
7.5
|
1.0
|
CG
|
A:HIS444
|
4.0
|
8.5
|
1.0
|
NE2
|
A:HIS396
|
4.1
|
10.9
|
1.0
|
CG
|
A:HIS137
|
4.1
|
12.5
|
0.7
|
CG
|
A:HIS95
|
4.3
|
8.0
|
1.0
|
CE1
|
A:HIS137
|
4.3
|
9.5
|
0.7
|
CE1
|
A:HIS95
|
4.4
|
10.3
|
1.0
|
CG2
|
A:VAL442
|
4.6
|
4.8
|
1.0
|
ND1
|
A:HIS137
|
4.7
|
16.1
|
0.7
|
ND1
|
A:HIS95
|
4.7
|
7.3
|
1.0
|
CG
|
A:HIS396
|
4.7
|
4.7
|
1.0
|
OE2
|
A:GLU451
|
4.8
|
12.7
|
0.4
|
OE1
|
A:GLU451
|
4.8
|
5.2
|
0.4
|
CD
|
A:GLU451
|
4.9
|
5.0
|
0.4
|
CU
|
A:CU1463
|
4.9
|
11.2
|
1.0
|
CB
|
A:HIS137
|
5.0
|
7.9
|
0.7
|
CD2
|
A:HIS446
|
5.0
|
3.9
|
1.0
|
|
Reference:
H.Serrano-Posada,
S.Centeno-Leija,
S.P.Rojas-Trejo,
C.Rodriguez-Almazan,
V.Stojanoff,
E.Rudino-Pinera.
X-Ray-Induced Catalytic Active-Site Reduction of A Multicopper Oxidase: Structural Insights Into the Proton- Relay Mechanism and O2-Reduction States. Acta Crystallogr.,Sect.D V. 71 2396 2015.
ISSN: ISSN 0907-4449
PubMed: 26627648
DOI: 10.1107/S1399004715018714
Page generated: Wed Jul 31 00:20:34 2024
|