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Copper in PDB 2yae: X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose)

Enzymatic activity of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose)

All present enzymatic activity of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose):
1.10.3.2;

Protein crystallography data

The structure of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose), PDB code: 2yae 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) 29.284 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.629, 110.304, 96.333, 90.00, 90.00, 90.00
R / Rfree (%) 14.68 / 17.38

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose) (pdb code 2yae). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose), PDB code: 2yae:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2yae

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Copper binding site 1 out of 4 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 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(0.0-12.5 Percent Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1463

b:18.9
occ:0.43
NE2 A:HIS398 1.8 5.7 1.0
NE2 A:HIS444 2.0 7.8 1.0
NE2 A:HIS137 2.1 7.3 0.3
O1 A:OXY1483 2.4 15.9 0.4
O2 A:OXY1483 2.6 20.9 0.4
CD2 A:HIS137 2.6 13.1 0.3
CE1 A:HIS398 2.7 5.4 1.0
CD2 A:HIS398 2.9 6.3 1.0
CD2 A:HIS444 2.9 9.0 1.0
CD2 A:HIS137 2.9 6.6 0.7
CE1 A:HIS444 3.1 10.0 1.0
NE2 A:HIS137 3.1 13.4 0.7
CE1 A:HIS137 3.3 14.8 0.3
CU A:CU1482 3.4 20.8 0.2
CD2 A:HIS396 3.6 7.5 1.0
CD2 A:HIS95 3.7 14.7 1.0
NE2 A:HIS95 3.8 15.1 1.0
ND1 A:HIS398 3.8 5.9 1.0
O A:HOH2500 3.8 15.1 1.0
CG A:HIS137 3.9 11.2 0.3
CG A:HIS398 3.9 6.2 1.0
CG A:HIS137 4.0 10.3 0.7
CG A:HIS444 4.1 7.1 1.0
ND1 A:HIS444 4.1 7.6 1.0
NE2 A:HIS396 4.2 10.7 1.0
CE1 A:HIS137 4.2 13.0 0.7
ND1 A:HIS137 4.2 9.9 0.3
CG A:HIS95 4.3 5.2 1.0
CG2 A:VAL442 4.5 6.1 1.0
CE1 A:HIS95 4.5 10.7 1.0
ND1 A:HIS137 4.6 17.8 0.7
OE1 A:GLU451 4.8 3.4 0.4
ND1 A:HIS95 4.8 5.6 1.0
CG A:HIS396 4.8 5.9 1.0
CB A:HIS137 4.9 7.8 0.7
CU A:CU1464 5.0 11.0 1.0
CD A:GLU451 5.0 6.4 0.4
OE2 A:GLU451 5.0 11.5 0.4

Copper binding site 2 out of 4 in 2yae

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Copper binding site 2 out of 4 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 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(0.0-12.5 Percent Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1464

b:11.0
occ:1.00
ND1 A:HIS97 2.0 8.1 1.0
NE2 A:HIS135 2.1 4.9 1.0
NE2 A:HIS446 2.1 4.6 1.0
O1 A:OXY1483 2.7 15.9 0.4
O2 A:OXY1483 2.9 20.9 0.4
CE1 A:HIS97 2.9 6.8 1.0
CE1 A:HIS446 3.0 3.0 1.0
CG A:HIS97 3.0 6.9 1.0
CD2 A:HIS135 3.1 4.6 1.0
CE1 A:HIS135 3.1 7.2 1.0
CD2 A:HIS446 3.2 6.0 1.0
CB A:HIS97 3.4 6.5 1.0
CZ2 A:TRP133 3.6 5.0 1.0
CD2 A:HIS95 3.8 14.7 1.0
CE2 A:TRP133 3.9 6.0 1.0
NE2 A:HIS97 4.1 6.7 1.0
NE1 A:TRP133 4.1 5.2 1.0
ND1 A:HIS446 4.1 3.7 1.0
CD2 A:HIS97 4.1 10.3 1.0
CU A:CU1482 4.1 20.8 0.2
ND1 A:HIS135 4.2 2.8 1.0
CG A:HIS135 4.2 3.9 1.0
CG A:HIS446 4.2 3.8 1.0
CH2 A:TRP133 4.3 3.8 1.0
NE2 A:HIS95 4.5 15.1 1.0
NE2 A:HIS396 4.5 10.7 1.0
CD2 A:HIS396 4.5 7.5 1.0
CA A:HIS97 4.7 6.7 1.0
CD2 A:TRP133 4.8 2.7 1.0
CU A:CU1463 5.0 18.9 0.4
CG A:HIS95 5.0 5.2 1.0
O A:HOH2500 5.0 15.1 1.0

Copper binding site 3 out of 4 in 2yae

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Copper binding site 3 out of 4 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 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(0.0-12.5 Percent Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1465

b:9.8
occ:1.00
ND1 A:HIS393 2.1 5.5 1.0
ND1 A:HIS450 2.1 6.2 1.0
SG A:CYS445 2.2 7.0 1.0
CE1 A:HIS393 2.9 6.8 1.0
CG A:HIS450 3.1 6.5 1.0
CE1 A:HIS450 3.1 8.6 1.0
CG A:HIS393 3.2 8.3 1.0
CB A:CYS445 3.2 5.4 1.0
CB A:HIS450 3.4 4.0 1.0
SD A:MET455 3.5 14.2 1.0
CB A:HIS393 3.6 7.7 1.0
CA A:HIS393 4.0 2.9 1.0
CB A:ILE447 4.0 4.3 1.0
CD1 A:ILE447 4.0 5.9 1.0
NE2 A:HIS393 4.1 9.1 1.0
NE2 A:HIS450 4.2 6.2 1.0
CD2 A:HIS450 4.2 7.7 1.0
CD2 A:HIS393 4.2 5.1 1.0
CG1 A:ILE447 4.5 2.0 1.0
O A:ASP392 4.5 6.4 1.0
CE A:MET455 4.5 12.7 1.0
CD A:PRO394 4.6 2.3 1.0
CA A:CYS445 4.6 4.8 1.0
O A:ILE447 4.7 5.8 1.0
CG2 A:ILE447 4.8 5.4 1.0
N A:ILE447 4.8 3.3 1.0
CA A:HIS450 4.9 3.6 1.0
CA A:ILE447 4.9 4.8 1.0
C A:HIS393 5.0 4.5 1.0

Copper binding site 4 out of 4 in 2yae

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Copper binding site 4 out of 4 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27(0.0-12.5 Percent Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1482

b:20.8
occ:0.16
NE2 A:HIS396 1.6 10.7 1.0
NE2 A:HIS95 1.7 15.1 1.0
CD2 A:HIS396 2.4 7.5 1.0
CD2 A:HIS95 2.6 14.7 1.0
CE1 A:HIS95 2.8 10.7 1.0
CE1 A:HIS396 2.8 6.3 1.0
CD2 A:HIS398 2.9 6.3 1.0
NE2 A:HIS398 3.1 5.7 1.0
O1 A:OXY1483 3.2 15.9 0.4
CU A:CU1463 3.4 18.9 0.4
O A:HOH2124 3.5 13.3 1.0
CG A:HIS398 3.6 6.2 1.0
CG A:HIS396 3.6 5.9 1.0
ND1 A:HIS97 3.6 8.1 1.0
CG A:HIS95 3.7 5.2 1.0
ND1 A:HIS95 3.8 5.6 1.0
ND1 A:HIS396 3.8 6.4 1.0
CE1 A:HIS398 3.8 5.4 1.0
CG A:HIS97 3.9 6.9 1.0
O2 A:OXY1483 3.9 20.9 0.4
CE1 A:HIS97 4.1 6.8 1.0
ND1 A:HIS398 4.1 5.9 1.0
CA A:HIS97 4.1 6.7 1.0
CU A:CU1464 4.1 11.0 1.0
CB A:HIS97 4.2 6.5 1.0
CA A:HIS398 4.3 4.9 1.0
CD2 A:HIS97 4.4 10.3 1.0
CB A:HIS398 4.5 4.8 1.0
NE2 A:HIS97 4.5 6.7 1.0
N A:GLY98 4.6 5.7 1.0
NE2 A:HIS444 4.6 7.8 1.0
N A:HIS398 4.6 4.1 1.0
O A:LEU397 4.8 3.9 1.0
C A:LEU397 4.9 4.8 1.0
C A:HIS97 4.9 5.2 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 Oct 28 14:22:33 2020
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