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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

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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 Oct 28 14:22:33 2020
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