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Copper in PDB 2yam: X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 Percent Dose)

Enzymatic activity of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 Percent Dose)

All present enzymatic activity of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 Percent Dose):
1.10.3.2;

Protein crystallography data

The structure of X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 Percent Dose), PDB code: 2yam 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) 27.897 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.625, 110.310, 96.308, 90.00, 90.00, 90.00
R / Rfree (%) 14.69 / 17.23

Copper Binding Sites:

The binding sites of Copper atom in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 Percent Dose) (pdb code 2yam). 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 (37.5-50.0 Percent Dose), PDB code: 2yam:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 2yam

Go back to Copper Binding Sites List in 2yam
Copper binding site 1 out of 3 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 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 (37.5-50.0 Percent Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1463

b:10.3
occ:1.00
ND1 A:HIS97 2.0 4.4 1.0
NE2 A:HIS135 2.1 6.3 1.0
NE2 A:HIS446 2.1 8.2 1.0
O A:OH1482 2.8 27.4 0.6
HO A:OH1482 2.8 32.8 0.6
CE1 A:HIS97 3.0 4.7 1.0
CE1 A:HIS446 3.0 4.5 1.0
CD2 A:HIS135 3.0 5.8 1.0
CG A:HIS97 3.0 5.0 1.0
CE1 A:HIS135 3.1 7.9 1.0
CD2 A:HIS446 3.2 5.9 1.0
CB A:HIS97 3.4 8.2 1.0
CZ2 A:TRP133 3.6 3.3 1.0
CD2 A:HIS95 3.7 15.7 1.0
CE2 A:TRP133 3.9 2.9 1.0
NE1 A:TRP133 4.0 4.5 1.0
NE2 A:HIS97 4.1 6.6 1.0
CD2 A:HIS97 4.1 5.5 1.0
ND1 A:HIS446 4.1 4.2 1.0
ND1 A:HIS135 4.2 3.5 1.0
CG A:HIS135 4.2 2.0 1.0
CG A:HIS446 4.3 5.7 1.0
CH2 A:TRP133 4.3 3.3 1.0
NE2 A:HIS95 4.3 15.8 1.0
NE2 A:HIS396 4.4 9.5 1.0
CD2 A:HIS396 4.5 7.5 1.0
CA A:HIS97 4.7 4.7 1.0
CD2 A:TRP133 4.8 1.2 1.0
CG A:HIS95 4.8 9.6 1.0
O A:HOH2478 5.0 17.9 1.0

Copper binding site 2 out of 3 in 2yam

Go back to Copper Binding Sites List in 2yam
Copper binding site 2 out of 3 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 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 (37.5-50.0 Percent Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1464

b:9.4
occ:1.00
ND1 A:HIS450 2.1 4.6 1.0
ND1 A:HIS393 2.1 6.3 1.0
SG A:CYS445 2.2 6.0 1.0
CE1 A:HIS393 3.0 10.3 1.0
CG A:HIS450 3.1 4.3 1.0
CE1 A:HIS450 3.1 7.3 1.0
CG A:HIS393 3.2 7.9 1.0
CB A:CYS445 3.2 4.6 1.0
CB A:HIS450 3.4 4.5 1.0
SD A:MET455 3.6 14.1 1.0
CB A:HIS393 3.6 8.0 1.0
CD1 A:ILE447 3.9 3.6 1.0
CB A:ILE447 3.9 3.5 1.0
CA A:HIS393 4.0 3.1 1.0
NE2 A:HIS393 4.2 8.8 1.0
NE2 A:HIS450 4.2 5.4 1.0
CD2 A:HIS450 4.2 7.3 1.0
CD2 A:HIS393 4.3 5.2 1.0
CG1 A:ILE447 4.4 1.7 1.0
O A:ASP392 4.5 6.1 1.0
CD A:PRO394 4.5 1.8 1.0
CA A:CYS445 4.6 3.7 1.0
CE A:MET455 4.6 13.8 1.0
O A:ILE447 4.7 6.4 1.0
CG2 A:ILE447 4.7 2.1 1.0
N A:ILE447 4.8 3.1 1.0
CA A:ILE447 4.9 5.4 1.0
CA A:HIS450 4.9 4.4 1.0
C A:HIS393 5.0 5.9 1.0

Copper binding site 3 out of 3 in 2yam

Go back to Copper Binding Sites List in 2yam
Copper binding site 3 out of 3 in the X-Ray Induced Reduction of Laccase From Thermus Thermophilus HB27 (37.5-50.0 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 (37.5-50.0 Percent Dose) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1465

b:18.7
occ:0.42
NE2 A:HIS398 1.8 5.6 1.0
NE2 A:HIS444 1.9 9.9 1.0
NE2 A:HIS137 2.2 10.8 0.4
O A:OH1482 2.3 27.4 0.6
CD2 A:HIS137 2.6 11.0 0.4
CE1 A:HIS398 2.6 5.4 1.0
CD2 A:HIS444 2.9 7.6 1.0
CD2 A:HIS398 2.9 7.2 1.0
HO A:OH1482 2.9 32.8 0.6
CE1 A:HIS444 2.9 7.6 1.0
CD2 A:HIS137 3.0 8.1 0.6
NE2 A:HIS137 3.1 12.3 0.6
CE1 A:HIS137 3.4 15.2 0.4
CD2 A:HIS396 3.6 7.5 1.0
CD2 A:HIS95 3.6 15.7 1.0
O A:HOH2478 3.7 17.9 1.0
NE2 A:HIS95 3.8 15.8 1.0
ND1 A:HIS398 3.8 6.0 1.0
CG A:HIS137 3.9 8.7 0.4
CG A:HIS398 3.9 5.9 1.0
CG A:HIS137 4.0 8.3 0.6
ND1 A:HIS444 4.0 4.7 1.0
CG A:HIS444 4.0 7.9 1.0
CE1 A:HIS137 4.1 14.6 0.6
NE2 A:HIS396 4.1 9.5 1.0
ND1 A:HIS137 4.2 12.8 0.4
CG A:HIS95 4.3 9.6 1.0
CG2 A:VAL442 4.4 2.3 1.0
CE1 A:HIS95 4.4 17.7 1.0
ND1 A:HIS137 4.5 16.9 0.6
OE2 A:GLU451 4.7 14.2 0.4
ND1 A:HIS95 4.7 9.8 1.0
OE1 A:GLU451 4.7 5.3 0.4
CG A:HIS396 4.8 4.6 1.0
CD A:GLU451 4.9 3.0 0.4
CB A:HIS137 4.9 7.6 0.6

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: Thu Sep 3 16:59:03 2020
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