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Copper in PDB 5afa: Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K.

Enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K.

All present enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K.:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K., PDB code: 5afa was solved by N.Jimenez-Arroyo, E.Rudino-Pinera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.346 / 2.19
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.706, 110.579, 96.547, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 19.43

Other elements in 5afa:

The structure of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K. also contains other interesting chemical elements:

Silver (Ag) 3 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K. (pdb code 5afa). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K., PDB code: 5afa:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5afa

Go back to Copper Binding Sites List in 5afa
Copper binding site 1 out of 4 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1480

b:21.2
occ:0.74
 NE2 A:HIS398 1.8 10.7 1.0
NE2 A:HIS444 2.0 10.0 1.0
NE2 A:HIS137 2.0 21.0 1.0
O A:OH1484 2.1 37.6 1.0
CE1 A:HIS398 2.6 18.2 1.0
CD2 A:HIS137 2.7 14.6 1.0
CE1 A:HIS444 2.9 10.7 1.0
CD2 A:HIS398 2.9 13.2 1.0
CD2 A:HIS444 3.1 12.4 1.0
CE1 A:HIS137 3.2 12.7 1.0
O A:HOH2144 3.5 52.1 1.0
CU A:CU1483 3.6 17.1 0.7
O A:HOH2146 3.7 32.2 1.0
CD2 A:HIS396 3.8 10.6 1.0
ND1 A:HIS398 3.8 13.9 1.0
CD2 A:HIS95 3.9 13.1 1.0
CG A:HIS137 3.9 15.1 1.0
CG A:HIS398 4.0 10.1 1.0
NE2 A:HIS95 4.0 20.6 1.0
ND1 A:HIS444 4.0 14.2 1.0
CG A:HIS444 4.1 11.5 1.0
ND1 A:HIS137 4.1 23.4 1.0
NE2 A:HIS396 4.2 9.3 1.0
CG2 A:VAL442 4.5 13.6 1.0
OE1 A:GLU451 4.7 10.0 0.5
CG A:HIS95 4.7 14.4 1.0
CE1 A:HIS95 4.8 16.3 1.0
OE2 A:GLU451 4.8 11.6 0.5
CD A:GLU451 4.9 11.0 0.5
CU A:CU1481 4.9 13.4 1.0
CG A:HIS396 5.0 12.8 1.0

Copper binding site 2 out of 4 in 5afa

Go back to Copper Binding Sites List in 5afa
Copper binding site 2 out of 4 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1481

b:13.4
occ:1.00
 ND1 A:HIS97 2.0 9.1 1.0
NE2 A:HIS135 2.1 14.3 1.0
NE2 A:HIS446 2.2 10.3 1.0
O A:OH1484 2.8 37.6 1.0
CE1 A:HIS97 2.9 10.9 1.0
CG A:HIS97 3.0 10.7 1.0
CD2 A:HIS135 3.0 11.2 1.0
CE1 A:HIS446 3.1 7.2 1.0
CE1 A:HIS135 3.1 11.9 1.0
CD2 A:HIS446 3.2 10.0 1.0
O A:HOH2144 3.3 52.1 1.0
CB A:HIS97 3.5 10.2 1.0
CZ2 A:TRP133 3.6 9.1 1.0
CD2 A:HIS95 4.0 13.1 1.0
CU A:CU1483 4.0 17.1 0.7
NE2 A:HIS97 4.0 12.2 1.0
CE2 A:TRP133 4.0 7.9 1.0
CD2 A:HIS97 4.1 9.4 1.0
ND1 A:HIS135 4.2 10.1 1.0
ND1 A:HIS446 4.2 9.6 1.0
CG A:HIS135 4.2 9.0 1.0
NE1 A:TRP133 4.3 6.2 1.0
CH2 A:TRP133 4.3 8.1 1.0
CG A:HIS446 4.3 13.5 1.0
NE2 A:HIS396 4.4 9.3 1.0
NE2 A:HIS95 4.5 20.6 1.0
CD2 A:HIS396 4.5 10.6 1.0
CA A:HIS97 4.7 12.7 1.0
CU A:CU1480 4.9 21.2 0.7
O A:HOH2146 5.0 32.2 1.0
CD2 A:TRP133 5.0 8.9 1.0

Copper binding site 3 out of 4 in 5afa

Go back to Copper Binding Sites List in 5afa
Copper binding site 3 out of 4 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1482

b:12.1
occ:1.00
 ND1 A:HIS450 2.1 10.2 1.0
ND1 A:HIS393 2.1 8.5 1.0
SG A:CYS445 2.2 10.7 1.0
CE1 A:HIS393 2.9 10.1 1.0
CG A:HIS450 3.0 12.2 1.0
CE1 A:HIS450 3.1 8.2 1.0
CG A:HIS393 3.1 10.9 1.0
CB A:CYS445 3.2 7.8 1.0
CB A:HIS450 3.3 7.7 1.0
SD A:MET455 3.5 16.5 1.0
CB A:HIS393 3.5 10.4 1.0
CA A:HIS393 4.0 7.2 1.0
CB A:ILE447 4.0 9.6 1.0
NE2 A:HIS393 4.1 15.4 1.0
CD1 A:ILE447 4.1 8.5 1.0
NE2 A:HIS450 4.2 12.9 1.0
CD2 A:HIS450 4.2 10.9 1.0
CD2 A:HIS393 4.2 9.1 1.0
CG1 A:ILE447 4.4 7.3 1.0
O A:ASP392 4.5 8.8 1.0
CE A:MET455 4.6 17.3 1.0
CD A:PRO394 4.6 5.1 1.0
CA A:CYS445 4.6 11.3 1.0
O A:ILE447 4.7 7.6 1.0
CG2 A:ILE447 4.8 5.2 1.0
CA A:HIS450 4.9 9.1 1.0
N A:ILE447 4.9 7.3 1.0
C A:HIS393 5.0 7.5 1.0
CA A:ILE447 5.0 7.6 1.0

Copper binding site 4 out of 4 in 5afa

Go back to Copper Binding Sites List in 5afa
Copper binding site 4 out of 4 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K.


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Laccase From Thermus Thermophilus HB27 Complexed with Ag, Crystal of the Holoenzyme Soaked For 30 M in 5 Mm AGNO3 at 278 K. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1483

b:17.1
occ:0.66
 NE2 A:HIS95 1.8 20.6 1.0
NE2 A:HIS396 2.0 9.3 1.0
CD2 A:HIS95 2.7 13.1 1.0
CE1 A:HIS95 2.8 16.3 1.0
CD2 A:HIS396 2.9 10.6 1.0
O A:OH1484 2.9 37.6 1.0
O A:HOH2092 2.9 16.1 1.0
CE1 A:HIS396 3.0 7.6 1.0
CD2 A:HIS398 3.2 13.2 1.0
NE2 A:HIS398 3.2 10.7 1.0
ND1 A:HIS97 3.5 9.1 1.0
CU A:CU1480 3.6 21.2 0.7
CG A:HIS97 3.7 10.7 1.0
CG A:HIS398 3.7 10.1 1.0
CE1 A:HIS398 3.8 18.2 1.0
CA A:HIS97 3.8 12.7 1.0
CG A:HIS95 3.9 14.4 1.0
ND1 A:HIS95 3.9 13.3 1.0
CE1 A:HIS97 4.0 10.9 1.0
CB A:HIS97 4.0 10.2 1.0
CU A:CU1481 4.0 13.4 1.0
ND1 A:HIS398 4.1 13.9 1.0
CG A:HIS396 4.1 12.8 1.0
ND1 A:HIS396 4.1 12.0 1.0
CD2 A:HIS97 4.2 9.4 1.0
N A:GLY98 4.3 15.1 1.0
NE2 A:HIS97 4.4 12.2 1.0
O A:HOH2094 4.4 34.3 1.0
CA A:HIS398 4.5 8.6 1.0
CB A:HIS398 4.6 8.8 1.0
C A:HIS97 4.6 10.9 1.0
N A:HIS97 4.8 12.0 1.0
O A:HOH2093 4.9 17.6 1.0
N A:HIS398 4.9 10.0 1.0
NE2 A:HIS444 4.9 10.0 1.0

Reference:

N.Jimenez-Arroyo, C.S.Cardona-Felix, S.P.Rojas-Trejo, E.Rudino-Pinera. Structural Function of the Methionine-Rich Beta-Hairpin in the Laccase For T. Thermophilus. To Be Published.
Page generated: Sun Dec 13 11:16:57 2020

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