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Copper in PDB 5k0d: Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min)

Enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min)

All present enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min):
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min), PDB code: 5k0d was solved by A.Diaz-Vilchis, R.R.Ruiz-Arellano, E.Rosas-Benitez, V.Stojanoff, E.Rudino-Pinera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.72 / 1.82
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.940, 110.330, 96.510, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 18.9

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min) (pdb code 5k0d). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min), PDB code: 5k0d:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5k0d

Go back to Copper Binding Sites List in 5k0d
Copper binding site 1 out of 3 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min)


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 (Cu(II)- Cyclophanes, 3 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:20.9
occ:0.24
NE2 A:HIS398 1.8 7.9 1.0
NE2 A:HIS444 1.9 10.2 1.0
CE1 A:HIS398 2.6 6.4 1.0
CE1 A:HIS137 2.7 13.0 1.0
ND1 A:HIS137 2.7 17.0 1.0
CD2 A:HIS444 2.9 7.0 1.0
CE1 A:HIS444 2.9 8.2 1.0
CD2 A:HIS398 3.0 6.3 1.0
CD2 A:HIS95 3.5 10.4 1.0
NE2 A:HIS137 3.7 21.1 1.0
NE2 A:HIS95 3.7 12.4 1.0
CD2 A:HIS396 3.7 7.3 1.0
O A:HOH631 3.8 17.1 1.0
ND1 A:HIS398 3.8 6.6 1.0
CG A:HIS137 3.8 10.3 1.0
ND1 A:HIS444 4.0 6.9 1.0
CG A:HIS398 4.0 8.1 1.0
CG A:HIS444 4.0 6.5 1.0
CG A:HIS95 4.2 6.6 1.0
NE2 A:HIS396 4.2 10.2 1.0
CD2 A:HIS137 4.3 16.3 1.0
CE1 A:HIS95 4.5 6.7 1.0
CG2 A:VAL442 4.5 5.3 1.0
OE2 A:GLU451 4.6 5.6 0.4
ND1 A:HIS95 4.7 6.5 1.0
CB A:HIS137 4.7 11.3 1.0
OE1 A:GLU451 4.9 14.3 0.4
CB A:HIS95 4.9 6.5 1.0
CD A:GLU451 4.9 7.3 0.4
CG A:HIS396 5.0 4.7 1.0

Copper binding site 2 out of 3 in 5k0d

Go back to Copper Binding Sites List in 5k0d
Copper binding site 2 out of 3 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min)


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 (Cu(II)- Cyclophanes, 3 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:10.8
occ:1.00
ND1 A:HIS97 2.0 5.9 1.0
NE2 A:HIS135 2.0 9.1 1.0
NE2 A:HIS446 2.1 6.0 1.0
CE1 A:HIS97 2.9 4.8 1.0
CD2 A:HIS135 2.9 4.8 1.0
CE1 A:HIS446 3.0 5.7 1.0
CG A:HIS97 3.0 6.9 1.0
CE1 A:HIS135 3.1 9.4 1.0
CD2 A:HIS446 3.2 9.5 1.0
CB A:HIS97 3.4 5.6 1.0
CZ2 A:TRP133 3.5 6.9 1.0
CD2 A:HIS95 3.7 10.4 1.0
CE2 A:TRP133 3.8 5.4 1.0
NE1 A:TRP133 3.9 3.5 1.0
NE2 A:HIS97 4.0 8.3 1.0
CG A:HIS135 4.1 4.5 1.0
CD2 A:HIS97 4.1 7.4 1.0
ND1 A:HIS446 4.1 6.3 1.0
ND1 A:HIS135 4.1 5.4 1.0
CG A:HIS446 4.3 8.0 1.0
CH2 A:TRP133 4.3 1.9 1.0
NE2 A:HIS95 4.3 12.4 1.0
NE2 A:HIS396 4.4 10.2 1.0
CD2 A:HIS396 4.5 7.3 1.0
CA A:HIS97 4.7 6.2 1.0
CD2 A:TRP133 4.8 5.0 1.0
CG A:HIS95 4.9 6.6 1.0
CD1 A:TRP133 4.9 3.0 1.0

Copper binding site 3 out of 3 in 5k0d

Go back to Copper Binding Sites List in 5k0d
Copper binding site 3 out of 3 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 (Cu(II)- Cyclophanes, 3 Min)


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 (Cu(II)- Cyclophanes, 3 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:13.2
occ:1.00
ND1 A:HIS393 2.1 8.1 1.0
ND1 A:HIS450 2.1 6.6 1.0
SG A:CYS445 2.2 7.5 1.0
CE1 A:HIS393 3.0 8.8 1.0
CG A:HIS450 3.1 5.2 1.0
CE1 A:HIS450 3.1 9.4 1.0
CG A:HIS393 3.2 7.6 1.0
CB A:CYS445 3.3 7.9 1.0
CB A:HIS450 3.4 5.3 1.0
SD A:MET455 3.4 5.2 0.3
CB A:HIS393 3.6 7.8 1.0
SD A:MET455 3.7 12.1 0.7
CE A:MET455 3.8 11.7 0.3
CA A:HIS393 4.0 7.3 1.0
CD1 A:ILE447 4.0 5.3 1.0
CB A:ILE447 4.0 7.5 1.0
NE2 A:HIS393 4.1 9.6 1.0
NE2 A:HIS450 4.2 6.1 1.0
CD2 A:HIS450 4.2 9.2 1.0
CD2 A:HIS393 4.2 8.0 1.0
CG1 A:ILE447 4.4 2.2 1.0
O A:ASP392 4.4 8.2 1.0
CE A:MET455 4.5 4.7 0.7
CD A:PRO394 4.6 1.9 1.0
CA A:CYS445 4.7 4.7 1.0
O A:ILE447 4.7 6.5 1.0
CG2 A:ILE447 4.8 3.0 1.0
N A:ILE447 4.8 4.4 1.0
CG A:MET455 4.9 8.2 0.3
CA A:HIS450 4.9 6.2 1.0
C A:HIS393 4.9 5.0 1.0
CA A:ILE447 4.9 8.0 1.0
N A:PRO394 5.0 6.2 1.0

Reference:

A.Diaz-Vilchis, R.R.Ruiz-Arelalno, E.Rosas-Benitez, V.Stojanoff, E.Rudino-Pinera. Preserving Metallic Sites Affected By Radiation Damage: the CUT2 Case in Thermus Thermophilus Multicopper Oxidase To Be Published.
Page generated: Sun Dec 13 11:18:10 2020

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