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Copper in PDB 9cpm: Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence

Enzymatic activity of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence

All present enzymatic activity of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence:
1.10.3.2;

Protein crystallography data

The structure of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence, PDB code: 9cpm was solved by J.Lee, B.Miranda-Zaragoza, C.Rodriguez-Almazan, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.17 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.927, 66.032, 74.057, 90, 100.14, 90
R / Rfree (%) 15.3 / 18.2

Copper Binding Sites:

The binding sites of Copper atom in the Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence (pdb code 9cpm). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 5 binding sites of Copper where determined in the Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence, PDB code: 9cpm:
Jump to Copper binding site number: 1; 2; 3; 4; 5;

Copper binding site 1 out of 5 in 9cpm

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Copper binding site 1 out of 5 in the Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:10.5
occ:1.00
 ND1 A:HIS450 2.0 10.0 1.0
ND1 A:HIS393 2.1 9.6 1.0
SG A:CYS445 2.2 12.8 1.0
CE1 A:HIS393 3.0 10.4 1.0
CE1 A:HIS450 3.0 8.8 1.0
CG A:HIS450 3.0 9.8 1.0
CG A:HIS393 3.1 9.9 1.0
CB A:CYS445 3.3 13.9 1.0
CB A:HIS450 3.3 9.6 1.0
CB A:HIS393 3.5 9.6 1.0
SD A:MET455 3.6 19.7 1.0
CA A:HIS393 3.9 8.7 1.0
CD1 A:ILE447 4.0 9.1 1.0
CB A:ILE447 4.0 8.3 1.0
NE2 A:HIS393 4.1 9.8 1.0
CD2 A:HIS450 4.1 9.6 1.0
NE2 A:HIS450 4.1 9.5 1.0
CD2 A:HIS393 4.2 9.5 1.0
CG1 A:ILE447 4.3 9.1 1.0
O A:ASP392 4.4 9.2 1.0
CD A:PRO394 4.4 8.6 1.0
CE A:MET455 4.5 16.8 1.0
CA A:CYS445 4.6 10.6 1.0
O A:ILE447 4.7 8.5 1.0
N A:ILE447 4.7 7.9 1.0
CA A:HIS450 4.8 9.5 1.0
CG2 A:ILE447 4.9 9.6 1.0
C A:HIS393 4.9 9.2 1.0
N A:HIS393 4.9 8.8 1.0
CA A:ILE447 4.9 8.4 1.0
N A:PRO394 5.0 9.2 1.0

Copper binding site 2 out of 5 in 9cpm

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Copper binding site 2 out of 5 in the Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:15.4
occ:1.00
 NE2 A:HIS95 2.0 12.3 1.0
NE2 A:HIS396 2.0 10.8 1.0
O A:HOH763 2.8 21.3 1.0
CD2 A:HIS95 2.9 13.2 1.0
CD2 A:HIS396 3.0 10.8 1.0
CE1 A:HIS396 3.0 9.7 1.0
CE1 A:HIS95 3.0 13.3 1.0
CD2 A:HIS398 3.1 15.3 1.0
NE2 A:HIS398 3.3 15.4 1.0
O A:HOH938 3.4 36.4 1.0
ND1 A:HIS97 3.6 9.7 1.0
CU A:CU503 3.7 22.0 1.0
CG A:HIS97 3.7 10.7 1.0
CG A:HIS398 3.8 13.4 1.0
CA A:HIS97 3.8 10.4 1.0
CE1 A:HIS398 3.9 14.1 1.0
CB A:HIS97 4.0 10.6 1.0
CU A:CU504 4.0 13.9 1.0
CG A:HIS95 4.0 12.7 1.0
ND1 A:HIS396 4.1 9.7 1.0
ND1 A:HIS95 4.1 12.3 1.0
CG A:HIS396 4.1 9.3 1.0
CE1 A:HIS97 4.1 11.1 1.0
ND1 A:HIS398 4.2 13.4 1.0
CD2 A:HIS97 4.2 11.8 1.0
N A:GLY98 4.3 12.2 1.0
NE2 A:HIS97 4.4 11.2 1.0
CA A:HIS398 4.5 13.5 1.0
O A:HOH755 4.6 22.5 1.0
CB A:HIS398 4.6 13.2 1.0
C A:HIS97 4.7 10.1 1.0
O A:HOH864 4.7 26.4 1.0
N A:HIS97 4.8 10.8 1.0
NE2 A:HIS444 4.9 11.4 1.0
N A:HIS398 4.9 11.6 1.0

Copper binding site 3 out of 5 in 9cpm

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Copper binding site 3 out of 5 in the Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu503

b:22.0
occ:1.00
 NE2 A:HIS398 2.0 15.4 1.0
NE2 A:HIS137 2.0 24.4 1.0
NE2 A:HIS444 2.0 11.4 1.0
O A:HOH938 2.2 36.4 1.0
CD2 A:HIS137 2.9 25.8 1.0
CE1 A:HIS398 2.9 14.1 1.0
CD2 A:HIS444 2.9 11.1 1.0
CD2 A:HIS398 3.0 15.3 1.0
CE1 A:HIS444 3.0 12.1 1.0
CE1 A:HIS137 3.1 26.9 1.0
O A:HOH652 3.7 30.3 1.0
CU A:CU502 3.7 15.4 1.0
CD2 A:HIS396 3.9 10.8 1.0
CD2 A:HIS95 4.0 13.2 1.0
ND1 A:HIS398 4.0 13.4 1.0
CG A:HIS398 4.1 13.4 1.0
CG A:HIS137 4.1 20.2 1.0
NE2 A:HIS95 4.1 12.3 1.0
ND1 A:HIS444 4.1 10.7 1.0
CG A:HIS444 4.1 10.0 1.0
ND1 A:HIS137 4.1 26.9 1.0
CG2 A:VAL442 4.3 13.5 1.0
NE2 A:HIS396 4.3 10.8 1.0
OE2 A:GLU451 4.5 26.4 1.0
CG A:HIS95 4.8 12.7 1.0
CE1 A:HIS95 4.8 13.3 1.0
OE1 A:GLU451 4.9 30.5 1.0
CD A:GLU451 4.9 22.8 1.0
CU A:CU504 5.0 13.9 1.0

Copper binding site 4 out of 5 in 9cpm

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Copper binding site 4 out of 5 in the Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu504

b:13.9
occ:1.00
 ND1 A:HIS97 2.0 9.7 1.0
NE2 A:HIS135 2.0 9.1 1.0
NE2 A:HIS446 2.1 12.0 1.0
O A:HOH938 2.8 36.4 1.0
CE1 A:HIS97 2.9 11.1 1.0
CE1 A:HIS135 2.9 9.2 1.0
CG A:HIS97 3.0 10.7 1.0
CE1 A:HIS446 3.0 12.6 1.0
CD2 A:HIS135 3.0 9.6 1.0
CD2 A:HIS446 3.2 12.3 1.0
CB A:HIS97 3.4 10.6 1.0
CZ2 A:TRP133 3.6 9.6 1.0
CE2 A:TRP133 4.0 9.9 1.0
NE2 A:HIS97 4.0 11.2 1.0
CD2 A:HIS95 4.0 13.2 1.0
CU A:CU502 4.0 15.4 1.0
CD2 A:HIS97 4.1 11.8 1.0
ND1 A:HIS135 4.1 9.2 1.0
NE1 A:TRP133 4.1 11.3 1.0
CG A:HIS135 4.2 8.9 1.0
ND1 A:HIS446 4.2 11.4 1.0
CG A:HIS446 4.3 10.8 1.0
CH2 A:TRP133 4.4 10.1 1.0
NE2 A:HIS396 4.4 10.8 1.0
CD2 A:HIS396 4.6 10.8 1.0
CA A:HIS97 4.6 10.4 1.0
NE2 A:HIS95 4.6 12.3 1.0
O A:HOH652 4.6 30.3 1.0
CD2 A:TRP133 4.9 9.6 1.0
CU A:CU503 5.0 22.0 1.0

Copper binding site 5 out of 5 in 9cpm

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Copper binding site 5 out of 5 in the Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Thermus Thermophilus HB27 Laccase (Tth-Lac) Mutant with Partial Deletion of Beta-Hairpin Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu505

b:18.8
occ:1.00
 NE2 A:GLN36 1.9 12.0 0.6
NE2 A:GLN36 2.6 13.7 0.5
O A:HOH966 2.7 32.1 1.0
OE1 A:GLN36 2.7 12.4 0.5
CD A:GLN36 3.0 15.7 0.5
CD A:GLN36 3.2 16.6 0.6
CG A:GLN36 4.0 14.7 0.6
OE1 A:GLN36 4.1 14.6 0.6
O A:HOH980 4.1 43.3 1.0
CG A:GLN36 4.5 13.3 0.5

Reference:

B.Miranda-Zaragoza, G.A.Huerta-Miranda, W.I.Garcia-Garcia, E.Hernandez-Alvarez, A.Solano-Peralta, J.Lee, N.Strynadka, M.Miranda-Hernandez, C.Rodriguez-Almazan. Structure-Function Relationship of the Beta-Hairpin of Thermus Thermophilus HB27 Laccase. Int J Mol Sci V. 26 2025.
ISSN: ESSN 1422-0067
PubMed: 39859450
DOI: 10.3390/IJMS26020735
Page generated: Mon Jul 14 09:46:50 2025

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