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Copper in PDB 6w2k: Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)

Enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)

All present enzymatic activity of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min):
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min), PDB code: 6w2k was solved by R.Miranda-Blancas, E.Rudino-Pinera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.25, 96.23, 72.29, 90, 99.36, 90
R / Rfree (%) 14.5 / 19.7

Copper Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min) (pdb code 6w2k). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 11 binding sites of Copper where determined in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min), PDB code: 6w2k:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 11 in 6w2k

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Copper binding site 1 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 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 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu507

b:10.4
occ:1.00
ND1 A:HIS97 2.0 5.4 1.0
NE2 A:HIS135 2.1 9.9 1.0
NE2 A:HIS446 2.1 7.1 1.0
CE1 A:HIS97 2.9 7.8 1.0
CD2 A:HIS135 3.0 7.9 1.0
CG A:HIS97 3.0 8.8 1.0
CE1 A:HIS135 3.1 4.8 1.0
CE1 A:HIS446 3.1 5.8 1.0
CD2 A:HIS446 3.2 5.8 1.0
CB A:HIS97 3.4 11.3 1.0
CZ2 A:TRP133 3.5 5.3 1.0
CD2 A:HIS95 3.8 8.2 1.0
CE2 A:TRP133 3.8 6.6 1.0
CU A:CU510 3.9 10.5 0.2
NE1 A:TRP133 4.0 4.6 1.0
NE2 A:HIS97 4.1 10.6 1.0
CD2 A:HIS97 4.1 8.4 1.0
CG A:HIS135 4.2 7.8 1.0
ND1 A:HIS135 4.2 7.9 1.0
ND1 A:HIS446 4.2 5.9 1.0
CH2 A:TRP133 4.2 3.2 1.0
CG A:HIS446 4.3 7.6 1.0
NE2 A:HIS95 4.4 13.7 1.0
NE2 A:HIS396 4.4 8.6 1.0
CD2 A:HIS396 4.5 8.2 1.0
CA A:HIS97 4.6 8.9 1.0
CD2 A:TRP133 4.8 4.1 1.0
CG A:HIS95 4.9 7.3 1.0
CD1 A:TRP133 5.0 3.0 1.0

Copper binding site 2 out of 11 in 6w2k

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Copper binding site 2 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 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 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu508

b:12.0
occ:0.94
ND1 A:HIS393 2.1 11.2 1.0
ND1 A:HIS450 2.1 5.9 1.0
SG A:CYS445 2.1 10.6 1.0
CE1 A:HIS393 2.9 13.1 1.0
CG A:HIS450 3.1 7.1 1.0
CE1 A:HIS450 3.1 8.5 1.0
CG A:HIS393 3.2 9.6 1.0
CB A:CYS445 3.3 7.9 1.0
CB A:HIS450 3.4 8.5 1.0
SD A:MET455 3.6 17.5 1.0
CB A:HIS393 3.7 9.1 1.0
CD1 A:ILE447 3.9 4.6 1.0
CB A:ILE447 3.9 7.7 1.0
CA A:HIS393 4.0 8.2 1.0
NE2 A:HIS393 4.1 16.1 1.0
NE2 A:HIS450 4.2 9.8 1.0
CD2 A:HIS450 4.2 7.0 1.0
CD2 A:HIS393 4.3 7.7 1.0
CG1 A:ILE447 4.3 3.2 1.0
O A:ASP392 4.5 5.5 1.0
CD A:PRO394 4.5 1.3 1.0
CA A:CYS445 4.6 7.5 1.0
CG2 A:ILE447 4.6 4.8 1.0
O A:ILE447 4.7 8.9 1.0
N A:ILE447 4.7 5.1 1.0
CE A:MET455 4.7 26.7 1.0
CA A:ILE447 4.8 8.6 1.0
CA A:HIS450 4.9 11.4 1.0
C A:HIS393 5.0 5.2 1.0

Copper binding site 3 out of 11 in 6w2k

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Copper binding site 3 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 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 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu509

b:13.9
occ:0.31
NE2 A:HIS398 1.8 9.8 1.0
NE2 A:HIS444 1.9 10.2 1.0
NE2 A:HIS137 2.3 22.8 1.0
CD2 A:HIS137 2.4 14.9 1.0
CE1 A:HIS398 2.6 8.5 1.0
CD2 A:HIS444 2.8 12.4 1.0
CD2 A:HIS398 2.9 9.4 1.0
CE1 A:HIS444 3.0 6.8 1.0
CE1 A:HIS137 3.5 26.1 1.0
CD2 A:HIS95 3.7 8.2 1.0
CG A:HIS137 3.7 16.0 1.0
ND1 A:HIS398 3.8 10.2 1.0
CU A:CU510 3.8 10.5 0.2
CD2 A:HIS396 3.9 8.2 1.0
NE2 A:HIS95 3.9 13.7 1.0
CG A:HIS398 3.9 11.0 1.0
CG A:HIS444 4.0 7.5 1.0
ND1 A:HIS444 4.0 10.5 1.0
ND1 A:HIS137 4.2 25.3 1.0
CG2 A:VAL442 4.3 7.9 1.0
CG A:HIS95 4.3 7.3 1.0
NE2 A:HIS396 4.3 8.6 1.0
OE2 A:GLU451 4.5 10.5 0.4
CE1 A:HIS95 4.6 8.5 1.0
CD A:GLU451 4.8 9.7 0.4
OE1 A:GLU451 4.8 13.0 0.4
ND1 A:HIS95 4.8 8.6 1.0
CB A:HIS137 4.9 13.0 1.0

Copper binding site 4 out of 11 in 6w2k

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Copper binding site 4 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)


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 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu510

b:10.5
occ:0.24
NE2 A:HIS95 1.5 13.7 1.0
NE2 A:HIS396 1.7 8.6 1.0
CD2 A:HIS95 2.4 8.2 1.0
CD2 A:HIS396 2.6 8.2 1.0
CE1 A:HIS95 2.7 8.5 1.0
CE1 A:HIS396 2.8 9.6 1.0
CD2 A:HIS398 3.1 9.4 1.0
NE2 A:HIS398 3.3 9.8 1.0
O A:HOH693 3.3 10.8 1.0
ND1 A:HIS97 3.4 5.4 1.0
CG A:HIS97 3.5 8.8 1.0
CG A:HIS95 3.6 7.3 1.0
ND1 A:HIS95 3.7 8.6 1.0
CU A:CU509 3.8 13.9 0.3
CG A:HIS396 3.8 8.0 1.0
CA A:HIS97 3.8 8.9 1.0
CE1 A:HIS97 3.8 7.8 1.0
ND1 A:HIS396 3.8 8.0 1.0
CG A:HIS398 3.9 11.0 1.0
CB A:HIS97 3.9 11.3 1.0
CU A:CU507 3.9 10.4 1.0
CE1 A:HIS398 4.0 8.5 1.0
CD2 A:HIS97 4.1 8.4 1.0
NE2 A:HIS97 4.2 10.6 1.0
ND1 A:HIS398 4.3 10.2 1.0
N A:GLY98 4.4 8.8 1.0
CA A:HIS398 4.5 4.6 1.0
C A:HIS97 4.7 11.5 1.0
CB A:HIS398 4.7 7.6 1.0
NE2 A:HIS444 4.8 10.2 1.0
N A:HIS97 4.8 6.1 1.0
N A:HIS398 4.9 8.9 1.0
CB A:HIS95 5.0 9.7 1.0

Copper binding site 5 out of 11 in 6w2k

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Copper binding site 5 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu511

b:27.4
occ:0.18
CE A:MET192 2.1 28.2 1.0
H13 A:MPD501 2.2 51.0 1.0
CG A:MET192 2.4 27.1 1.0
H11 A:MPD501 2.4 51.0 1.0
CB A:MET192 2.4 15.6 1.0
H31 A:MPD501 2.6 45.3 1.0
C1 A:MPD501 2.7 42.5 1.0
SD A:MET192 2.9 44.8 1.0
CA A:MET192 3.1 14.8 1.0
C3 A:MPD501 3.5 37.7 1.0
H12 A:MPD501 3.6 51.0 1.0
C2 A:MPD501 3.7 44.5 1.0
CE A:MET195 3.8 16.5 1.0
N A:MET192 3.9 9.6 1.0
H32 A:MPD501 4.0 45.3 1.0
CG A:MET295 4.2 24.8 1.0
O2 A:MPD501 4.3 55.7 1.0
O A:HOH850 4.3 18.2 1.0
H53 A:MPD501 4.3 43.7 1.0
C A:MET192 4.3 12.0 1.0
O A:MET192 4.6 11.4 1.0
O A:MET293 4.7 20.5 1.0
HO2 A:MPD501 4.7 66.9 1.0
C4 A:MPD501 4.7 41.6 1.0
SD A:MET195 4.7 17.8 1.0
H4 A:MPD501 4.9 49.9 1.0
C A:PRO191 4.9 13.4 1.0
CM A:MPD501 5.0 41.8 1.0

Copper binding site 6 out of 11 in 6w2k

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Copper binding site 6 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu512

b:46.1
occ:0.23
CG A:MET293 2.1 26.1 1.0
CE A:MET293 2.4 26.5 1.0
SD A:MET293 2.7 41.2 1.0
CB A:MET293 3.0 18.9 1.0
O A:HOH906 3.4 27.6 1.0
CE A:MET354 3.5 15.1 1.0
O A:HOH629 3.8 27.6 1.0
CG A:MET354 4.0 16.4 1.0
CB A:ALA304 4.0 34.6 1.0
CB A:MET354 4.3 13.6 1.0
O A:HOH710 4.4 27.7 1.0
CA A:MET293 4.4 15.8 1.0
SD A:MET354 4.6 16.3 1.0
CE A:MET355 4.9 37.0 1.0

Copper binding site 7 out of 11 in 6w2k

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Copper binding site 7 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu504

b:10.2
occ:1.00
ND1 B:HIS97 2.0 6.8 1.0
NE2 B:HIS446 2.0 8.4 1.0
NE2 B:HIS135 2.1 8.2 1.0
CE1 B:HIS97 2.9 8.5 1.0
CE1 B:HIS446 2.9 5.8 1.0
CD2 B:HIS135 3.0 5.5 1.0
CG B:HIS97 3.0 8.5 1.0
CD2 B:HIS446 3.1 9.4 1.0
CE1 B:HIS135 3.2 6.0 1.0
CB B:HIS97 3.5 9.8 1.0
CZ2 B:TRP133 3.6 6.5 1.0
CD2 B:HIS95 3.8 7.1 1.0
CE2 B:TRP133 3.9 6.3 1.0
CU B:CU507 4.0 11.0 0.2
NE2 B:HIS97 4.0 6.6 1.0
NE1 B:TRP133 4.0 5.3 1.0
ND1 B:HIS446 4.1 4.9 1.0
CD2 B:HIS97 4.1 6.9 1.0
CG B:HIS446 4.2 6.0 1.0
CG B:HIS135 4.2 7.5 1.0
ND1 B:HIS135 4.2 9.8 1.0
CH2 B:TRP133 4.4 3.8 1.0
NE2 B:HIS95 4.4 11.4 1.0
NE2 B:HIS396 4.4 9.8 1.0
CD2 B:HIS396 4.4 10.0 1.0
CA B:HIS97 4.7 8.5 1.0
CD2 B:TRP133 4.9 5.9 1.0
CG B:HIS95 4.9 12.1 1.0

Copper binding site 8 out of 11 in 6w2k

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Copper binding site 8 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu505

b:11.7
occ:0.92
ND1 B:HIS393 2.0 8.3 1.0
ND1 B:HIS450 2.1 6.1 1.0
SG B:CYS445 2.2 10.2 1.0
CE1 B:HIS393 2.8 13.2 1.0
CG B:HIS450 3.1 9.0 1.0
CE1 B:HIS450 3.1 8.8 1.0
CG B:HIS393 3.2 9.3 1.0
CB B:CYS445 3.3 9.8 1.0
CB B:HIS450 3.4 8.4 1.0
SD B:MET455 3.5 16.9 1.0
CB B:HIS393 3.7 10.6 1.0
CD1 B:ILE447 3.9 6.8 1.0
NE2 B:HIS393 4.0 12.5 1.0
CB B:ILE447 4.0 6.8 1.0
CA B:HIS393 4.1 9.9 1.0
CD2 B:HIS393 4.2 7.5 1.0
NE2 B:HIS450 4.2 9.9 1.0
CD2 B:HIS450 4.2 10.6 1.0
CG1 B:ILE447 4.4 7.0 1.0
O B:ASP392 4.5 6.2 1.0
CD B:PRO394 4.6 2.3 1.0
CE B:MET455 4.7 19.7 1.0
CA B:CYS445 4.7 7.3 1.0
O B:ILE447 4.8 10.4 1.0
N B:ILE447 4.8 5.5 1.0
CG2 B:ILE447 4.8 8.9 1.0
CA B:HIS450 4.9 8.0 1.0
CA B:ILE447 5.0 7.5 1.0

Copper binding site 9 out of 11 in 6w2k

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Copper binding site 9 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu506

b:15.5
occ:0.36
NE2 B:HIS398 1.8 10.8 1.0
NE2 B:HIS444 1.8 9.8 1.0
NE2 B:HIS137 2.3 21.6 1.0
CD2 B:HIS137 2.5 16.3 1.0
CE1 B:HIS398 2.5 9.8 1.0
CD2 B:HIS444 2.8 12.5 1.0
CE1 B:HIS444 2.9 13.3 1.0
CD2 B:HIS398 3.0 10.3 1.0
CE1 B:HIS137 3.5 30.6 1.0
ND1 B:HIS398 3.7 10.5 1.0
CD2 B:HIS95 3.8 7.1 1.0
CG B:HIS137 3.8 12.8 1.0
CD2 B:HIS396 3.8 10.0 1.0
CU B:CU507 3.9 11.0 0.2
CG B:HIS444 3.9 9.6 1.0
ND1 B:HIS444 3.9 11.0 1.0
NE2 B:HIS95 3.9 11.4 1.0
CG B:HIS398 4.0 10.0 1.0
ND1 B:HIS137 4.2 21.1 1.0
CG2 B:VAL442 4.2 8.0 1.0
NE2 B:HIS396 4.4 9.8 1.0
OE1 B:GLU451 4.5 10.5 0.4
CG B:HIS95 4.5 12.1 1.0
OE2 B:GLU451 4.6 11.3 0.4
CD B:GLU451 4.7 11.3 0.4
CE1 B:HIS95 4.7 8.2 1.0
CB B:HIS137 5.0 11.1 1.0
ND1 B:HIS95 5.0 6.8 1.0

Copper binding site 10 out of 11 in 6w2k

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Copper binding site 10 out of 11 in the Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Laccase From Thermus Thermophilus HB27 in Reducing Conditions (NA2,S2,O2, 20 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu507

b:11.0
occ:0.24
NE2 B:HIS95 1.5 11.4 1.0
NE2 B:HIS396 1.7 9.8 1.0
CD2 B:HIS95 2.5 7.1 1.0
CE1 B:HIS95 2.6 8.2 1.0
CD2 B:HIS396 2.6 10.0 1.0
CE1 B:HIS396 2.8 10.5 1.0
CD2 B:HIS398 3.1 10.3 1.0
O B:HOH687 3.2 11.3 1.0
NE2 B:HIS398 3.2 10.8 1.0
ND1 B:HIS97 3.5 6.8 1.0
CG B:HIS97 3.6 8.5 1.0
CG B:HIS95 3.6 12.1 1.0
ND1 B:HIS95 3.7 6.8 1.0
CG B:HIS398 3.7 10.0 1.0
CA B:HIS97 3.8 8.5 1.0
CG B:HIS396 3.8 8.2 1.0
ND1 B:HIS396 3.8 5.9 1.0
CU B:CU506 3.9 15.5 0.4
CE1 B:HIS398 3.9 9.8 1.0
CB B:HIS97 3.9 9.8 1.0
CE1 B:HIS97 3.9 8.5 1.0
CU B:CU504 4.0 10.2 1.0
CD2 B:HIS97 4.1 6.9 1.0
ND1 B:HIS398 4.2 10.5 1.0
NE2 B:HIS97 4.3 6.6 1.0
N B:GLY98 4.4 6.9 1.0
CA B:HIS398 4.4 5.0 1.0
CB B:HIS398 4.5 8.3 1.0
C B:HIS97 4.6 9.9 1.0
N B:HIS97 4.8 5.9 1.0
N B:HIS398 4.8 6.9 1.0
NE2 B:HIS444 4.9 9.8 1.0
O B:LEU397 4.9 5.5 1.0

Reference:

R.Miranda-Blancas, E.Rudino-Pinera. Dynamic Behavior of Alpha-Beta Loop at Laccase of Thermus Thermophilus To Be Published.
Page generated: Wed Jul 31 07:42:59 2024

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