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Copper in PDB 5z1x: Crystal Structure of Laccase From Cerrena Sp. RSD1

Enzymatic activity of Crystal Structure of Laccase From Cerrena Sp. RSD1

All present enzymatic activity of Crystal Structure of Laccase From Cerrena Sp. RSD1:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of Laccase From Cerrena Sp. RSD1, PDB code: 5z1x was solved by C.C.Lee, M.H.Wu, T.H.Ho, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.626, 88.795, 147.815, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 14.9

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Laccase From Cerrena Sp. RSD1 (pdb code 5z1x). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 8 binding sites of Copper where determined in the Crystal Structure of Laccase From Cerrena Sp. RSD1, PDB code: 5z1x:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Copper binding site 1 out of 8 in 5z1x

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Copper binding site 1 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu509

b:12.3
occ:1.00
 ND1 A:HIS454 2.1 12.0 1.0
ND1 A:HIS393 2.1 11.8 1.0
SG A:CYS449 2.2 11.6 1.0
CE1 A:HIS393 3.0 12.6 1.0
CE1 A:HIS454 3.0 12.3 1.0
CG A:HIS454 3.1 11.7 1.0
CG A:HIS393 3.2 11.2 1.0
CB A:CYS449 3.3 11.3 1.0
CB A:HIS454 3.4 11.4 1.0
CD1 A:ILE451 3.5 12.5 1.0
CB A:HIS393 3.5 10.9 1.0
CD2 A:PHE459 3.7 11.6 1.0
CB A:ILE451 3.7 11.5 1.0
CE2 A:PHE459 3.9 12.1 1.0
CG1 A:ILE451 4.0 12.1 1.0
CA A:HIS393 4.0 10.6 1.0
NE2 A:HIS393 4.1 12.3 1.0
NE2 A:HIS454 4.1 13.0 1.0
CD2 A:HIS454 4.2 12.7 1.0
CD2 A:HIS393 4.2 11.5 1.0
CG2 A:ILE451 4.5 11.9 1.0
CA A:CYS449 4.6 10.9 1.0
O A:GLY390 4.7 16.6 1.0
N A:ILE451 4.7 11.2 1.0
CD A:PRO394 4.7 10.5 1.0
CA A:ILE451 4.8 11.5 1.0
O A:ILE451 4.8 12.2 1.0
CA A:HIS454 4.9 11.8 1.0
CG A:PHE459 5.0 11.3 1.0
C A:HIS393 5.0 10.6 1.0

Copper binding site 2 out of 8 in 5z1x

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Copper binding site 2 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu510

b:13.9
occ:1.00
 NE2 A:HIS396 1.9 10.1 1.0
NE2 A:HIS64 2.0 10.7 1.0
O A:HOH964 2.5 13.2 1.0
O2 A:OXY513 2.8 26.4 1.0
CE1 A:HIS64 2.9 10.9 1.0
CD2 A:HIS396 2.9 11.0 1.0
CE1 A:HIS396 2.9 10.7 1.0
CD2 A:HIS64 3.0 11.2 1.0
NE2 A:HIS398 3.4 11.1 1.0
CE1 A:HIS398 3.5 10.5 1.0
ND1 A:HIS66 3.5 10.4 1.0
CD2 A:HIS398 3.6 11.1 1.0
O1 A:OXY513 3.7 22.8 1.0
CG A:HIS66 3.7 10.0 1.0
ND1 A:HIS398 3.7 10.6 1.0
CG A:HIS398 3.8 10.6 1.0
CA A:HIS66 3.9 9.8 1.0
CE1 A:HIS66 3.9 10.8 1.0
ND1 A:HIS64 4.0 10.7 1.0
ND1 A:HIS396 4.0 10.6 1.0
CG A:HIS396 4.0 10.8 1.0
N A:GLY67 4.0 10.1 1.0
CU A:CU511 4.1 13.6 1.0
CG A:HIS64 4.1 10.6 1.0
CB A:HIS66 4.1 9.7 1.0
CD2 A:HIS66 4.2 9.7 1.0
NE2 A:HIS66 4.3 10.3 1.0
CU A:CU512 4.3 17.6 1.0
C A:HIS66 4.5 10.0 1.0
O A:HOH763 4.5 13.8 1.0
O A:HOH700 4.6 12.3 1.0
CA A:HIS398 4.6 10.4 1.0
CB A:HIS398 4.7 10.9 1.0
N A:HIS66 4.9 9.7 1.0

Copper binding site 3 out of 8 in 5z1x

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Copper binding site 3 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu511

b:13.6
occ:1.00
 ND1 A:HIS66 2.0 10.4 1.0
NE2 A:HIS109 2.0 11.2 1.0
NE2 A:HIS450 2.2 11.2 1.0
O2 A:OXY513 2.4 26.4 1.0
CE1 A:HIS66 2.9 10.8 1.0
CD2 A:HIS109 3.0 10.8 1.0
CE1 A:HIS450 3.0 11.7 1.0
CE1 A:HIS109 3.0 10.8 1.0
CG A:HIS66 3.0 10.0 1.0
O1 A:OXY513 3.3 22.8 1.0
CD2 A:HIS450 3.3 11.2 1.0
CZ2 A:TRP107 3.4 9.8 1.0
CB A:HIS66 3.4 9.7 1.0
CE2 A:TRP107 3.7 9.8 1.0
CD2 A:HIS64 3.9 11.2 1.0
NE1 A:TRP107 3.9 10.2 1.0
NE2 A:HIS66 4.1 10.3 1.0
CU A:CU510 4.1 13.9 1.0
ND1 A:HIS109 4.1 10.7 1.0
CD2 A:HIS66 4.1 9.7 1.0
CG A:HIS109 4.1 10.6 1.0
CH2 A:TRP107 4.2 9.8 1.0
ND1 A:HIS450 4.2 11.5 1.0
NE2 A:HIS64 4.3 10.7 1.0
CG A:HIS450 4.4 11.5 1.0
CD2 A:HIS396 4.4 11.0 1.0
NE2 A:HIS396 4.4 10.1 1.0
O A:HOH1116 4.5 18.8 1.0
CA A:HIS66 4.6 9.8 1.0
CD2 A:TRP107 4.7 9.6 1.0
CD1 A:TRP107 4.9 9.7 1.0
CU A:CU512 4.9 17.6 1.0

Copper binding site 4 out of 8 in 5z1x

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Copper binding site 4 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu512

b:17.6
occ:1.00
 O1 A:OXY513 1.7 22.8 1.0
NE2 A:HIS448 2.0 12.5 1.0
NE2 A:HIS398 2.0 11.1 1.0
NE2 A:HIS111 2.1 10.7 1.0
O2 A:OXY513 2.7 26.4 1.0
CE1 A:HIS398 2.9 10.5 1.0
CE1 A:HIS448 3.0 12.7 1.0
CD2 A:HIS448 3.0 12.5 1.0
CE1 A:HIS111 3.0 11.5 1.0
CD2 A:HIS111 3.1 10.6 1.0
CD2 A:HIS398 3.2 11.1 1.0
O A:HOH1116 3.6 18.8 1.0
CD2 A:HIS396 3.9 11.0 1.0
ND1 A:HIS398 4.0 10.6 1.0
ND1 A:HIS448 4.1 12.3 1.0
CG A:HIS448 4.1 11.8 1.0
ND1 A:HIS111 4.2 11.3 1.0
CG A:HIS398 4.2 10.6 1.0
CG A:HIS111 4.2 10.9 1.0
CU A:CU510 4.3 13.9 1.0
CD2 A:PHE446 4.4 13.0 1.0
CD2 A:HIS64 4.4 11.2 1.0
NE2 A:HIS396 4.6 10.1 1.0
CB A:PHE446 4.6 12.0 1.0
NE2 A:HIS64 4.6 10.7 1.0
CE1 A:HIS109 4.8 10.8 1.0
CG A:PRO79 4.8 11.1 1.0
NE2 A:HIS450 4.9 11.2 1.0
CU A:CU511 4.9 13.6 1.0
CG A:PHE446 5.0 11.9 1.0

Copper binding site 5 out of 8 in 5z1x

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Copper binding site 5 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu509

b:12.9
occ:1.00
 ND1 B:HIS454 2.1 13.1 1.0
ND1 B:HIS393 2.1 12.5 1.0
SG B:CYS449 2.2 12.3 1.0
CE1 B:HIS393 3.0 13.0 1.0
CE1 B:HIS454 3.0 13.3 1.0
CG B:HIS454 3.1 12.0 1.0
CG B:HIS393 3.2 12.4 1.0
CB B:CYS449 3.3 11.6 1.0
CB B:HIS454 3.4 12.2 1.0
CD1 B:ILE451 3.5 12.6 1.0
CB B:HIS393 3.5 12.3 1.0
CD2 B:PHE459 3.7 12.9 1.0
CB B:ILE451 3.7 12.2 1.0
CE2 B:PHE459 3.9 13.2 1.0
CG1 B:ILE451 4.0 12.6 1.0
CA B:HIS393 4.0 12.0 1.0
NE2 B:HIS393 4.1 14.0 1.0
NE2 B:HIS454 4.1 13.3 1.0
CD2 B:HIS454 4.2 12.7 1.0
CD2 B:HIS393 4.2 13.3 1.0
CG2 B:ILE451 4.5 12.2 1.0
CA B:CYS449 4.6 11.3 1.0
CD B:PRO394 4.7 11.3 1.0
N B:ILE451 4.7 11.5 1.0
O B:GLY390 4.8 16.9 1.0
CA B:ILE451 4.8 12.0 1.0
O B:ILE451 4.8 11.8 1.0
CA B:HIS454 4.9 12.3 1.0
CG B:PHE459 5.0 13.0 1.0
C B:HIS393 5.0 12.0 1.0

Copper binding site 6 out of 8 in 5z1x

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Copper binding site 6 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu510

b:15.2
occ:1.00
 NE2 B:HIS396 1.9 12.0 1.0
NE2 B:HIS64 1.9 11.2 1.0
O B:HOH917 2.5 13.9 1.0
CE1 B:HIS64 2.9 11.5 1.0
CD2 B:HIS396 2.9 12.1 1.0
CE1 B:HIS396 2.9 11.8 1.0
CD2 B:HIS64 3.0 11.8 1.0
O2 B:OXY513 3.0 61.9 1.0
NE2 B:HIS398 3.4 11.8 1.0
ND1 B:HIS66 3.5 10.6 1.0
CE1 B:HIS398 3.5 11.3 1.0
CD2 B:HIS398 3.6 11.7 1.0
CG B:HIS66 3.7 10.8 1.0
ND1 B:HIS398 3.7 11.8 1.0
O1 B:OXY513 3.8 45.5 1.0
CG B:HIS398 3.8 11.5 1.0
CA B:HIS66 3.9 11.1 1.0
CE1 B:HIS66 3.9 10.8 1.0
ND1 B:HIS64 4.0 11.8 1.0
ND1 B:HIS396 4.0 11.8 1.0
CG B:HIS396 4.0 11.8 1.0
CG B:HIS64 4.0 11.3 1.0
N B:GLY67 4.1 11.8 1.0
CU B:CU511 4.1 14.5 1.0
CB B:HIS66 4.1 10.8 1.0
CD2 B:HIS66 4.2 11.3 1.0
NE2 B:HIS66 4.3 11.6 1.0
CU B:CU512 4.3 19.3 1.0
C B:HIS66 4.5 11.1 1.0
O B:HOH765 4.5 14.8 1.0
O B:HOH696 4.6 13.7 1.0
CA B:HIS398 4.6 11.4 1.0
CB B:HIS398 4.7 11.5 1.0
N B:HIS66 4.9 10.7 1.0

Copper binding site 7 out of 8 in 5z1x

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Copper binding site 7 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu511

b:14.5
occ:1.00
 ND1 B:HIS66 2.0 10.6 1.0
O2 B:OXY513 2.0 61.9 1.0
NE2 B:HIS109 2.1 11.5 1.0
NE2 B:HIS450 2.2 11.8 1.0
CE1 B:HIS66 2.9 10.8 1.0
CD2 B:HIS109 3.0 11.2 1.0
CE1 B:HIS450 3.0 11.6 1.0
CG B:HIS66 3.0 10.8 1.0
O1 B:OXY513 3.1 45.5 1.0
CE1 B:HIS109 3.1 11.0 1.0
CD2 B:HIS450 3.3 11.7 1.0
CB B:HIS66 3.4 10.8 1.0
CZ2 B:TRP107 3.4 10.1 1.0
CE2 B:TRP107 3.7 9.7 1.0
CD2 B:HIS64 3.9 11.8 1.0
NE1 B:TRP107 3.9 10.3 1.0
NE2 B:HIS66 4.1 11.6 1.0
CU B:CU510 4.1 15.2 1.0
CD2 B:HIS66 4.1 11.3 1.0
ND1 B:HIS109 4.1 11.4 1.0
CG B:HIS109 4.1 10.7 1.0
CH2 B:TRP107 4.2 10.9 1.0
ND1 B:HIS450 4.2 11.6 1.0
NE2 B:HIS64 4.3 11.2 1.0
CG B:HIS450 4.4 11.7 1.0
CD2 B:HIS396 4.5 12.1 1.0
NE2 B:HIS396 4.5 12.0 1.0
O B:HOH1026 4.6 19.1 1.0
CA B:HIS66 4.6 11.1 1.0
CD2 B:TRP107 4.7 10.0 1.0
CD1 B:TRP107 4.9 9.9 1.0
CU B:CU512 4.9 19.3 1.0

Copper binding site 8 out of 8 in 5z1x

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Copper binding site 8 out of 8 in the Crystal Structure of Laccase From Cerrena Sp. RSD1


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 Cerrena Sp. RSD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu512

b:19.3
occ:1.00
 O1 B:OXY513 1.9 45.5 1.0
NE2 B:HIS398 2.0 11.8 1.0
NE2 B:HIS448 2.1 14.0 1.0
NE2 B:HIS111 2.1 12.1 1.0
CE1 B:HIS398 2.8 11.3 1.0
O2 B:OXY513 2.9 61.9 1.0
CD2 B:HIS448 3.0 13.5 1.0
CE1 B:HIS111 3.0 12.0 1.0
CE1 B:HIS448 3.0 13.6 1.0
CD2 B:HIS111 3.1 11.7 1.0
CD2 B:HIS398 3.2 11.7 1.0
O B:HOH1026 3.6 19.1 1.0
CD2 B:HIS396 3.9 12.1 1.0
ND1 B:HIS398 4.0 11.8 1.0
ND1 B:HIS448 4.1 12.7 1.0
CG B:HIS448 4.1 12.7 1.0
ND1 B:HIS111 4.2 11.9 1.0
CG B:HIS398 4.2 11.5 1.0
CG B:HIS111 4.2 11.6 1.0
CU B:CU510 4.3 15.2 1.0
CD2 B:HIS64 4.4 11.8 1.0
CD2 B:PHE446 4.4 13.4 1.0
NE2 B:HIS396 4.5 12.0 1.0
NE2 B:HIS64 4.6 11.2 1.0
CB B:PHE446 4.7 12.7 1.0
CG B:PRO79 4.8 12.2 1.0
CE1 B:HIS109 4.8 11.0 1.0
NE2 B:HIS450 4.9 11.8 1.0
CU B:CU511 4.9 14.5 1.0

Reference:

M.H.Wu, C.C.Lee, A.S.Hsiao, S.M.Yu, A.H.J.Wang, T.D.Ho. Kinetic Analysis and Structural Studies of A High-Efficiency Laccase Fromcerrenasp. RSD1. Febs Open Bio V. 8 1230 2018.
ISSN: ESSN 2211-5463
PubMed: 30087829
DOI: 10.1002/2211-5463.12459
Page generated: Wed Jul 31 05:31:54 2024

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