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Xenon in PDB 3qpk: Probing Oxygen Channels in Melanocarpus Albomyces Laccase

Enzymatic activity of Probing Oxygen Channels in Melanocarpus Albomyces Laccase

All present enzymatic activity of Probing Oxygen Channels in Melanocarpus Albomyces Laccase:
1.10.3.2;

Protein crystallography data

The structure of Probing Oxygen Channels in Melanocarpus Albomyces Laccase, PDB code: 3qpk was solved by J.P.Kallio, J.Rouvinen, N.Hakulinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.83 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.150, 60.200, 114.440, 90.00, 99.79, 90.00
R / Rfree (%) 21.4 / 27

Other elements in 3qpk:

The structure of Probing Oxygen Channels in Melanocarpus Albomyces Laccase also contains other interesting chemical elements:

Copper (Cu) 8 atoms
Chlorine (Cl) 2 atoms

Xenon Binding Sites:

The binding sites of Xenon atom in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase (pdb code 3qpk). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 6 binding sites of Xenon where determined in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase, PDB code: 3qpk:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6;

Xenon binding site 1 out of 6 in 3qpk

Go back to Xenon Binding Sites List in 3qpk
Xenon binding site 1 out of 6 in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Probing Oxygen Channels in Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe574

b:19.5
occ:1.00
 CZ A:PHE501 3.9 15.3 1.0
CZ A:PHE517 3.9 9.4 1.0
CE2 A:PHE501 4.0 12.4 1.0
CE1 A:PHE501 4.0 15.9 1.0
CD1 A:LEU489 4.0 9.5 1.0
CD1 A:PHE491 4.1 13.6 1.0
CD1 A:TRP417 4.1 11.4 1.0
CE2 A:PHE517 4.1 12.2 1.0
CD2 A:LEU435 4.1 16.6 1.0
CB A:LEU489 4.2 11.8 1.0
CE1 A:PHE491 4.2 11.5 1.0
CB A:TRP417 4.3 12.0 1.0
CG A:TRP417 4.3 11.9 1.0
CD2 A:PHE501 4.3 12.6 1.0
CD1 A:PHE501 4.3 11.6 1.0
CG A:PHE501 4.4 10.7 1.0
CG A:LEU489 4.7 6.9 1.0
CD1 A:LEU435 4.7 8.5 1.0
CD2 A:PHE440 4.8 7.5 1.0
CG A:LEU435 4.9 10.1 1.0
NE1 A:TRP417 4.9 11.0 1.0
CE1 A:PHE517 4.9 12.4 1.0

Xenon binding site 2 out of 6 in 3qpk

Go back to Xenon Binding Sites List in 3qpk
Xenon binding site 2 out of 6 in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Probing Oxygen Channels in Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe575

b:18.8
occ:0.40
 CE A:MET433 3.4 16.2 1.0
CG1 A:VAL375 3.7 13.1 1.0
CD2 A:PHE501 3.7 12.6 1.0
CE2 A:PHE501 3.8 12.4 1.0
O A:PHE501 3.9 7.5 1.0
CG2 A:VAL375 4.0 18.0 1.0
CD1 A:LEU359 4.1 14.1 1.0
N A:VAL515 4.4 9.6 1.0
CD2 A:LEU513 4.4 11.4 1.0
CG1 A:VAL515 4.4 9.4 1.0
CG2 A:VAL515 4.4 8.9 1.0
CB A:VAL375 4.5 17.3 1.0
C A:SER514 4.6 12.0 1.0
C A:PHE501 4.6 8.5 1.0
CB A:LEU359 4.6 9.2 1.0
CA A:SER514 4.6 10.7 1.0
CG A:PHE501 4.7 10.7 1.0
CG2 A:VAL361 4.7 9.7 1.0
CZ A:PHE501 4.7 15.3 1.0
CB A:VAL515 4.9 11.1 1.0
CG2 A:ILE419 4.9 8.3 1.0
CG A:LEU359 4.9 16.2 1.0
N A:SER514 4.9 9.8 1.0
CA A:HIS502 4.9 7.8 1.0

Xenon binding site 3 out of 6 in 3qpk

Go back to Xenon Binding Sites List in 3qpk
Xenon binding site 3 out of 6 in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Probing Oxygen Channels in Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe576

b:21.9
occ:0.49
 CD2 A:TYR416 3.8 16.6 1.0
O A:SER350 3.8 14.9 1.0
CD1 A:LEU468 3.9 9.2 1.0
CA A:VAL348 3.9 14.1 1.0
CD2 A:LEU488 3.9 11.4 1.0
CE2 A:TYR416 4.0 20.0 1.0
CB A:PHE351 4.0 19.5 1.0
O A:PRO347 4.0 20.2 1.0
CD1 A:PHE351 4.1 15.5 1.0
CD1 A:LEU443 4.2 10.3 1.0
CG1 A:VAL348 4.2 10.3 1.0
CB A:VAL348 4.3 14.3 1.0
CG A:PHE351 4.3 16.6 1.0
C A:VAL348 4.5 14.3 1.0
O A:VAL348 4.6 13.7 1.0
CG A:TYR416 4.6 15.3 1.0
C A:SER350 4.7 18.0 1.0
O A:HOH1115 4.7 30.7 1.0
C A:PRO347 4.9 20.1 1.0
CZ A:TYR416 4.9 21.7 1.0
N A:VAL348 4.9 19.8 1.0
CA A:PHE351 4.9 18.7 1.0
CG A:LEU488 5.0 9.6 1.0

Xenon binding site 4 out of 6 in 3qpk

Go back to Xenon Binding Sites List in 3qpk
Xenon binding site 4 out of 6 in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Probing Oxygen Channels in Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe574

b:18.3
occ:1.00
 CE1 B:PHE491 3.7 16.5 1.0
CD1 B:PHE491 3.8 14.4 1.0
CE2 B:PHE517 3.8 13.1 1.0
CZ B:PHE501 3.9 12.3 1.0
CE2 B:PHE501 4.0 8.6 1.0
CE1 B:PHE501 4.0 11.7 1.0
CD1 B:LEU489 4.0 11.8 1.0
CD1 B:TRP417 4.1 12.3 1.0
CZ B:PHE517 4.1 11.9 1.0
CD2 B:PHE501 4.3 9.6 1.0
CD1 B:PHE501 4.3 12.4 1.0
CG B:TRP417 4.3 11.2 1.0
CD2 B:LEU435 4.3 11.7 1.0
CB B:LEU489 4.3 10.2 1.0
CB B:TRP417 4.3 12.6 1.0
CG B:PHE501 4.4 9.1 1.0
CD1 B:LEU435 4.8 9.3 1.0
CG B:LEU489 4.8 8.2 1.0
NE1 B:TRP417 4.8 9.5 1.0
CD2 B:PHE517 4.9 11.0 1.0
CG B:LEU435 4.9 8.6 1.0
CZ B:PHE491 4.9 14.3 1.0
CD2 B:PHE440 5.0 14.4 1.0

Xenon binding site 5 out of 6 in 3qpk

Go back to Xenon Binding Sites List in 3qpk
Xenon binding site 5 out of 6 in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Probing Oxygen Channels in Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe575

b:18.6
occ:0.41
 CE B:MET433 3.4 14.9 1.0
CD1 B:PHE501 3.7 12.4 1.0
O B:PHE501 3.8 10.8 1.0
CE1 B:PHE501 3.8 11.7 1.0
CG2 B:VAL375 3.9 14.9 1.0
CG1 B:VAL375 3.9 16.9 1.0
CG1 B:VAL515 4.1 16.3 1.0
CD2 B:LEU513 4.3 11.0 1.0
CG2 B:VAL515 4.4 12.2 1.0
CB B:VAL375 4.5 17.7 1.0
N B:VAL515 4.5 13.4 1.0
CD1 B:LEU359 4.5 10.5 1.0
C B:PHE501 4.6 9.7 1.0
CG B:PHE501 4.6 9.1 1.0
C B:SER514 4.7 13.1 1.0
CG2 B:VAL361 4.7 13.7 1.0
CA B:SER514 4.7 11.9 1.0
CG2 B:ILE419 4.7 9.0 1.0
CB B:LEU359 4.7 9.8 1.0
CB B:VAL515 4.8 17.4 1.0
CZ B:PHE501 4.9 12.3 1.0
CA B:HIS502 5.0 10.4 1.0
SD B:MET433 5.0 14.1 1.0

Xenon binding site 6 out of 6 in 3qpk

Go back to Xenon Binding Sites List in 3qpk
Xenon binding site 6 out of 6 in the Probing Oxygen Channels in Melanocarpus Albomyces Laccase


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Probing Oxygen Channels in Melanocarpus Albomyces Laccase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe576

b:23.8
occ:0.49
 O B:SER350 3.6 17.3 1.0
CD2 B:LEU488 3.8 17.0 1.0
CA B:VAL348 3.9 16.1 1.0
CD1 B:LEU468 3.9 11.1 1.0
CB B:PHE351 3.9 20.8 1.0
CD2 B:TYR416 4.0 15.4 1.0
CD1 B:PHE351 4.0 15.1 1.0
O B:PRO347 4.0 18.4 1.0
CG1 B:VAL348 4.1 15.3 1.0
CD1 B:LEU443 4.1 14.2 1.0
CB B:VAL348 4.1 13.6 1.0
CE2 B:TYR416 4.3 15.1 1.0
CG B:PHE351 4.3 18.5 1.0
O B:HOH880 4.5 22.6 1.0
C B:SER350 4.6 20.4 1.0
C B:VAL348 4.6 15.8 1.0
CG B:TYR416 4.7 17.2 1.0
CG B:LEU488 4.8 10.1 1.0
O B:VAL348 4.8 11.1 1.0
C B:PRO347 4.9 17.4 1.0
N B:VAL348 4.9 16.7 1.0
CA B:PHE351 4.9 19.9 1.0
CE1 B:PHE351 5.0 16.5 1.0

Reference:

J.P.Kallio, J.Rouvinen, K.Kruus, N.Hakulinen. Probing the Dioxygen Route in Melanocarpus Albomyces Laccase with Pressurized Xenon Gas. Biochemistry V. 50 4396 2011.
ISSN: ISSN 0006-2960
PubMed: 21524088
DOI: 10.1021/BI200486B
Page generated: Sat Oct 12 19:00:48 2024

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