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Xenon in PDB 3fz6: Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon

Enzymatic activity of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon

All present enzymatic activity of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon:
4.1.1.15;

Protein crystallography data

The structure of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon, PDB code: 3fz6 was solved by V.N.Malashkevich, D.De Biase, F.Bossa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.85 / 2.82
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 116.729, 116.729, 208.423, 90.00, 90.00, 120.00
R / Rfree (%) 13.5 / 20.3

Xenon Binding Sites:

The binding sites of Xenon atom in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon (pdb code 3fz6). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 6 binding sites of Xenon where determined in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon, PDB code: 3fz6:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6;

Xenon binding site 1 out of 6 in 3fz6

Go back to Xenon Binding Sites List in 3fz6
Xenon binding site 1 out of 6 in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe501

b:11.4
occ:0.30
 O A:GLY120 3.6 9.7 1.0
CD2 A:LEU295 3.9 4.7 1.0
CB A:PHE313 4.2 27.2 1.0
C A:GLY120 4.3 8.8 1.0
N A:PHE313 4.3 27.9 1.0
N A:GLY120 4.5 8.4 1.0
CB A:THR121 4.5 8.1 1.0
O A:GLY311 4.6 37.7 1.0
CA A:GLY120 4.8 7.8 1.0
CA A:PHE313 4.8 27.1 1.0
CZ3 A:TRP289 4.9 12.2 1.0

Xenon binding site 2 out of 6 in 3fz6

Go back to Xenon Binding Sites List in 3fz6
Xenon binding site 2 out of 6 in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe501

b:19.0
occ:0.30
 CB B:PHE313 3.8 33.6 1.0
O B:GLY120 3.9 6.3 1.0
CD2 B:LEU295 3.9 11.5 1.0
N B:PHE313 4.0 34.7 1.0
C B:GLY120 4.3 7.3 1.0
CB B:THR121 4.4 15.6 1.0
CA B:PHE313 4.5 33.3 1.0
N B:GLY120 4.6 6.0 1.0
O B:GLY311 4.8 38.0 1.0
C B:THR312 4.8 35.7 1.0
CA B:GLY120 4.9 5.6 1.0
CZ3 B:TRP289 4.9 5.8 1.0
N B:THR121 4.9 10.1 1.0

Xenon binding site 3 out of 6 in 3fz6

Go back to Xenon Binding Sites List in 3fz6
Xenon binding site 3 out of 6 in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe501

b:2.1
occ:0.30
 O C:GLY120 3.7 9.9 1.0
CD2 C:LEU295 3.9 11.3 1.0
CB C:PHE313 4.0 25.5 1.0
C C:GLY120 4.2 8.3 1.0
N C:PHE313 4.2 26.9 1.0
O C:GLY311 4.4 38.2 1.0
CB C:THR121 4.4 6.8 1.0
O E:HOH737 4.4 17.7 1.0
N C:GLY120 4.5 8.3 1.0
CA C:GLY120 4.7 7.6 1.0
CA C:PHE313 4.8 25.8 1.0
CG1 C:VAL119 4.8 2.0 1.0
CZ3 C:TRP289 4.8 11.9 1.0
C C:THR312 4.9 29.2 1.0
CG2 C:VAL300 4.9 2.0 1.0
N C:THR121 4.9 7.3 1.0
OG1 C:THR121 5.0 3.5 1.0

Xenon binding site 4 out of 6 in 3fz6

Go back to Xenon Binding Sites List in 3fz6
Xenon binding site 4 out of 6 in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe501

b:15.0
occ:0.30
 O D:GLY120 3.7 6.8 1.0
CD2 D:LEU295 3.9 14.4 1.0
CB D:PHE313 4.1 24.1 1.0
N D:PHE313 4.2 26.1 1.0
C D:GLY120 4.2 6.6 1.0
O E:HOH720 4.3 22.3 1.0
N D:GLY120 4.5 7.5 1.0
CB D:THR121 4.5 8.7 1.0
CG1 D:VAL119 4.7 2.0 1.0
CA D:GLY120 4.7 6.5 1.0
CA D:PHE313 4.8 24.1 1.0
CZ3 D:TRP289 4.9 9.1 1.0
N D:THR121 5.0 6.7 1.0
O D:GLY311 5.0 36.4 1.0
C D:THR312 5.0 28.0 1.0

Xenon binding site 5 out of 6 in 3fz6

Go back to Xenon Binding Sites List in 3fz6
Xenon binding site 5 out of 6 in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe501

b:7.5
occ:0.30
 O E:GLY120 3.8 7.9 1.0
CB E:PHE313 4.0 26.0 1.0
CD2 E:LEU295 4.1 12.1 1.0
N E:PHE313 4.1 27.5 1.0
O E:HOH765 4.3 27.9 1.0
C E:GLY120 4.4 7.2 1.0
O E:HOH656 4.4 22.9 1.0
CB E:THR121 4.4 6.9 1.0
N E:GLY120 4.6 6.6 1.0
O E:GLY311 4.6 34.7 1.0
CA E:PHE313 4.7 26.3 1.0
C E:THR312 4.9 29.6 1.0
CA E:GLY120 4.9 6.7 1.0
CZ3 E:TRP289 5.0 10.0 1.0

Xenon binding site 6 out of 6 in 3fz6

Go back to Xenon Binding Sites List in 3fz6
Xenon binding site 6 out of 6 in the Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Xe501

b:22.6
occ:0.30
 N F:PHE313 3.8 28.0 1.0
CB F:PHE313 4.0 28.2 1.0
CD2 F:LEU295 4.0 11.2 1.0
O F:GLY120 4.2 3.9 1.0
O E:HOH749 4.3 10.1 1.0
CA F:PHE313 4.5 26.9 1.0
O F:GLY311 4.5 35.6 1.0
C F:THR312 4.7 30.0 1.0
C F:GLY120 4.7 4.4 1.0
N F:GLY120 4.8 6.0 1.0
O F:PHE313 4.8 25.7 1.0
CB F:THR121 4.8 6.8 1.0
CA F:THR312 4.9 32.5 1.0

Reference:

V.N.Malashkevich, D.De Biase, F.Bossa. Crystal Structure of Glutamate Decarboxylase Beta From Escherichia Coli: Complex with Xenon To Be Published.
Page generated: Sat Oct 12 18:43:28 2024

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