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Xenon in PDB 7b2c: Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon

Enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon

All present enzymatic activity of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon, PDB code: 7b2c was solved by T.Wagner, O.N.Lemaire, S.Engilberge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.90 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.791, 147.186, 113.376, 90, 107.2, 90
R / Rfree (%) 17.4 / 20.1

Other elements in 7b2c:

The structure of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Potassium (K) 17 atoms
Nickel (Ni) 2 atoms
Chlorine (Cl) 5 atoms
Sodium (Na) 5 atoms

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Xenon atom in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon (pdb code 7b2c). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 16 binding sites of Xenon where determined in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon, PDB code: 7b2c:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 16 in 7b2c

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Xenon binding site 1 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed 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 the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1208

b:13.8
occ:0.60
 CB A:ALA452 3.6 10.5 1.0
CA A:GLY532 3.8 8.1 1.0
CS A:SMC354 3.8 8.4 1.0
CG1 A:VAL380 3.8 10.3 1.0
SG A:SMC354 3.9 9.7 1.0
N A:GLY532 4.0 7.6 1.0
CB A:VAL380 4.1 9.9 1.0
CH2 A:TRP472 4.3 11.8 1.0
CZ3 A:TRP472 4.3 11.6 1.0
CD2 A:LEU350 4.3 9.3 1.0
CD2 A:LEU386 4.4 13.7 1.0
CD1 A:LEU350 4.4 11.6 1.0
CG2 A:VAL380 4.6 11.2 1.0
O A:SER448 4.8 13.6 1.0
CG A:LEU350 4.9 11.9 1.0
C A:GLY531 4.9 8.8 1.0
O A:GLY528 4.9 12.7 1.0

Xenon binding site 2 out of 16 in 7b2c

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Xenon binding site 2 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed 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 the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1209

b:11.6
occ:0.80
 CE2 A:TRP373 3.7 8.9 1.0
CD2 A:TRP373 3.8 8.2 1.0
CE2 A:TYR376 3.9 15.5 1.0
C7 A:TP71204 3.9 7.9 1.0
S1 A:COM1205 3.9 8.9 1.0
CG A:TRP373 3.9 7.1 1.0
NE1 A:TRP373 3.9 9.3 1.0
S7 A:TP71204 4.0 9.7 1.0
OH B:TYR391 4.0 14.3 1.0
CD1 A:TRP373 4.1 8.9 1.0
CZ B:TYR391 4.1 14.1 1.0
CE1 B:TYR391 4.1 11.8 1.0
CZ2 A:TRP373 4.2 10.9 1.0
CE3 A:TRP373 4.2 9.6 1.0
CG2 A:VAL527 4.2 8.9 1.0
CG1 A:VAL527 4.3 7.9 1.0
CD2 A:TYR376 4.4 14.2 1.0
CZ A:TYR376 4.4 16.4 1.0
OH A:TYR376 4.5 14.5 1.0
CH2 A:TRP373 4.6 11.8 1.0
CZ3 A:TRP373 4.6 12.2 1.0
CB A:TRP373 4.7 7.2 1.0
CE2 B:TYR391 4.8 13.1 1.0
CD1 B:TYR391 4.9 11.3 1.0
CB A:VAL527 4.9 8.3 1.0
C1 A:COM1205 5.0 8.9 1.0
CHA A:USN1201 5.0 10.7 1.0

Xenon binding site 3 out of 16 in 7b2c

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Xenon binding site 3 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed 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 the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe1210

b:32.5
occ:0.30
 O A:HOH1607 3.4 13.3 1.0
NH2 C:ARG253 3.5 11.7 1.0
O B:HOH752 3.7 15.2 1.0
CB A:PRO477 3.8 11.2 1.0
CD A:PRO477 3.8 10.5 1.0
CG2 C:ILE249 3.8 14.2 1.0
O A:HOH1341 3.9 15.3 1.0
SD A:MET499 4.0 13.8 1.0
CZ C:ARG253 4.0 9.5 1.0
CG A:PRO477 4.0 10.9 1.0
CE A:MET499 4.0 10.6 1.0
OE1 B:GLU363 4.1 13.7 1.0
OE1 A:GLN496 4.3 10.2 1.0
N A:PRO477 4.3 10.5 1.0
CA A:PRO477 4.3 11.0 1.0
CH2 C:TRP245 4.4 13.8 1.0
NH1 C:ARG253 4.4 9.2 1.0
NE C:ARG253 4.5 8.6 1.0
CZ3 C:TRP245 4.5 13.7 1.0
CB C:ILE249 4.6 12.8 1.0
CG2 A:THR476 4.7 12.1 1.0

Xenon binding site 4 out of 16 in 7b2c

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Xenon binding site 4 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed 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 the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe509

b:12.7
occ:0.70
 O B:HIS223 3.7 15.0 1.0
CZ B:PHE42 3.8 15.8 1.0
C B:HIS223 3.9 15.2 1.0
CB B:ALA227 3.9 16.6 1.0
CD2 B:LEU202 4.0 16.8 1.0
CE2 B:PHE42 4.0 16.6 1.0
N B:ILE224 4.0 13.3 1.0
CB B:HIS223 4.1 16.7 1.0
CA B:ILE224 4.1 13.3 1.0
CG2 B:ILE219 4.2 14.9 1.0
CD2 B:LEU238 4.3 12.7 1.0
CG1 B:ILE224 4.3 13.2 1.0
CG2 B:ILE449 4.5 16.9 1.0
CG1 B:VAL439 4.6 25.8 1.0
CD1 B:LEU202 4.6 15.2 1.0
CA B:HIS223 4.6 15.2 1.0
CG B:LEU202 4.8 14.9 1.0
CB B:ILE224 4.9 11.5 1.0
CE1 B:PHE42 5.0 14.3 1.0

Xenon binding site 5 out of 16 in 7b2c

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Xenon binding site 5 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed 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 the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe510

b:46.8
occ:0.40
 SG B:CYS267 3.1 21.3 1.0
ND2 B:ASN273 3.7 25.9 1.0
CG2 B:ILE8 3.7 19.5 1.0
CB B:ALA272 3.8 15.1 1.0
SD B:MET325 3.9 16.4 1.0
CE B:MET325 4.0 12.5 1.0
O B:HOH876 4.1 37.3 1.0
CG B:ASN273 4.3 23.9 1.0
O B:HOH843 4.4 42.2 1.0
CD2 B:LEU263 4.6 12.0 1.0
CB B:ILE8 4.6 17.3 1.0
CB B:CYS267 4.7 14.4 1.0
O B:ALA272 4.7 18.3 1.0
CE1 B:TYR329 4.7 16.6 1.0
C B:ALA272 4.8 18.3 1.0
OD1 B:ASN273 4.8 23.4 1.0
CB B:ASN273 4.9 21.3 1.0
CA B:ALA272 4.9 16.6 1.0

Xenon binding site 6 out of 16 in 7b2c

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Xenon binding site 6 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed 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 the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe511

b:41.5
occ:0.50
 NH2 D:ARG152 1.5 40.1 0.5
CZ D:ARG152 1.7 38.9 0.5
NH1 D:ARG152 2.2 37.8 0.5
NE D:ARG152 2.5 36.6 0.5
CG D:ARG153 3.4 19.9 1.0
O B:ALA428 3.5 23.2 1.0
CD D:ARG152 3.6 32.7 0.5
O B:THR427 3.7 21.9 1.0
C B:ALA428 3.7 21.4 1.0
C B:THR427 3.7 21.3 1.0
CG D:ARG152 3.8 28.7 0.5
O B:GLY426 3.9 19.9 1.0
CG2 C:VAL55 3.9 22.7 1.0
N B:ALA428 4.0 22.3 1.0
CG2 B:VAL429 4.0 20.5 1.0
CD D:ARG153 4.1 21.6 1.0
CA B:ALA428 4.2 22.7 1.0
N B:VAL429 4.2 18.5 1.0
CB D:ARG152 4.2 24.9 0.5
CB D:ARG152 4.3 24.3 0.5
CA B:THR427 4.4 18.4 1.0
O D:HOH826 4.5 27.6 1.0
CB D:ARG153 4.6 21.1 1.0
CA B:VAL429 4.6 17.9 1.0
O C:VAL55 4.7 20.9 1.0
C B:GLY426 4.7 18.6 1.0
N D:ARG153 4.7 22.1 1.0
CA D:ARG153 4.8 22.2 1.0
C D:ARG152 4.8 23.4 1.0
O B:HOH759 4.9 34.4 1.0
CB B:VAL429 5.0 19.5 1.0
N B:THR427 5.0 17.5 1.0
NE D:ARG153 5.0 21.9 1.0

Xenon binding site 7 out of 16 in 7b2c

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Xenon binding site 7 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe304

b:18.1
occ:0.50
 OE2 C:GLU224 3.7 18.8 1.0
CD C:GLU224 3.7 21.4 1.0
CG C:ASP12 3.8 18.8 1.0
OD2 C:ASP12 3.8 22.0 1.0
CB C:ASP12 3.9 17.6 1.0
O C:HOH608 4.0 21.3 1.0
CG2 C:VAL14 4.0 19.2 1.0
CG C:GLU224 4.0 18.7 1.0
OE1 C:GLU224 4.1 21.6 1.0
CB C:GLU224 4.1 16.9 1.0
NH1 C:ARG240 4.1 20.0 1.0
CE1 C:TYR218 4.2 15.4 1.0
OD1 C:ASP12 4.2 18.3 1.0
NH1 C:ARG13 4.3 20.9 1.0
CZ C:ARG240 4.5 18.4 1.0
N C:VAL14 4.5 17.3 1.0
NH2 C:ARG240 4.5 16.5 1.0
CB C:VAL14 4.5 18.0 1.0
N C:ARG13 4.6 17.6 1.0
CD1 C:TYR218 4.7 14.9 1.0
CB C:ARG13 5.0 17.7 1.0

Xenon binding site 8 out of 16 in 7b2c

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Xenon binding site 8 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Xe305

b:34.1
occ:0.30
 CG2 C:VAL153 2.9 18.7 0.7
OH C:TYR187 3.4 21.0 1.0
CE C:MET202 3.6 22.4 1.0
O C:HOH464 3.6 15.0 1.0
CE1 C:TYR187 3.9 18.4 1.0
CD2 C:LEU42 3.9 21.9 1.0
CZ C:TYR187 3.9 19.9 1.0
CD1 C:PHE141 3.9 19.4 1.0
SG C:CYS146 4.0 21.9 1.0
CG C:PHE141 4.2 18.0 1.0
CB C:VAL153 4.2 18.4 1.0
CE C:MET90 4.2 15.4 1.0
N C:VAL153 4.3 17.2 1.0
CE1 C:PHE141 4.3 18.5 1.0
SD C:MET202 4.5 21.2 1.0
O C:ASP151 4.5 15.5 1.0
CB C:PHE141 4.6 18.1 1.0
CA C:PHE141 4.7 18.7 1.0
CD2 C:PHE141 4.7 17.1 1.0
CZ C:PHE141 4.9 17.8 1.0
C C:GLN152 4.9 17.9 1.0
CA C:GLN152 4.9 16.9 1.0
CA C:VAL153 4.9 17.1 1.0
CG C:LEU42 5.0 22.4 1.0
CD1 C:TYR187 5.0 17.4 1.0
CE2 C:TYR187 5.0 18.1 1.0

Xenon binding site 9 out of 16 in 7b2c

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Xenon binding site 9 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 9 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe708

b:10.0
occ:0.80
 CE2 D:TRP373 3.7 9.2 1.0
CD2 D:TRP373 3.7 8.3 1.0
S1 F:COM1102 3.8 11.3 1.0
S7 D:TP7701 3.9 10.8 1.0
OH E:TYR391 3.9 11.3 1.0
CE2 D:TYR376 3.9 9.3 1.0
NE1 D:TRP373 3.9 9.4 1.0
CG D:TRP373 4.0 8.0 1.0
C7 D:TP7701 4.0 11.1 1.0
CZ E:TYR391 4.1 10.8 1.0
CD1 D:TRP373 4.1 9.7 1.0
CE1 E:TYR391 4.1 10.9 1.0
CZ2 D:TRP373 4.2 9.5 1.0
CE3 D:TRP373 4.3 7.9 1.0
CG2 D:VAL527 4.3 8.8 1.0
CG1 D:VAL527 4.3 10.0 1.0
CZ D:TYR376 4.4 8.5 1.0
CD2 D:TYR376 4.4 9.7 1.0
OH D:TYR376 4.4 8.7 1.0
CH2 D:TRP373 4.6 7.8 1.0
CZ3 D:TRP373 4.7 7.8 1.0
CB D:TRP373 4.7 8.1 1.0
CE2 E:TYR391 4.8 11.2 1.0
CD1 E:TYR391 4.8 10.1 1.0
CHA F:USN1101 4.9 8.5 1.0
CB D:VAL527 4.9 9.7 1.0
C6 D:TP7701 5.0 10.3 1.0

Xenon binding site 10 out of 16 in 7b2c

Go back to Xenon Binding Sites List in 7b2c
Xenon binding site 10 out of 16 in the Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 10 of Crystal Structure of the Ethyl-Coenzyme M Reductase From Candidatus Ethanoperedens Thermophilum Gassed with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe709

b:13.3
occ:0.60
 CB D:ALA452 3.6 11.7 1.0
CA D:GLY532 3.8 10.3 1.0
CG1 D:VAL380 3.8 14.9 1.0
CS D:SMC354 3.8 9.1 1.0
SG D:SMC354 3.8 10.3 1.0
N D:GLY532 4.0 11.4 1.0
CB D:VAL380 4.1 14.4 1.0
CH2 D:TRP472 4.3 8.6 1.0
CD2 D:LEU350 4.3 9.2 1.0
CD2 D:LEU386 4.4 9.8 1.0
CZ3 D:TRP472 4.4 9.8 1.0
CD1 D:LEU350 4.4 12.6 1.0
CG2 D:VAL380 4.6 14.5 1.0
CG D:LEU350 4.9 11.0 1.0
O D:SER448 4.9 9.0 1.0
O D:GLY528 4.9 10.1 1.0
C D:GLY531 4.9 9.9 1.0

Reference:

C.J.Hahn, O.N.Lemaire, J.Kahnt, S.Engilberge, G.Wegener, T.Wagner. Crystal Structure of A Key Enzyme For Anaerobic Ethane Activation. Science V. 373 118 2021.
ISSN: ESSN 1095-9203
PubMed: 34210888
DOI: 10.1126/SCIENCE.ABG1765
Page generated: Sat Oct 12 19:56:34 2024

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