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Xenon in PDB 7b2h: Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon

Enzymatic activity of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon

All present enzymatic activity of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon:
2.8.4.1;

Protein crystallography data

The structure of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon, PDB code: 7b2h 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) 48.17 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.719, 116.386, 123.07, 90, 92.36, 90
R / Rfree (%) 17.7 / 20.4

Other elements in 7b2h:

The structure of Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 15 atoms
Potassium (K) 4 atoms
Chlorine (Cl) 2 atoms

Xenon Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Xenon atom in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon (pdb code 7b2h). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 12 binding sites of Xenon where determined in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon, PDB code: 7b2h:
Jump to Xenon binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Xenon binding site 1 out of 12 in 7b2h

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Xenon binding site 1 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe613

b:64.8
occ:0.60
 O A:ASP501 3.5 45.3 1.0
NE2 A:GLN192 3.7 50.7 1.0
O A:SER293 3.8 45.0 1.0
CA A:ALA497 3.9 46.6 1.0
CB A:TYR297 4.0 56.0 1.0
CB A:SER293 4.0 42.4 1.0
CA A:TYR297 4.1 55.6 1.0
O A:ALA497 4.2 47.9 1.0
CA A:SER293 4.2 43.5 1.0
C A:GLY500 4.3 58.1 1.0
CA A:GLY500 4.3 59.2 1.0
O A:HOH801 4.4 40.4 1.0
C A:SER293 4.4 43.7 1.0
O A:HIS496 4.4 48.1 1.0
O A:GLY500 4.5 62.5 1.0
O A:TYR297 4.5 58.5 1.0
C A:ASP501 4.5 47.0 1.0
CB A:ALA497 4.6 46.2 1.0
C A:ALA497 4.6 46.9 1.0
N A:ASP501 4.6 53.0 1.0
CG1 A:VAL303 4.7 39.8 1.0
N A:ALA497 4.8 45.4 1.0
CG2 A:VAL303 4.8 41.8 1.0
CD A:GLN192 4.8 51.2 1.0
C A:TYR297 4.9 58.7 1.0
N A:GLY500 4.9 56.6 1.0
C A:HIS496 4.9 45.2 1.0

Xenon binding site 2 out of 12 in 7b2h

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Xenon binding site 2 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe507

b:71.1
occ:0.40
 ND2 C:ASN247 3.6 64.7 1.0
OD1 C:ASN247 3.6 67.2 1.0
CG C:ASN247 3.7 64.4 1.0
CZ B:PHE349 3.8 52.2 1.0
N B:ALA300 4.1 45.3 1.0
O B:HOH636 4.2 44.5 1.0
O B:HOH642 4.2 48.5 1.0
CB B:LEU299 4.3 48.0 1.0
CB B:ALA300 4.3 44.4 1.0
CE2 B:PHE349 4.3 52.0 1.0
CA B:ALA300 4.3 43.5 1.0
SD B:MET236 4.3 63.5 1.0
CB B:MET236 4.5 52.3 1.0
C B:LEU299 4.7 45.4 1.0
CB C:ASN247 4.7 60.7 1.0
O B:HOH682 4.9 31.6 1.0
O C:GLY244 5.0 43.5 1.0
CG B:MET236 5.0 58.3 1.0
CE1 B:PHE349 5.0 52.6 1.0

Xenon binding site 3 out of 12 in 7b2h

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Xenon binding site 3 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe508

b:68.1
occ:0.25
 CB B:PHE121 3.6 47.5 1.0
CG B:PHE121 3.6 47.7 1.0
CB B:GLN40 3.7 57.5 1.0
CD2 B:PHE121 3.7 48.6 1.0
CG B:GLN40 3.7 61.8 1.0
O B:GLN40 3.8 51.3 1.0
CA B:GLN40 3.9 52.2 1.0
CD B:GLN40 4.1 66.0 1.0
CE B:LYS43 4.3 40.0 1.0
CB B:LYS43 4.3 41.5 1.0
C B:GLN40 4.3 50.6 1.0
CD B:LYS43 4.3 39.9 1.0
CD1 B:PHE121 4.3 46.8 1.0
OE1 B:GLN40 4.4 67.3 1.0
CE2 B:PHE121 4.4 48.7 1.0
CA B:SER118 4.6 55.6 1.0
NZ B:LYS43 4.7 39.7 1.0
OG B:SER118 4.7 60.0 1.0
CB B:SER118 4.7 58.4 1.0
CB B:ARG44 4.7 44.4 1.0
CD B:ARG44 4.7 51.0 1.0
NE2 B:GLN40 4.8 66.8 1.0
O B:SER118 4.8 53.6 1.0
CG B:LYS43 4.9 40.6 1.0

Xenon binding site 4 out of 12 in 7b2h

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Xenon binding site 4 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe509

b:71.9
occ:0.40
 SD B:MET405 3.5 64.1 1.0
CG2 C:VAL52 3.6 61.5 1.0
C B:THR403 3.6 48.6 1.0
O B:THR403 3.6 48.5 1.0
O B:GLY402 3.8 58.2 1.0
N B:GLN404 3.9 45.8 1.0
C B:GLN404 4.0 47.3 1.0
CA B:THR403 4.1 50.3 1.0
O B:GLN404 4.1 47.2 1.0
N B:MET405 4.1 49.2 1.0
CG B:MET405 4.2 60.5 1.0
O B:HOH735 4.3 72.6 1.0
CB D:ARG119 4.3 52.3 1.0
CA D:ARG119 4.4 56.4 1.0
CA B:GLN404 4.4 45.5 1.0
O D:LYS118 4.6 66.9 1.0
O C:VAL52 4.6 59.3 1.0
C B:GLY402 4.6 57.0 1.0
N D:ARG119 4.6 60.4 1.0
CA B:MET405 4.6 52.8 1.0
C D:LYS118 4.6 63.5 1.0
CG D:ARG119 4.7 51.2 1.0
N B:THR403 4.7 54.0 1.0
CD D:ARG119 4.8 49.5 1.0
CB D:LYS118 4.9 63.1 1.0
O B:HOH712 4.9 68.1 1.0

Xenon binding site 5 out of 12 in 7b2h

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Xenon binding site 5 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe510

b:100.3
occ:0.40
 CE1 B:PHE419 0.4 83.7 0.6
CZ B:PHE419 1.5 78.3 0.6
CD1 B:PHE419 1.7 78.4 0.6
CE2 B:PHE419 2.7 57.0 0.6
CG B:PHE419 2.8 55.2 0.6
CD2 B:PHE419 3.1 50.7 0.6
O B:ALA176 3.6 43.7 1.0
N B:ALA47 3.6 45.5 1.0
CB B:ALA47 3.6 46.9 1.0
CD1 B:ILE415 3.6 53.5 1.0
C B:VAL46 4.1 44.3 1.0
CB B:PHE419 4.2 47.5 0.6
CA B:ALA47 4.2 46.7 1.0
CG2 B:THR45 4.3 45.5 1.0
C B:ALA176 4.3 42.5 1.0
CA B:THR177 4.3 42.4 1.0
CA B:VAL46 4.4 43.0 1.0
O B:THR45 4.5 38.7 1.0
N B:PHE419 4.5 49.9 1.0
CG1 B:VAL418 4.6 55.2 1.0
N B:VAL46 4.6 41.8 1.0
C B:THR45 4.7 40.4 1.0
CB B:VAL418 4.7 55.3 1.0
N B:THR177 4.7 42.2 1.0
CA B:PHE419 4.7 49.2 1.0
C B:THR177 4.8 43.8 1.0
N B:MET178 4.8 45.2 1.0
O B:VAL46 4.8 43.5 1.0
CA B:ILE415 4.9 55.4 1.0

Xenon binding site 6 out of 12 in 7b2h

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Xenon binding site 6 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe511

b:47.1
occ:0.20
 CA B:THR136 3.4 39.4 1.0
N B:THR136 3.4 37.5 1.0
CB B:THR136 3.4 38.4 1.0
CE B:LYS157 3.6 35.2 1.0
O D:ILE460 3.7 38.2 1.0
N D:GLY462 3.8 40.2 1.0
CD B:LYS157 3.8 36.5 1.0
OG1 B:THR136 3.9 39.9 1.0
C B:ALA135 3.9 39.5 1.0
CA D:GLY462 4.0 38.3 1.0
CB B:ALA135 4.0 40.9 1.0
C D:ARG461 4.2 41.9 1.0
CD2 B:LEU161 4.3 34.5 1.0
O B:ALA135 4.3 41.3 1.0
O E:HOH616 4.4 37.9 1.0
CG2 B:VAL139 4.5 44.6 1.0
CA D:ARG461 4.5 42.0 1.0
O B:LEU132 4.5 41.0 1.0
CA B:ALA135 4.6 41.0 1.0
CG2 B:THR136 4.8 38.6 1.0
C B:THR136 4.8 42.8 1.0
C D:ILE460 4.8 38.0 1.0
CB B:VAL139 4.9 44.9 1.0
O D:ARG461 4.9 41.6 1.0

Xenon binding site 7 out of 12 in 7b2h

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Xenon binding site 7 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe609

b:62.5
occ:0.60
 O D:ASP501 3.5 40.4 1.0
O D:SER293 3.7 36.7 1.0
NE2 D:GLN192 3.7 44.5 1.0
CB D:TYR297 4.0 49.3 1.0
CB D:SER293 4.0 34.1 1.0
CA D:ALA497 4.0 42.9 1.0
CA D:TYR297 4.1 49.2 1.0
CA D:SER293 4.2 33.6 1.0
O D:ALA497 4.3 44.8 1.0
C D:GLY500 4.3 44.5 1.0
C D:SER293 4.3 35.6 1.0
CA D:GLY500 4.4 44.1 1.0
O D:HIS496 4.4 39.0 1.0
O D:HOH809 4.5 35.8 1.0
O D:TYR297 4.5 53.1 1.0
O D:GLY500 4.5 45.1 1.0
C D:ASP501 4.6 40.8 1.0
CB D:ALA497 4.6 42.2 1.0
C D:ALA497 4.6 46.4 1.0
CG1 D:VAL303 4.7 36.2 1.0
N D:ASP501 4.7 43.6 1.0
CG2 D:VAL303 4.7 37.5 1.0
CD D:GLN192 4.8 44.6 1.0
C D:TYR297 4.8 53.2 1.0
N D:ALA497 4.9 39.6 1.0
N D:GLY500 5.0 43.9 1.0

Xenon binding site 8 out of 12 in 7b2h

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Xenon binding site 8 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe506

b:62.3
occ:0.20
 SD E:MET405 3.0 70.4 1.0
O E:THR403 3.6 69.2 1.0
C E:THR403 3.7 68.0 1.0
O E:GLY402 3.7 90.5 1.0
C E:GLN404 3.9 63.3 1.0
C3 E:PEG502 4.0 91.3 1.0
N E:GLN404 4.0 65.9 1.0
CG E:MET405 4.0 66.9 1.0
O4 E:PEG502 4.0 92.8 1.0
N E:MET405 4.0 62.5 1.0
O E:GLN404 4.0 63.2 1.0
CA E:THR403 4.2 72.7 1.0
CB A:ARG119 4.3 56.5 0.9
CD A:ARG119 4.3 54.1 0.9
CA E:GLN404 4.3 64.0 1.0
CA A:ARG119 4.4 58.9 0.9
CG A:ARG119 4.4 55.5 0.9
CA E:MET405 4.5 61.7 1.0
CE E:MET405 4.6 72.0 1.0
C4 E:PEG502 4.6 92.2 1.0
C E:GLY402 4.6 88.0 1.0
N A:ARG119 4.7 60.1 0.9
O F:VAL52 4.8 78.3 1.0
CB E:MET405 4.8 63.9 1.0
O A:LYS118 4.9 65.0 1.0
N E:THR403 4.9 81.8 1.0
C A:LYS118 4.9 61.6 1.0

Xenon binding site 9 out of 12 in 7b2h

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Xenon binding site 9 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe507

b:46.0
occ:0.20
 CB E:ALA203 2.9 55.3 1.0
SD E:MET178 3.2 63.0 1.0
CD1 E:LEU214 3.4 59.9 1.0
CE E:MET178 3.8 66.0 1.0
O E:HIS199 4.0 51.3 1.0
CA E:VAL200 4.1 54.4 1.0
CG E:LEU214 4.3 60.7 1.0
CA E:ALA203 4.3 57.0 1.0
O E:VAL200 4.4 53.0 1.0
CB E:PHE425 4.4 68.1 1.0
C E:HIS199 4.6 51.9 1.0
O E:PHE425 4.6 70.2 1.0
N E:VAL200 4.7 52.4 1.0
C E:VAL200 4.7 55.5 1.0
N E:ALA203 4.8 58.8 1.0
CG2 E:VAL200 4.9 54.4 1.0
CB E:VAL200 4.9 54.5 1.0
C E:ALA203 4.9 55.4 1.0
CG E:MET178 5.0 56.5 1.0
CG E:PHE425 5.0 67.1 1.0

Xenon binding site 10 out of 12 in 7b2h

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Xenon binding site 10 out of 12 in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized 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 Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe508

b:65.4
occ:0.40
 CE1 E:PHE419 0.3 62.1 0.6
CZ E:PHE419 1.1 60.4 0.6
CD1 E:PHE419 1.6 60.6 0.6
CE2 E:PHE419 2.2 55.9 0.6
CG E:PHE419 2.5 55.3 0.6
CD2 E:PHE419 2.7 54.0 0.6
CD1 E:ILE415 3.4 56.9 1.0
N E:ALA47 3.9 43.4 1.0
O E:ALA176 3.9 38.5 1.0
CB E:ALA47 3.9 44.8 1.0
CB E:PHE419 3.9 55.2 0.6
CA E:THR177 4.4 43.8 1.0
C E:VAL46 4.4 43.3 1.0
C E:ALA176 4.4 41.5 1.0
CG2 E:THR45 4.5 41.2 1.0
CA E:ALA47 4.5 45.0 1.0
N E:PHE419 4.5 60.1 1.0
O E:THR45 4.7 39.5 1.0
N E:THR177 4.7 42.8 1.0
CA E:PHE419 4.7 58.0 1.0
CA E:VAL46 4.7 41.1 1.0
C E:THR177 4.7 42.8 1.0
CG1 E:VAL418 4.8 66.2 1.0
N E:MET178 4.8 44.4 1.0
CG1 E:ILE415 4.8 57.5 1.0
CA E:ILE415 4.8 61.4 1.0
CB E:VAL418 4.8 65.4 1.0
CG E:MET178 4.8 56.5 1.0
C E:THR45 4.9 41.0 1.0
N E:VAL46 4.9 41.5 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 19:57:44 2024

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