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Xenon in PDB 7sxm: Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis

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

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

Protein crystallography data

The structure of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis, PDB code: 7sxm was solved by P.Y.-T.Chen, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.63 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.956, 115.741, 123.4, 90, 92.53, 90
R / Rfree (%) 17.8 / 21.8

Other elements in 7sxm:

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

Magnesium (Mg) 2 atoms
Nickel (Ni) 2 atoms
Sodium (Na) 1 atom

Xenon Binding Sites:

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

Xenon binding site 1 out of 8 in 7sxm

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Xenon binding site 1 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe610

b:46.7
occ:0.40
 O A:SER293 3.6 36.8 1.0
O A:ASP501 3.7 36.4 1.0
NE2 A:GLN192 3.7 39.4 1.0
O A:HOH856 3.7 42.7 1.0
CB A:SER293 3.9 31.7 1.0
CA A:ALA497 4.0 35.1 1.0
CA A:SER293 4.1 34.0 1.0
O A:ALA497 4.2 35.3 1.0
CB A:TYR297 4.2 42.2 1.0
CA A:TYR297 4.2 41.7 1.0
O A:HOH803 4.2 32.4 1.0
C A:SER293 4.3 37.2 1.0
CA A:GLY500 4.4 35.3 1.0
C A:GLY500 4.4 38.4 1.0
O A:HIS496 4.5 36.4 1.0
CB A:ALA497 4.5 33.3 1.0
C A:ALA497 4.6 35.7 1.0
O A:TYR297 4.6 47.4 1.0
O A:GLY500 4.7 42.0 1.0
CG1 A:VAL303 4.7 30.0 1.0
N A:ASP501 4.7 37.0 1.0
CG2 A:VAL303 4.7 34.7 1.0
C A:ASP501 4.7 35.9 1.0
N A:ALA497 4.8 34.3 1.0
CD A:GLN192 4.9 39.7 1.0
C A:TYR297 5.0 44.1 1.0
N A:GLY500 5.0 41.1 1.0

Xenon binding site 2 out of 8 in 7sxm

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Xenon binding site 2 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe501

b:51.4
occ:0.40
 CE2 B:PHE419 2.5 53.7 0.4
CD2 B:PHE419 2.8 53.6 0.4
CD2 B:LEU214 3.6 54.1 1.0
CB B:ALA203 3.6 55.3 1.0
CE B:MET178 3.6 56.2 1.0
CZ B:PHE419 3.8 51.9 0.4
CB B:PHE425 3.9 57.1 1.0
SD B:MET178 4.0 56.2 1.0
CG B:PHE419 4.2 52.2 0.4
O B:HIS199 4.3 50.2 1.0
CA B:VAL200 4.4 50.1 1.0
O B:PHE425 4.4 58.8 1.0
CG B:PHE425 4.5 56.0 1.0
CG B:LEU214 4.7 49.1 1.0
O B:VAL200 4.7 49.1 1.0
CA B:PHE425 4.8 57.7 1.0
CA B:ALA203 4.8 59.5 1.0
C B:PHE425 4.8 60.2 1.0
CE1 B:PHE419 4.9 50.5 0.4
C B:HIS199 4.9 50.2 1.0
CG2 B:VAL200 5.0 46.6 1.0

Xenon binding site 3 out of 8 in 7sxm

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Xenon binding site 3 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe502

b:47.9
occ:0.40
 CE1 B:PHE419 0.5 47.4 0.6
CZ B:PHE419 1.2 45.4 0.6
CD1 B:PHE419 1.7 50.0 0.6
CE2 B:PHE419 2.3 46.1 0.6
CG B:PHE419 2.7 50.2 0.6
CD2 B:PHE419 2.9 49.1 0.6
O B:ALA176 3.6 39.9 1.0
N B:ALA47 3.7 35.2 1.0
CB B:ALA47 3.7 36.1 1.0
CD1 B:PHE419 3.8 50.4 0.4
CD1 B:ILE415 4.0 48.3 1.0
CB B:PHE419 4.1 52.7 0.6
CB B:PHE419 4.1 52.7 0.4
C B:VAL46 4.2 37.4 1.0
CA B:THR177 4.2 40.1 1.0
C B:ALA176 4.3 38.4 1.0
CA B:ALA47 4.3 36.9 1.0
O B:THR45 4.3 37.6 1.0
CG B:PHE419 4.4 52.2 0.4
CA B:VAL46 4.4 37.1 1.0
CG2 B:THR45 4.5 38.6 1.0
CG1 B:VAL418 4.5 44.7 1.0
N B:PHE419 4.6 53.0 1.0
C B:THR177 4.6 41.7 1.0
N B:THR177 4.6 41.3 1.0
C B:THR45 4.6 38.5 1.0
CA B:PHE419 4.7 54.3 0.4
CA B:PHE419 4.7 54.4 0.6
N B:VAL46 4.7 36.9 1.0
CE1 B:PHE419 4.7 50.5 0.4
N B:MET178 4.8 41.6 1.0
CB B:VAL418 4.8 50.3 1.0
CG B:MET178 4.8 45.3 1.0
O B:VAL46 5.0 38.5 1.0

Xenon binding site 4 out of 8 in 7sxm

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Xenon binding site 4 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 4 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Xe503

b:40.5
occ:0.20
 CG2 B:VAL393 3.6 39.6 1.0
CG2 B:THR382 3.7 30.7 1.0
CB B:ALA389 3.8 26.4 1.0
CG2 B:THR355 3.8 26.4 1.0
CD2 B:PHE359 3.8 34.4 1.0
CD1 B:LEU331 4.0 34.8 1.0
CD1 B:ILE390 4.0 32.6 1.0
C B:ALA389 4.0 34.0 1.0
CB B:THR382 4.1 30.2 1.0
O B:ALA389 4.1 32.0 1.0
N B:ILE390 4.2 33.0 1.0
CG B:PHE359 4.2 31.0 1.0
CE2 B:PHE359 4.2 34.9 1.0
CA B:ILE390 4.4 33.5 1.0
CG1 B:ILE390 4.5 33.3 1.0
CB B:PHE359 4.5 29.4 1.0
CA B:ALA389 4.6 31.2 1.0
CB B:VAL393 4.8 41.7 1.0
CD1 B:PHE359 4.9 36.7 1.0
CZ B:PHE359 4.9 37.0 1.0
CA B:THR382 5.0 28.4 1.0

Xenon binding site 5 out of 8 in 7sxm

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Xenon binding site 5 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 5 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Xe603

b:49.6
occ:0.40
 O D:SER293 3.5 35.8 1.0
NE2 D:GLN192 3.6 33.5 1.0
O D:ASP501 3.7 33.2 1.0
CB D:SER293 3.9 27.9 1.0
O D:HOH864 3.9 40.7 1.0
CA D:ALA497 3.9 30.6 1.0
CA D:SER293 4.1 28.8 1.0
CB D:TYR297 4.1 35.9 1.0
CA D:TYR297 4.1 37.2 1.0
C D:SER293 4.2 30.3 1.0
O D:ALA497 4.2 34.7 1.0
O D:HIS496 4.4 29.2 1.0
CB D:ALA497 4.5 28.1 1.0
CA D:GLY500 4.5 28.6 1.0
O D:TYR297 4.5 43.9 1.0
C D:GLY500 4.5 34.6 1.0
O D:HOH853 4.5 28.0 1.0
C D:ALA497 4.6 34.2 1.0
CG2 D:VAL303 4.6 30.6 1.0
CG1 D:VAL303 4.6 25.9 1.0
C D:ASP501 4.8 33.1 1.0
O D:GLY500 4.8 36.2 1.0
CD D:GLN192 4.8 32.3 1.0
N D:ASP501 4.8 30.9 1.0
N D:ALA497 4.8 32.8 1.0
C D:TYR297 4.8 39.8 1.0

Xenon binding site 6 out of 8 in 7sxm

Go back to Xenon Binding Sites List in 7sxm
Xenon binding site 6 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 6 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe501

b:45.4
occ:0.40
 CE2 E:PHE419 3.4 59.0 0.4
CD2 E:PHE419 3.5 59.5 0.4
CD2 E:LEU214 3.6 66.3 1.0
CE E:MET178 3.7 53.5 1.0
CB E:ALA203 3.7 64.8 1.0
CA E:VAL200 3.9 63.1 1.0
O E:HIS199 4.0 59.2 1.0
CB E:PHE425 4.2 69.0 1.0
SD E:MET178 4.3 54.5 1.0
O E:VAL200 4.3 62.5 1.0
CG2 E:VAL200 4.3 61.7 1.0
CB E:VAL200 4.5 62.8 1.0
N E:VAL200 4.6 62.4 1.0
CG E:LEU214 4.6 62.9 1.0
C E:HIS199 4.6 58.1 1.0
C E:VAL200 4.6 59.4 1.0
CG E:PHE425 4.7 66.0 1.0
CZ E:PHE419 4.7 55.9 0.4
CG1 E:VAL200 4.7 58.0 1.0
O E:PHE425 4.8 72.1 1.0
CA E:ALA203 4.8 68.5 1.0
CG E:PHE419 4.9 57.7 0.4
C E:ALA203 4.9 67.7 1.0
CG2 E:THR204 4.9 67.4 1.0

Xenon binding site 7 out of 8 in 7sxm

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Xenon binding site 7 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 7 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe502

b:47.7
occ:0.40
 CE1 E:PHE419 0.4 49.0 0.6
CZ E:PHE419 1.2 47.2 0.6
CD1 E:PHE419 1.8 56.5 0.6
CE2 E:PHE419 2.4 49.6 0.6
CG E:PHE419 2.7 58.0 0.6
CD2 E:PHE419 2.9 55.4 0.6
O E:ALA176 3.6 37.2 1.0
CD1 E:PHE419 3.7 56.2 0.4
CD1 E:ILE415 3.8 51.6 1.0
CB E:ALA47 3.8 41.1 1.0
N E:ALA47 3.8 36.5 1.0
CA E:THR177 4.1 35.2 1.0
CB E:PHE419 4.1 61.1 0.6
C E:ALA176 4.2 37.1 1.0
CB E:PHE419 4.2 61.0 0.4
CG E:PHE419 4.3 57.7 0.4
C E:VAL46 4.4 39.4 1.0
O E:THR45 4.4 40.2 1.0
CA E:ALA47 4.4 40.0 1.0
CE1 E:PHE419 4.4 54.8 0.4
C E:THR177 4.5 34.0 1.0
N E:THR177 4.5 35.4 1.0
CA E:VAL46 4.6 38.6 1.0
CG E:MET178 4.6 46.5 1.0
N E:MET178 4.6 37.5 1.0
CG2 E:THR45 4.7 39.3 1.0
CG1 E:VAL418 4.7 55.2 1.0
C E:THR45 4.7 39.5 1.0
N E:PHE419 4.8 65.5 1.0
CG2 E:ILE415 4.8 57.3 1.0
CA E:ILE415 4.8 64.8 1.0
CA E:PHE419 4.8 64.1 0.4
N E:VAL46 4.8 36.3 1.0
CA E:PHE419 4.8 64.1 0.6
CB E:ALA176 4.9 34.3 1.0
CB E:VAL418 5.0 63.5 1.0

Xenon binding site 8 out of 8 in 7sxm

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Xenon binding site 8 out of 8 in the Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 8 of Structure of Xenon-Derivatized Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Xe503

b:40.4
occ:0.20
 CG2 E:VAL393 3.7 44.2 1.0
CD2 E:PHE359 3.7 40.5 1.0
CG2 E:THR355 3.8 28.7 1.0
CG2 E:THR382 3.8 32.9 1.0
CB E:ALA389 3.8 35.0 1.0
CD1 E:LEU331 3.9 39.4 1.0
CD1 E:ILE390 4.0 40.1 1.0
C E:ALA389 4.0 44.1 1.0
O E:ALA389 4.0 45.2 1.0
CG E:PHE359 4.1 37.2 1.0
CE2 E:PHE359 4.1 44.2 1.0
CB E:THR382 4.1 34.4 1.0
N E:ILE390 4.2 39.6 1.0
CB E:PHE359 4.4 33.5 1.0
CA E:ILE390 4.4 42.7 1.0
CG1 E:ILE390 4.5 40.0 1.0
CA E:ALA389 4.6 40.3 1.0
CD1 E:PHE359 4.8 38.7 1.0
CZ E:PHE359 4.8 44.1 1.0
CB E:VAL393 5.0 48.0 1.0
CB E:THR355 5.0 28.9 1.0

Reference:

C.J.Ohmer, M.Dasgupta, A.Patwardhan, I.Bogacz, C.Kaminsky, M.D.Doyle, P.Y.Chen, S.M.Keable, H.Makita, P.S.Simon, R.Massad, T.Fransson, R.Chatterjee, A.Bhowmick, D.W.Paley, N.W.Moriarty, A.S.Brewster, L.B.Gee, R.Alonso-Mori, F.Moss, F.D.Fuller, A.Batyuk, N.K.Sauter, U.Bergmann, C.L.Drennan, V.K.Yachandra, J.Yano, J.F.Kern, S.W.Ragsdale. Xfel Serial Crystallography Reveals the Room Temperature Structure of Methyl-Coenzyme M Reductase. J.Inorg.Biochem. V. 230 11768 2022.
ISSN: ISSN 0162-0134
PubMed: 35202981
DOI: 10.1016/J.JINORGBIO.2022.111768
Page generated: Sat Oct 12 20:05:52 2024

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