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Potassium 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
Xenon (Xe) 12 atoms
Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis Derivatized with Xenon, PDB code: 7b2h:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 7b2h

Go back to Potassium Binding Sites List in 7b2h
Potassium binding site 1 out of 4 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 Potassium with other atoms in the K 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:K603

b:47.3
occ:1.00
 O D:CYS218 2.6 30.5 1.0
O A:CYS218 2.8 27.5 1.0
O A:ARG216 2.9 29.0 1.0
O D:ARG216 2.9 31.0 1.0
O A:SER215 3.4 30.6 1.0
O D:SER215 3.4 29.8 1.0
NH1 A:ARG102 3.4 29.4 1.0
NH1 D:ARG102 3.4 29.4 1.0
C A:ARG216 3.6 28.9 1.0
C D:ARG216 3.6 29.3 1.0
O A:HOH750 3.7 27.7 1.0
O A:HOH736 3.8 29.3 1.0
C D:CYS218 3.8 30.0 1.0
CA A:ARG216 3.9 29.0 1.0
C A:CYS218 3.9 27.3 1.0
CA D:ARG216 3.9 29.3 1.0
CZ D:ARG102 4.0 26.4 1.0
CZ A:ARG102 4.0 29.0 1.0
NH2 D:ARG102 4.0 24.7 1.0
NH2 A:ARG102 4.1 29.3 1.0
N A:CYS218 4.4 26.0 1.0
C A:SER215 4.4 29.8 1.0
C D:SER215 4.4 30.9 1.0
C A:THR217 4.5 25.1 1.0
N D:CYS218 4.6 26.5 1.0
CA D:ASP219 4.6 27.6 1.0
C D:THR217 4.6 27.4 1.0
N A:THR217 4.6 28.5 1.0
CA A:ASP219 4.6 27.2 1.0
N A:ARG216 4.7 28.9 1.0
N D:ARG216 4.7 30.6 1.0
N A:ASP219 4.7 26.0 1.0
N D:THR217 4.7 27.1 1.0
N D:ASP219 4.7 28.8 1.0
O D:THR217 4.7 29.4 1.0
CA A:CYS218 4.8 26.5 1.0
CA D:CYS218 4.8 28.1 1.0
O A:THR217 4.8 25.9 1.0

Potassium binding site 2 out of 4 in 7b2h

Go back to Potassium Binding Sites List in 7b2h
Potassium binding site 2 out of 4 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 Potassium with other atoms in the K 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
A:K615

b:70.2
occ:1.00
 O A:ILE60 2.5 49.2 1.0
O A:HOH836 2.6 40.3 1.0
O A:THR62 2.6 43.3 1.0
O A:PRO58 2.7 45.2 1.0
C A:PRO58 3.6 48.0 1.0
C A:THR62 3.7 45.0 1.0
C A:ILE60 3.7 49.4 1.0
O D:HOH727 3.8 43.6 1.0
O A:HOH858 3.9 48.4 1.0
CA A:PRO58 4.0 44.6 1.0
N A:THR62 4.2 45.3 1.0
C A:GLY61 4.2 47.5 1.0
N A:ILE60 4.3 51.2 1.0
CA A:PRO63 4.3 46.1 1.0
O A:HOH794 4.4 44.6 1.0
N A:PRO63 4.4 46.0 1.0
O A:ASN57 4.4 43.2 1.0
N A:LEU64 4.5 48.1 1.0
O D:ALA144 4.5 40.3 1.0
O A:GLY61 4.5 48.4 1.0
N A:ASP59 4.5 52.3 1.0
CA A:THR62 4.6 44.9 1.0
CA A:ILE60 4.6 49.2 1.0
CA A:GLY61 4.6 48.7 1.0
N A:GLY61 4.6 49.4 1.0
C A:ASP59 4.7 53.5 1.0
CA A:ASP59 4.9 55.6 1.0
CG A:LEU64 4.9 45.5 1.0
C A:PRO63 5.0 47.0 1.0
CB A:PRO58 5.0 43.0 1.0

Potassium binding site 3 out of 4 in 7b2h

Go back to Potassium Binding Sites List in 7b2h
Potassium binding site 3 out of 4 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 Potassium with other atoms in the K 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:K513

b:77.5
occ:1.00
 OD1 B:ASN303 3.0 38.3 1.0
O B:SER346 3.1 38.2 1.0
CE1 B:PHE349 3.1 52.6 1.0
CD1 B:PHE349 3.3 51.5 1.0
CB B:ASN303 3.5 39.4 1.0
O B:PRO345 3.5 41.5 1.0
CG B:ASN303 3.6 38.5 1.0
CD1 B:TRP302 3.8 46.1 1.0
CA B:ASN303 3.8 40.2 1.0
C B:SER346 4.0 38.8 1.0
CG B:PRO345 4.0 46.2 1.0
C B:PRO345 4.1 42.1 1.0
NE1 B:TRP302 4.2 45.6 1.0
CZ B:PHE349 4.2 52.2 1.0
N B:ASN303 4.2 42.4 1.0
N B:PHE349 4.3 42.4 1.0
CB B:PRO345 4.4 45.2 1.0
CD2 B:LEU299 4.4 49.4 1.0
CG B:PHE349 4.5 49.5 1.0
N B:ASP348 4.5 39.9 1.0
O B:LEU299 4.5 44.0 1.0
CA B:VAL347 4.6 38.7 1.0
N B:VAL347 4.7 38.8 1.0
N B:SER346 4.7 39.2 1.0
CA B:PHE349 4.8 44.1 1.0
CA B:PRO345 4.8 44.1 1.0
CA B:SER346 4.8 39.1 1.0
C B:VAL347 4.8 38.9 1.0
ND2 B:ASN303 4.9 37.0 1.0
CG B:TRP302 4.9 46.6 1.0

Potassium binding site 4 out of 4 in 7b2h

Go back to Potassium Binding Sites List in 7b2h
Potassium binding site 4 out of 4 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 Potassium with other atoms in the K 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
D:K610

b:82.9
occ:1.00
 O A:ALA144 2.8 45.8 1.0
O D:THR62 2.8 57.5 1.0
O A:HOH751 3.1 44.3 1.0
O D:ILE60 3.3 58.7 1.0
C A:ALA144 3.6 45.9 1.0
CA A:VAL145 4.0 49.1 1.0
C D:THR62 4.0 58.6 1.0
CG D:LEU64 4.1 55.2 1.0
N A:VAL145 4.1 47.1 1.0
N D:THR62 4.2 53.6 1.0
C A:VAL145 4.4 49.8 1.0
C D:ILE60 4.5 57.2 1.0
CD1 D:LEU64 4.5 54.1 1.0
CB A:ALA144 4.6 43.1 1.0
CD2 D:LEU64 4.6 54.6 1.0
NE2 A:HIS138 4.6 37.2 1.0
C D:GLY61 4.6 52.6 1.0
CA A:ALA144 4.6 43.6 1.0
O D:PRO58 4.7 65.9 1.0
O A:VAL145 4.7 51.7 1.0
CA D:THR62 4.7 56.6 1.0
N D:LEU64 4.7 57.4 1.0
OG1 D:THR62 4.7 53.8 1.0
CA D:GLY61 4.8 51.5 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: Mon Aug 12 18:43:36 2024

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