Sodium in PDB 5a0y: Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution

All present enzymatic activity of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution:
2.8.4.1;

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y was solved by T.Wagner, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.35 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.227, 118.300, 122.560, 90.00, 91.90, 90.00
R / Rfree (%)	11.1 / 12.9

The structure of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Magnesium	(Mg)	16 atoms
Potassium	(K)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution (pdb code 5a0y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution, PDB code: 5a0y:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na564 b:15.9 occ:1.00 O A:HOH2161 2.3 14.1 1.0 O A:THR62 2.3 12.5 1.0 O A:ILE60 2.4 13.8 1.0 O A:HOH2178 2.4 12.2 1.0 O A:HOH2169 2.9 19.3 1.0 O A:HOH2168 3.2 16.1 1.0 O A:PRO58 3.2 15.9 1.0 C A:THR62 3.4 11.6 1.0 C A:ILE60 3.5 12.9 1.0 N A:THR62 3.8 11.3 1.0 C A:GLY61 3.8 12.0 1.0 O A:HOH2160 4.0 11.4 1.0 C A:PRO58 4.0 13.2 1.0 O A:GLY61 4.1 14.0 1.0 CA A:THR62 4.2 11.4 1.0 N A:ILE60 4.2 12.8 1.0 N A:PRO63 4.2 11.7 1.0 O D:ALA144 4.3 8.7 1.0 CA A:PRO63 4.3 12.7 1.0 CA A:GLY61 4.4 12.2 1.0 O A:HOH2177 4.4 13.2 1.0 N A:GLY61 4.4 12.3 1.0 CA A:ILE60 4.5 12.8 1.0 N A:LEU64 4.6 12.1 1.0 CA A:PRO58 4.6 12.8 1.0 O A:HOH2159 4.6 16.7 1.0 C A:ASP59 4.7 13.0 1.0 O A:ASN57 4.7 10.5 1.0 N A:ASP59 4.8 12.0 1.0 CA A:ASP59 5.0 13.4 1.0 C A:PRO63 5.0 12.0 1.0

Sodium binding site 2 out of 2 in the Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Methyl-Coenzyme M Reductase From Methanothermobacter Marburgensis at 1.1 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Na558 b:14.6 occ:1.00 O A:HOH2291 2.3 12.4 1.0 O D:ILE60 2.3 12.3 1.0 O A:HOH2288 2.3 16.1 1.0 O D:THR62 2.3 11.2 1.0 O D:HOH2178 2.8 20.2 1.0 O D:PRO58 3.0 15.8 1.0 O D:HOH2179 3.3 14.5 1.0 C D:THR62 3.3 10.0 1.0 C D:ILE60 3.5 10.6 1.0 N D:THR62 3.7 10.9 1.0 C D:GLY61 3.8 12.4 1.0 C D:PRO58 3.8 12.8 1.0 O A:HOH2289 4.0 11.2 1.0 O D:GLY61 4.0 15.7 1.0 CA D:THR62 4.1 10.4 1.0 N D:ILE60 4.2 10.6 1.0 N D:PRO63 4.2 10.6 1.0 CA D:PRO63 4.3 10.8 1.0 O A:ALA144 4.3 7.6 1.0 CA D:GLY61 4.4 12.1 1.0 N D:GLY61 4.4 11.9 1.0 O A:HOH2293 4.4 11.0 1.0 CA D:ILE60 4.4 11.5 1.0 C D:ASP59 4.5 11.7 1.0 CA D:PRO58 4.5 12.0 1.0 N D:ASP59 4.6 11.9 1.0 N D:LEU64 4.6 10.5 1.0 CA D:ASP59 4.7 13.1 1.0 O D:ASN57 4.7 9.0 1.0 O D:HOH2172 4.8 15.2 1.0 C D:PRO63 5.0 10.5 1.0

T.Wagner, J.Kahnt, U.Ermler, S.Shima. Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation. Angew.Chem.Int.Ed.Engl. V. 55 10630 2016.
ISSN: ISSN 1433-7851
PubMed: 27467699
DOI: 10.1002/ANIE.201603882