Atomistry » Sodium » PDB 5fje-5g3f » 5g0r
Atomistry »
  Sodium »
    PDB 5fje-5g3f »
      5g0r »

Sodium in PDB 5g0r: Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol

Enzymatic activity of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol

All present enzymatic activity of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol:
2.8.4.1;

Protein crystallography data

The structure of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol, PDB code: 5g0r was solved by T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.80 / 1.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.200, 118.101, 122.640, 90.00, 92.03, 90.00
R / Rfree (%) 10.5 / 12.4

Other elements in 5g0r:

The structure of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol also contains other interesting chemical elements:

Nickel (Ni) 2 atoms
Magnesium (Mg) 18 atoms
Potassium (K) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol (pdb code 5g0r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol, PDB code: 5g0r:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 5g0r

Go back to Sodium Binding Sites List in 5g0r
Sodium binding site 1 out of 3 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


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 I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na564

b:14.1
occ:1.00
 O A:HOH2148 2.3 13.4 1.0
O A:ILE60 2.3 13.5 1.0
O A:THR62 2.3 13.1 1.0
O A:HOH2163 2.4 11.1 1.0
O A:HOH2155 2.9 20.4 1.0
O A:HOH2154 3.1 14.8 1.0
O A:PRO58 3.2 16.6 1.0
C A:THR62 3.4 12.0 1.0
C A:ILE60 3.5 12.3 1.0
N A:THR62 3.8 11.3 1.0
C A:GLY61 3.8 11.7 1.0
C A:PRO58 4.0 13.7 1.0
O A:HOH2147 4.0 11.4 1.0
O A:GLY61 4.1 13.4 1.0
CA A:THR62 4.2 11.2 1.0
N A:ILE60 4.2 12.7 1.0
N A:PRO63 4.2 12.7 1.0
CA A:PRO63 4.3 13.2 1.0
O D:ALA144 4.3 9.2 1.0
CA A:GLY61 4.4 11.6 1.0
N A:GLY61 4.4 11.9 1.0
O A:HOH2162 4.4 12.0 1.0
CA A:ILE60 4.5 12.5 1.0
N A:LEU64 4.5 13.0 1.0
CA A:PRO58 4.6 13.5 1.0
C A:ASP59 4.6 14.2 1.0
O A:HOH2146 4.7 15.5 1.0
O A:ASN57 4.7 11.1 1.0
N A:ASP59 4.8 12.7 1.0
CA A:ASP59 5.0 14.6 1.0
C A:PRO63 5.0 13.3 1.0

Sodium binding site 2 out of 3 in 5g0r

Go back to Sodium Binding Sites List in 5g0r
Sodium binding site 2 out of 3 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


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 I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1502

b:16.7
occ:1.00
 O A:HOH2256 3.1 12.1 1.0
O D:HOH2169 3.2 32.5 1.0
N D:GLY61 3.2 10.9 1.0
CE1 A:HIS131 3.5 15.7 1.0
CA D:ILE60 3.9 10.9 1.0
NE2 A:HIS131 4.0 14.9 1.0
C D:ILE60 4.0 10.6 1.0
CA D:GLY61 4.1 11.7 1.0
O D:ASP59 4.2 14.3 1.0
O A:HOH2255 4.3 17.4 1.0
CD1 D:ILE60 4.3 15.5 1.0
CG2 D:ILE60 4.4 11.6 1.0
ND1 A:HIS131 4.6 15.3 1.0
CB D:ILE60 4.7 11.2 1.0
OG1 A:THR135 4.7 10.0 1.0
OG A:SER237 4.8 10.8 1.0
O D:GLY61 4.8 13.7 1.0
N D:ILE60 5.0 11.4 1.0
C D:GLY61 5.0 11.6 1.0

Sodium binding site 3 out of 3 in 5g0r

Go back to Sodium Binding Sites List in 5g0r
Sodium binding site 3 out of 3 in the Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Methyl-Coenzyme M Reductase I From Methanothermobacter Marburgensis Exposed to 3-Nitrooxypropanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na558

b:13.6
occ:1.00
 O A:HOH2265 2.3 15.1 1.0
O D:ILE60 2.3 12.0 1.0
O D:THR62 2.3 11.7 1.0
O A:HOH2268 2.4 12.1 1.0
O D:HOH2166 2.8 20.4 1.0
O D:PRO58 3.0 16.1 1.0
O D:HOH2167 3.2 16.7 1.0
C D:THR62 3.4 11.2 1.0
C D:ILE60 3.5 10.6 1.0
N D:THR62 3.8 10.6 1.0
C D:GLY61 3.8 11.6 1.0
C D:PRO58 3.9 13.7 1.0
O A:HOH2266 4.0 11.9 1.0
O D:GLY61 4.1 13.7 1.0
N D:ILE60 4.2 11.4 1.0
CA D:THR62 4.2 10.9 1.0
N D:PRO63 4.3 11.7 1.0
CA D:PRO63 4.3 11.6 1.0
O A:ALA144 4.3 8.4 1.0
CA D:GLY61 4.4 11.7 1.0
N D:GLY61 4.4 10.9 1.0
O A:HOH2270 4.4 11.8 1.0
CA D:ILE60 4.5 10.9 1.0
N D:LEU64 4.5 11.4 1.0
CA D:PRO58 4.5 12.3 1.0
C D:ASP59 4.6 12.1 1.0
O D:HOH2161 4.7 16.3 1.0
N D:ASP59 4.7 12.7 1.0
O D:ASN57 4.8 10.5 1.0
CA D:ASP59 4.9 14.2 1.0
C D:PRO63 4.9 11.7 1.0

Reference:

E.C.Duin, T.Wagner, S.Shima, D.Prakash, B.Cronin, D.R.Yanez-Ruiz, S.Duval, R.Rumbeli, R.T.Stemmler, R.K.Thauer, M.Kindermann. Mode of Action Uncovered For the Specific Reduction of Methane Emissions From Ruminants By the Small Molecule 3-Nitrooxypropanol. Proc.Natl.Acad.Sci.Usa V. 113 6172 2016.
ISSN: ISSN 0027-8424
PubMed: 27140643
DOI: 10.1073/PNAS.1600298113
Page generated: Mon Oct 7 21:07:57 2024

Last articles

I in 3QF1
I in 3QH9
I in 3QGN
I in 3Q7S
I in 3Q5M
I in 3Q1E
I in 3PMC
I in 3PM6
I in 3PY4
I in 3PP1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy