Sodium in PDB 8a8o: Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A

The structure of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A, PDB code: 8a8o was solved by M.Jespersen, T.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.04 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.714, 123.65, 88.842, 90, 104.44, 90
R / Rfree (%)	15.1 / 17.8

The structure of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Iron	(Fe)	16 atoms

The binding sites of Sodium atom in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A (pdb code 8a8o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A, PDB code: 8a8o:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:29.9 occ:0.78 O A:HOH1046 2.3 31.1 1.0 O A:HOH1035 2.3 46.8 1.0 O A:HOH982 2.4 39.5 1.0 O A:GLU472 2.4 28.7 1.0 OG A:SER475 2.4 27.7 1.0 O A:HOH802 2.6 26.6 1.0 CB A:SER475 3.3 28.1 1.0 C A:GLU472 3.4 25.4 1.0 CA A:GLU472 3.9 25.3 1.0 N A:SER475 4.2 23.0 1.0 CA A:SER475 4.4 23.6 1.0 O A:HOH935 4.5 34.0 1.0 N A:ASP473 4.6 22.2 1.0 O A:HOH819 4.6 32.6 1.0 CB A:GLU472 4.6 35.3 1.0 O A:GLU471 4.7 24.0 1.0 CA A:ASP473 5.0 21.5 1.0

Sodium binding site 2 out of 3 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na607 b:29.9 occ:0.49 OD2 B:ASP300 2.2 106.6 1.0 CG B:ASP300 3.0 93.1 1.0 OD1 B:ASP300 3.6 92.5 1.0 CB B:ASP300 4.0 74.1 1.0 NZ B:LYS329 4.6 73.9 1.0

Sodium binding site 3 out of 3 in the Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Paps Reductase From Methanothermococcus Thermolithotrophicus Refined to 1.45 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na204 b:29.9 occ:0.56 O A:HOH822 2.2 40.1 0.9 O A:HOH897 2.3 45.0 1.0 O C:HOH381 2.4 41.1 1.0 O A:HOH769 2.5 29.1 1.0 O C:ASN87 2.6 35.4 1.0 O C:HOH323 3.0 34.3 1.0 C C:ASN87 3.4 31.6 1.0 NZ A:LYS476 3.9 32.7 1.0 OE1 A:GLU428 3.9 48.1 1.0 CA C:ASN87 3.9 29.5 1.0 OE2 A:GLU428 4.1 44.1 1.0 O C:ASP86 4.3 30.4 1.0 N C:ASN88 4.4 32.9 1.0 O C:GLY68 4.4 22.6 1.0 O C:HOH389 4.4 45.2 1.0 CD A:GLU428 4.5 45.2 1.0 N C:GLY89 4.5 38.6 1.0 CA C:ASN88 4.7 38.8 1.0 CB C:ASN87 4.8 30.4 1.0 C C:ASN88 4.8 42.3 1.0 C C:GLY68 4.9 23.0 1.0 O C:HOH387 4.9 45.7 1.0 CE A:LYS476 4.9 29.5 1.0 CA C:GLY68 4.9 21.6 1.0

M.Jespersen, T.Wagner. How A Methanogen Assimilates Sulfate: Structural and Functional Elucidation of the Complete Sulfate-Reduction Pathway. To Be Published.