Sodium in PDB 8uas: Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A

The structure of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A, PDB code: 8uas was solved by L.A.Wilson, L.W.Guddat, G.Schenk, C.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	78.144, 157.745, 272.429, 90, 91.06, 90
R / Rfree (%)	18.2 / 21

The structure of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A also contains other interesting chemical elements:

Silicon	(Si)	10 atoms
Zinc	(Zn)	26 atoms

The binding sites of Sodium atom in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A (pdb code 8uas). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A, PDB code: 8uas:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:17.4 occ:1.00 H A:GLY224 2.5 44.0 1.0 HB2 A:SER223 3.0 50.8 1.0 HG22 A:THR252 3.1 36.7 1.0 OG1 A:THR255 3.2 35.7 1.0 HA A:THR252 3.2 34.3 1.0 N A:GLY224 3.4 36.6 1.0 HB3 A:ALA227 3.4 42.6 1.0 HG1 A:THR255 3.4 43.0 1.0 HA A:SER223 3.4 48.4 1.0 HG21 A:THR255 3.4 33.1 1.0 HB A:THR255 3.5 43.0 1.0 HB2 A:ALA227 3.6 42.6 1.0 HG11 A:VAL202 3.7 42.7 1.0 CB A:SER223 3.7 42.2 1.0 CB A:THR255 3.8 35.8 1.0 CB A:ALA227 3.8 35.4 1.0 HB1 A:ALA227 3.9 42.6 1.0 CA A:SER223 3.9 40.2 1.0 HB3 A:SER223 4.0 50.8 1.0 HG12 A:VAL202 4.0 42.7 1.0 CG2 A:THR252 4.1 30.5 1.0 CG2 A:THR255 4.1 27.5 1.0 O A:GLY224 4.1 36.6 1.0 CA A:THR252 4.1 28.5 1.0 C A:SER223 4.2 37.0 1.0 HA2 A:GLY224 4.2 46.8 1.0 HD13 A:ILE178 4.3 35.7 1.0 CG1 A:VAL202 4.3 35.5 1.0 CA A:GLY224 4.3 39.0 1.0 O A:SER251 4.3 34.3 1.0 HG21 A:ILE178 4.4 41.1 1.0 HG23 A:THR252 4.4 36.7 1.0 HG23 A:ILE178 4.4 41.1 1.0 HG22 A:THR255 4.5 33.1 1.0 CB A:THR252 4.6 32.8 1.0 C A:GLY224 4.6 39.3 1.0 HG21 A:THR252 4.6 36.7 1.0 HB A:THR252 4.6 39.4 1.0 N A:THR252 4.7 33.9 1.0 HG13 A:VAL202 4.7 42.7 1.0 C A:SER251 4.7 32.9 1.0 O A:HOH556 4.8 39.0 1.0 HG23 A:THR255 4.8 33.1 1.0 CG2 A:ILE178 4.9 34.2 1.0 OG A:SER223 4.9 50.5 1.0

Sodium binding site 2 out of 4 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na406 b:19.4 occ:1.00 H D:GLY224 2.9 58.3 1.0 OG D:SER223 3.0 50.8 1.0 HG22 D:THR252 3.2 36.9 1.0 O D:HOH540 3.2 46.7 1.0 HA D:THR252 3.3 41.3 1.0 OG1 D:THR255 3.3 41.4 1.0 HG21 D:THR255 3.4 41.8 1.0 HA D:SER223 3.4 49.4 1.0 HB D:THR255 3.5 42.6 1.0 HG D:SER223 3.5 61.0 1.0 HG1 D:THR255 3.5 49.8 1.0 HB3 D:ALA227 3.5 47.3 1.0 N D:GLY224 3.6 48.5 1.0 CB D:THR255 3.8 35.5 1.0 HG11 D:VAL202 3.8 41.2 1.0 HB2 D:ALA227 3.9 47.3 1.0 CG2 D:THR255 4.0 34.8 1.0 O D:GLY224 4.0 43.8 1.0 CB D:SER223 4.0 42.6 1.0 HG12 D:VAL202 4.0 41.2 1.0 CB D:ALA227 4.0 39.4 1.0 CA D:SER223 4.1 41.1 1.0 CG2 D:THR252 4.1 30.7 1.0 HG23 D:ILE178 4.1 41.0 1.0 HG21 D:ILE178 4.2 41.0 1.0 HD13 D:ILE178 4.2 38.7 1.0 CA D:THR252 4.2 34.4 1.0 HB1 D:ALA227 4.2 47.3 1.0 HB2 D:SER223 4.2 51.1 1.0 C D:SER223 4.3 46.3 1.0 O D:HOH687 4.4 50.1 1.0 CG1 D:VAL202 4.4 34.2 1.0 HG22 D:THR255 4.4 41.8 1.0 HG23 D:THR252 4.4 36.9 1.0 O D:HOH529 4.4 42.6 1.0 O D:SER251 4.5 39.1 1.0 CA D:GLY224 4.5 42.4 1.0 HA2 D:GLY224 4.6 51.0 1.0 CB D:THR252 4.6 32.1 1.0 HB D:THR252 4.6 38.7 1.0 CG2 D:ILE178 4.6 34.1 1.0 C D:GLY224 4.6 44.3 1.0 HG21 D:THR252 4.7 36.9 1.0 N D:THR252 4.7 33.5 1.0 HG23 D:THR255 4.8 41.8 1.0 HB3 D:SER223 4.8 51.1 1.0 C D:SER251 4.8 37.6 1.0 HG13 D:VAL202 4.9 41.2 1.0

Sodium binding site 3 out of 4 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ I:Na406 b:20.6 occ:1.00 H I:GLY224 2.5 44.9 1.0 HB2 I:SER223 2.6 37.7 1.0 OG1 I:THR255 3.1 33.0 1.0 HA I:THR252 3.1 39.6 1.0 O I:HOH551 3.1 40.3 1.0 HA I:SER223 3.2 39.7 1.0 HG1 I:THR255 3.2 39.6 1.0 HG22 I:THR252 3.2 34.5 1.0 N I:GLY224 3.3 37.3 1.0 CB I:SER223 3.4 31.4 1.0 HB I:THR255 3.4 36.9 1.0 HG21 I:THR255 3.4 37.2 1.0 HB3 I:ALA227 3.5 36.6 1.0 HB3 I:SER223 3.6 37.7 1.0 CB I:THR255 3.7 30.7 1.0 CA I:SER223 3.7 33.0 1.0 HB2 I:ALA227 3.7 36.6 1.0 HG11 I:VAL202 3.7 31.9 1.0 CB I:ALA227 3.9 30.4 1.0 O I:GLY224 4.0 33.9 1.0 C I:SER223 4.0 33.0 1.0 HB1 I:ALA227 4.0 36.6 1.0 CG2 I:THR255 4.0 31.0 1.0 CA I:THR252 4.0 32.9 1.0 HG12 I:VAL202 4.0 31.9 1.0 CG2 I:THR252 4.1 28.7 1.0 O I:SER251 4.2 35.2 1.0 HG21 I:ILE178 4.2 39.5 1.0 HG23 I:THR252 4.3 34.5 1.0 CA I:GLY224 4.3 34.2 1.0 HA2 I:GLY224 4.3 41.2 1.0 CG1 I:VAL202 4.3 26.5 1.0 HD13 I:ILE178 4.4 34.5 1.0 HG23 I:ILE178 4.4 39.5 1.0 HG22 I:THR255 4.5 37.2 1.0 CB I:THR252 4.5 35.1 1.0 N I:THR252 4.5 36.5 1.0 O I:HOH623 4.5 43.9 1.0 OG I:SER223 4.5 44.7 1.0 C I:GLY224 4.5 34.8 1.0 HB I:THR252 4.6 42.1 1.0 C I:SER251 4.6 32.5 1.0 HG13 I:VAL202 4.7 31.9 1.0 HG23 I:THR255 4.7 37.2 1.0 HG I:SER223 4.8 53.7 1.0 HG21 I:THR252 4.8 34.5 1.0 CG2 I:ILE178 4.8 32.8 1.0 O I:HOH547 4.8 35.8 1.0 H I:THR255 4.9 36.0 1.0 O I:HOH632 4.9 49.8 1.0 O I:HOH586 4.9 35.2 1.0 HB2 I:SER251 5.0 38.2 1.0

Sodium binding site 4 out of 4 in the Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Rhodococcus Ruber Alcohol Dehydrogenase Nadh Biomimetic Complex - Compound 1A within 5.0Å range: probe atom residue distance (Å) B Occ J:Na504 b:23.4 occ:1.00 H J:GLY224 2.8 57.5 1.0 HG22 J:THR252 3.1 45.9 1.0 OG J:SER223 3.2 67.1 1.0 HA J:THR252 3.2 47.0 1.0 OG1 J:THR255 3.2 37.9 1.0 O J:HOH615 3.3 44.6 1.0 HG1 J:THR255 3.3 45.6 1.0 HB3 J:ALA227 3.3 50.4 1.0 HG21 J:THR255 3.4 44.1 1.0 HB J:THR255 3.5 44.5 1.0 HA J:SER223 3.5 58.2 1.0 N J:GLY224 3.6 47.9 1.0 HG J:SER223 3.6 80.6 1.0 HG11 J:VAL202 3.6 46.8 1.0 CB J:THR255 3.7 37.0 1.0 HB2 J:ALA227 3.7 50.4 1.0 O J:GLY224 3.9 41.9 1.0 CB J:ALA227 3.9 41.9 1.0 HB1 J:ALA227 4.0 50.4 1.0 HG12 J:VAL202 4.0 46.8 1.0 CB J:SER223 4.0 54.1 1.0 CG2 J:THR252 4.0 38.2 1.0 CG2 J:THR255 4.0 36.7 1.0 CA J:SER223 4.1 48.5 1.0 CA J:THR252 4.1 39.1 1.0 HB2 J:SER223 4.1 65.0 1.0 HD13 J:ILE178 4.2 40.0 1.0 HG21 J:ILE178 4.2 47.5 1.0 CG1 J:VAL202 4.3 39.0 1.0 HG23 J:THR252 4.3 45.9 1.0 HG23 J:ILE178 4.3 47.5 1.0 C J:SER223 4.3 53.8 1.0 O J:SER251 4.4 39.2 1.0 CA J:GLY224 4.4 49.2 1.0 HA2 J:GLY224 4.4 59.1 1.0 HG22 J:THR255 4.5 44.1 1.0 O J:HOH648 4.5 42.6 1.0 C J:GLY224 4.6 47.9 1.0 CB J:THR252 4.6 34.9 1.0 N J:THR252 4.6 38.2 1.0 HG13 J:VAL202 4.7 46.8 1.0 HG21 J:THR252 4.7 45.9 1.0 HB J:THR252 4.7 42.0 1.0 CG2 J:ILE178 4.7 39.5 1.0 C J:SER251 4.7 39.9 1.0 HG23 J:THR255 4.8 44.1 1.0 HB3 J:SER223 4.9 65.0 1.0 H J:THR255 5.0 36.9 1.0 HB2 J:SER251 5.0 46.7 1.0

R.A.Rocha, L.A.Wilson, B.D.Schwartz, A.C.Warden, L.W.Guddat, R.E.Speight, L.Malins, G.Schenk, C.Scott. Structural Characterization of Enzymatic Interactions with Functional Nicotinamide Cofactor Biomimetics Catalysts V. 14 2024.
ISSN: ESSN 2073-4344
DOI: 10.3390/CATAL14070399