Sodium in PDB 4ehu: Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp, PDB code: 4ehu was solved by S.H.Knauer, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.17 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	66.105, 158.259, 62.988, 90.00, 111.97, 90.00
R / Rfree (%)	17.1 / 19.7

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	4 atoms

The binding sites of Sodium atom in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp (pdb code 4ehu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp, PDB code: 4ehu:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na305 b:34.7 occ:1.00 H8 A:ANP302 2.4 28.1 1.0 HE21 A:GLN241 2.6 23.8 1.0 HB2 A:ALA12 2.8 31.6 1.0 OG A:SER31 3.1 52.5 1.0 H5'1 A:ANP302 3.2 23.6 1.0 H4' A:ANP302 3.2 31.4 1.0 O A:HOH607 3.2 62.4 1.0 O A:HOH649 3.3 50.8 1.0 HG A:SER31 3.3 62.9 1.0 NE2 A:GLN241 3.4 19.9 1.0 HA A:SER31 3.4 48.5 1.0 HB3 A:SER31 3.4 45.0 1.0 C8 A:ANP302 3.5 23.5 1.0 CB A:ALA12 3.6 26.4 1.0 HE22 A:GLN241 3.6 23.8 1.0 H3' A:ANP302 3.7 27.9 1.0 HG22 A:THR11 3.7 33.5 1.0 CB A:SER31 3.7 37.6 1.0 HB1 A:ALA12 3.8 31.6 1.0 HB3 A:ALA12 3.9 31.6 1.0 CA A:SER31 4.1 40.5 1.0 N7 A:ANP302 4.1 23.5 1.0 C5' A:ANP302 4.2 19.7 1.0 C4' A:ANP302 4.3 26.3 1.0 HG21 A:THR29 4.4 36.1 1.0 HG22 A:THR29 4.5 36.1 1.0 HG21 A:THR11 4.5 33.5 1.0 C3' A:ANP302 4.5 23.3 1.0 CD A:GLN241 4.5 26.9 1.0 CG2 A:THR11 4.5 28.0 1.0 N9 A:ANP302 4.6 22.0 1.0 O4' A:ANP302 4.6 22.8 1.0 HB2 A:SER31 4.6 45.0 1.0 OE1 A:GLN241 4.7 22.9 1.0 O1A A:ANP302 4.8 19.7 1.0 CA A:ALA12 4.8 23.5 1.0 H5'2 A:ANP302 4.8 23.6 1.0 H2' A:ANP302 4.9 30.6 1.0 CG2 A:THR29 4.9 30.1 1.0 O A:THR11 4.9 32.0 1.0 HA A:ALA12 4.9 28.1 1.0 N A:SER31 4.9 31.4 1.0 O5' A:ANP302 5.0 18.3 1.0

Sodium binding site 2 out of 3 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:25.4 occ:1.00 H A:GLN241 2.5 23.8 1.0 HA A:ILE239 2.8 29.4 1.0 HB3 A:GLN241 2.9 24.3 1.0 HD2 A:PRO240 2.9 26.4 1.0 O A:HOH524 3.0 40.0 1.0 O A:HOH444 3.1 29.2 1.0 N A:GLN241 3.3 19.9 1.0 C A:ILE239 3.4 21.1 1.0 HD2 A:ARG218 3.4 26.2 1.0 HD12 A:LEU242 3.5 46.7 1.0 HB2 A:GLN241 3.5 24.3 1.0 CA A:ILE239 3.5 24.6 1.0 CB A:GLN241 3.5 20.3 1.0 N A:PRO240 3.5 19.9 1.0 CD A:PRO240 3.6 22.1 1.0 HG2 A:PRO240 3.6 22.3 1.0 H A:LEU242 3.7 21.6 1.0 HB A:ILE239 3.7 34.3 1.0 HG A:LEU242 3.8 35.6 1.0 O A:ILE239 3.9 22.9 1.0 CA A:GLN241 3.9 20.8 1.0 HG2 A:ARG218 4.0 23.6 1.0 HG22 A:ILE239 4.1 37.9 1.0 CG A:PRO240 4.1 18.6 1.0 CB A:ILE239 4.1 28.6 1.0 CD A:ARG218 4.2 21.9 1.0 N A:LEU242 4.2 18.1 1.0 CD1 A:LEU242 4.2 39.0 1.0 C A:PRO240 4.3 18.3 1.0 HB2 A:LEU242 4.3 26.7 1.0 HD11 A:LEU242 4.3 46.7 1.0 CG A:LEU242 4.4 29.7 1.0 HE A:ARG218 4.4 30.0 1.0 HD3 A:PRO240 4.4 26.4 1.0 CA A:PRO240 4.4 17.8 1.0 CG A:ARG218 4.4 19.8 1.0 NE A:ARG218 4.4 25.1 1.0 C A:GLN241 4.5 19.9 1.0 HG3 A:ARG218 4.5 23.6 1.0 O A:ASP238 4.6 26.7 1.0 OE1 A:GLN241 4.6 22.9 1.0 CG2 A:ILE239 4.6 31.6 1.0 HG1 A:THR29 4.7 38.0 1.0 N A:ILE239 4.7 25.0 1.0 CB A:LEU242 4.8 22.4 1.0 HA A:GLN241 4.8 24.8 1.0 HG3 A:PRO240 4.8 22.3 1.0 CG A:GLN241 4.9 20.5 1.0 CZ A:ARG218 4.9 37.7 1.0 CB A:PRO240 5.0 18.1 1.0

Sodium binding site 3 out of 3 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:27.8 occ:1.00 H B:GLN241 2.5 29.4 1.0 HA B:ILE239 2.8 30.8 1.0 HD2 B:PRO240 2.9 29.5 1.0 HB3 B:GLN241 3.0 27.5 1.0 O B:HOH407 3.0 32.6 1.0 O B:HOH443 3.1 45.4 1.0 HB2 B:GLN241 3.3 27.5 1.0 N B:GLN241 3.3 24.5 1.0 HD2 B:ARG218 3.3 30.9 1.0 HG B:LEU242 3.4 41.1 1.0 C B:ILE239 3.4 25.1 1.0 CB B:GLN241 3.5 23.0 1.0 CA B:ILE239 3.5 25.8 1.0 N B:PRO240 3.6 27.3 1.0 CD B:PRO240 3.6 24.7 1.0 H B:LEU242 3.7 25.9 1.0 HD12 B:LEU242 3.7 55.9 1.0 HG2 B:ARG218 3.8 30.9 1.0 HB B:ILE239 3.8 35.1 1.0 HG2 B:PRO240 3.9 29.3 1.0 CA B:GLN241 3.9 23.1 1.0 O B:ILE239 3.9 26.5 1.0 CD B:ARG218 4.1 25.8 1.0 CG B:LEU242 4.2 34.3 1.0 HG22 B:ILE239 4.2 42.9 1.0 N B:LEU242 4.2 21.7 1.0 CB B:ILE239 4.2 29.3 1.0 HD11 B:LEU242 4.2 55.9 1.0 CD1 B:LEU242 4.2 46.6 1.0 CG B:PRO240 4.3 24.5 1.0 CG B:ARG218 4.3 25.8 1.0 C B:PRO240 4.3 23.9 1.0 NE B:ARG218 4.3 26.5 1.0 HD3 B:PRO240 4.4 29.5 1.0 HG3 B:ARG218 4.4 30.9 1.0 O B:ASP238 4.4 31.1 1.0 HE B:ARG218 4.4 31.7 1.0 C B:GLN241 4.4 23.6 1.0 HB2 B:LEU242 4.5 29.3 1.0 CA B:PRO240 4.5 27.1 1.0 OE1 B:GLN241 4.5 28.1 1.0 N B:ILE239 4.7 31.1 1.0 HG1 B:THR29 4.7 36.6 1.0 CG2 B:ILE239 4.7 35.8 1.0 HA B:GLN241 4.8 27.7 1.0 CB B:LEU242 4.8 24.5 1.0 O B:HOH508 4.8 53.6 1.0 CZ B:ARG218 4.9 42.0 1.0 HD3 B:ARG218 4.9 30.9 1.0 CG B:GLN241 4.9 25.8 1.0 HH11 B:ARG218 4.9 40.7 1.0 C B:ASP238 5.0 32.0 1.0

S.H.Knauer, W.Buckel, H.Dobbek. On the Atp-Dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-Coa Dehydratase. Biochemistry V. 51 6609 2012.
ISSN: ISSN 0006-2960
PubMed: 22827463
DOI: 10.1021/BI300571Z