Magnesium 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:

Iron	(Fe)	4 atoms
Sodium	(Na)	3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adpnp, PDB code: 4ehu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg303 b:15.6 occ:1.00 O2B A:ANP302 2.1 17.4 1.0 O2G A:ANP302 2.1 19.3 1.0 O A:HOH531 2.1 15.5 1.0 O A:HOH532 2.1 17.3 1.0 O A:HOH534 2.1 17.0 1.0 O A:HOH533 2.2 18.6 1.0 HE2 A:HIS83 3.2 23.9 1.0 PB A:ANP302 3.4 19.1 1.0 PG A:ANP302 3.4 18.6 1.0 HZ3 A:LYS14 3.5 26.6 1.0 O A:HOH536 3.8 21.5 1.0 N3B A:ANP302 3.8 18.0 1.0 O A:HOH537 3.9 20.2 1.0 O2A A:ANP302 3.9 18.0 1.0 HA3 A:GLY101 4.0 22.8 1.0 HA3 A:GLY9 4.1 28.4 1.0 OE1 A:GLU79 4.1 19.5 1.0 NE2 A:HIS83 4.1 20.0 1.0 O A:HOH403 4.1 18.3 1.0 O1G A:ANP302 4.1 19.9 1.0 O3A A:ANP302 4.1 18.3 1.0 OD2 A:ASP99 4.2 18.0 1.0 OD2 A:ASP7 4.3 20.5 1.0 OD1 A:ASP99 4.3 19.5 1.0 NZ A:LYS14 4.3 22.3 1.0 OD1 A:ASP7 4.4 22.3 1.0 HZ1 A:LYS14 4.5 26.6 1.0 O3G A:ANP302 4.5 20.6 1.0 O1B A:ANP302 4.6 21.2 1.0 PA A:ANP302 4.6 18.8 1.0 CG A:ASP99 4.7 17.1 1.0 HA2 A:GLY9 4.7 28.4 1.0 HA2 A:GLY101 4.8 22.8 1.0 CG A:ASP7 4.8 20.9 1.0 HZ2 A:LYS14 4.8 26.6 1.0 HE1 A:HIS83 4.8 24.1 1.0 CA A:GLY101 4.8 19.0 1.0 CA A:GLY9 4.8 23.7 1.0 HNB1 A:ANP302 4.8 21.5 1.0 HE3 A:LYS14 4.9 23.9 1.0 CE1 A:HIS83 4.9 20.2 1.0 CD A:GLU79 5.0 22.9 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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 B:Mg302 b:19.7 occ:1.00 O3G B:ANP301 2.1 20.3 1.0 O B:HOH476 2.1 19.1 1.0 O1B B:ANP301 2.1 20.9 1.0 O B:HOH475 2.1 17.2 1.0 O B:HOH474 2.2 21.2 1.0 O B:HOH477 2.2 21.0 1.0 HE2 B:HIS83 3.2 25.5 1.0 PG B:ANP301 3.4 19.9 1.0 PB B:ANP301 3.4 21.0 1.0 HZ3 B:LYS14 3.5 26.8 1.0 O B:HOH404 3.8 22.2 1.0 N3B B:ANP301 3.8 21.6 1.0 O B:HOH408 3.9 22.4 1.0 O1A B:ANP301 3.9 20.3 1.0 OE1 B:GLU79 4.0 19.6 1.0 HA3 B:GLY101 4.0 22.6 1.0 NE2 B:HIS83 4.0 21.3 1.0 HA3 B:GLY9 4.1 31.4 1.0 O B:HOH406 4.1 23.4 1.0 O2G B:ANP301 4.1 19.5 1.0 O3A B:ANP301 4.1 20.7 1.0 OD2 B:ASP99 4.2 21.3 1.0 OD2 B:ASP7 4.3 22.2 1.0 OD1 B:ASP99 4.3 20.2 1.0 NZ B:LYS14 4.3 22.4 1.0 OD1 B:ASP7 4.4 24.1 1.0 HZ1 B:LYS14 4.4 26.8 1.0 O1G B:ANP301 4.5 19.4 1.0 PA B:ANP301 4.6 21.4 1.0 O2B B:ANP301 4.6 22.1 1.0 CG B:ASP99 4.7 19.4 1.0 HA2 B:GLY9 4.7 31.4 1.0 CG B:ASP7 4.8 26.4 1.0 HA2 B:GLY101 4.8 22.6 1.0 CA B:GLY101 4.8 18.9 1.0 CA B:GLY9 4.8 26.2 1.0 HNB1 B:ANP301 4.8 25.9 1.0 HE3 B:LYS14 4.9 24.1 1.0 HE1 B:HIS83 4.9 25.9 1.0 HZ2 B:LYS14 4.9 26.8 1.0 CE1 B:HIS83 4.9 21.7 1.0 CD B:GLU79 4.9 19.1 1.0 CD2 B:HIS83 5.0 21.2 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