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Magnesium in PDB 4eht: Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp

Protein crystallography data

The structure of Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp, PDB code: 4eht 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) 19.70 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 66.154, 161.005, 63.576, 90.00, 110.75, 90.00
R / Rfree (%) 17.6 / 20.5

Other elements in 4eht:

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

Iron (Fe) 4 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp (pdb code 4eht). 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 Adp, PDB code: 4eht:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4eht

Go back to Magnesium Binding Sites List in 4eht
Magnesium binding site 1 out of 2 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:31.4
occ:1.00
O3B A:ADP302 2.2 26.2 1.0
O A:HOH522 2.2 24.5 1.0
O A:HOH462 2.2 22.9 1.0
O A:HOH521 2.2 28.3 1.0
O A:HOH465 2.2 23.8 1.0
O A:HOH463 2.3 26.1 1.0
HE2 A:HIS83 3.2 34.1 1.0
PB A:ADP302 3.4 29.4 1.0
HZ1 A:LYS14 3.4 42.3 1.0
O2B A:ADP302 3.6 26.7 1.0
O2A A:ADP302 3.9 25.3 1.0
O A:HOH470 3.9 44.9 1.0
O A:HOH472 3.9 44.2 1.0
OE2 A:GLU79 4.0 32.9 1.0
HZ2 A:LYS106 4.0 70.1 1.0
NE2 A:HIS83 4.0 28.5 1.0
O A:HOH423 4.1 25.6 1.0
OD2 A:ASP99 4.1 27.8 1.0
O3A A:ADP302 4.2 27.6 1.0
NZ A:LYS14 4.3 35.3 1.0
OD1 A:ASP99 4.3 26.4 1.0
HZ3 A:LYS106 4.3 70.1 1.0
HA3 A:GLY9 4.3 40.5 1.0
OD2 A:ASP7 4.3 28.8 1.0
O A:HOH476 4.4 40.5 1.0
OD1 A:ASP7 4.4 35.5 1.0
HZ2 A:LYS14 4.4 42.3 1.0
HA3 A:GLY101 4.5 30.6 1.0
PA A:ADP302 4.6 28.6 1.0
NZ A:LYS106 4.6 58.5 1.0
O1B A:ADP302 4.6 31.5 1.0
CG A:ASP99 4.7 28.9 1.0
HZ3 A:LYS14 4.8 42.3 1.0
HE3 A:LYS14 4.8 36.6 1.0
CG A:ASP7 4.8 35.5 1.0
CD A:GLU79 4.8 40.0 1.0
HZ1 A:LYS106 4.9 70.1 1.0
CE1 A:HIS83 4.9 27.1 1.0
HE1 A:HIS83 4.9 32.4 1.0
CD2 A:HIS83 4.9 27.4 1.0
HA2 A:GLY9 4.9 40.5 1.0
HD2 A:HIS83 4.9 32.8 1.0

Magnesium binding site 2 out of 2 in 4eht

Go back to Magnesium Binding Sites List in 4eht
Magnesium binding site 2 out of 2 in the Activator of the 2-Hydroxyisocaproyl-Coa Dehydratase From Clostridium Difficile with Bound Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:38.3
occ:1.00
O3B B:ADP301 2.2 35.4 1.0
O B:HOH475 2.2 32.7 1.0
O B:HOH473 2.2 34.0 1.0
O B:HOH474 2.2 35.0 1.0
O B:HOH430 2.3 30.6 1.0
O B:HOH429 2.3 33.8 1.0
HE2 B:HIS83 3.1 45.9 1.0
HZ1 B:LYS14 3.4 40.4 1.0
PB B:ADP301 3.5 37.5 1.0
OE2 B:GLU79 3.8 39.6 1.0
O2B B:ADP301 3.8 42.3 1.0
NE2 B:HIS83 3.9 38.3 1.0
O B:HOH436 3.9 42.6 1.0
O2A B:ADP301 4.0 34.6 1.0
O B:HOH432 4.0 34.8 1.0
O B:HOH439 4.1 42.3 1.0
OD2 B:ASP99 4.1 35.3 1.0
NZ B:LYS14 4.2 33.8 1.0
OD2 B:ASP7 4.2 33.9 1.0
O3A B:ADP301 4.3 35.8 1.0
HZ2 B:LYS106 4.3 56.8 1.0
HA3 B:GLY9 4.3 63.6 1.0
OD1 B:ASP7 4.4 35.5 1.0
OD1 B:ASP99 4.4 35.4 1.0
HZ2 B:LYS14 4.4 40.4 1.0
HA3 B:GLY101 4.5 40.4 1.0
O B:HOH441 4.6 41.7 1.0
CD B:GLU79 4.6 44.5 1.0
PA B:ADP301 4.6 36.0 1.0
O1B B:ADP301 4.6 40.3 1.0
HE1 B:HIS83 4.7 42.2 1.0
CG B:ASP99 4.7 33.8 1.0
CE1 B:HIS83 4.7 35.2 1.0
HE3 B:LYS14 4.7 39.4 1.0
CG B:ASP7 4.7 34.6 1.0
HZ3 B:LYS14 4.8 40.4 1.0
CD2 B:HIS83 4.9 36.6 1.0
HB2 B:GLU79 4.9 38.3 1.0
HA2 B:GLY9 4.9 63.6 1.0
HD2 B:HIS83 4.9 43.8 1.0
CE B:LYS14 5.0 32.9 1.0

Reference:

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
Page generated: Mon Dec 14 14:05:33 2020

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