Magnesium in PDB 9dk3: Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound

The structure of Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound, PDB code: 9dk3 was solved by G.T.Randall, G.Bashiri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.75 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.175, 91.583, 151.372, 90, 90, 90
R / Rfree (%)	20.8 / 25.7

The structure of Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound (pdb code 9dk3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound, PDB code: 9dk3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:48.0 occ:1.00 OE1 A:GLN226 2.0 48.0 1.0 O2A A:ADP501 2.0 52.4 1.0 O4 A:PO4502 2.0 56.2 1.0 O1B A:ADP501 2.0 44.1 1.0 OD2 A:ASP241 2.1 40.0 1.0 O A:HOH616 2.2 48.5 1.0 CD A:GLN226 3.0 44.4 1.0 CG A:ASP241 3.0 35.4 1.0 PB A:ADP501 3.3 47.5 1.0 PA A:ADP501 3.4 47.3 1.0 NE2 A:GLN226 3.4 38.3 1.0 CB A:ASP241 3.4 37.2 1.0 P A:PO4502 3.5 64.7 1.0 O3A A:ADP501 3.6 43.6 1.0 MG A:MG504 3.6 40.4 1.0 O3 A:PO4502 3.7 45.0 1.0 O3B A:ADP501 3.8 44.0 1.0 NH2 A:ARG223 4.0 56.7 1.0 OD1 A:ASP241 4.1 36.9 1.0 O1A A:ADP501 4.3 41.3 1.0 CG A:GLN226 4.3 39.6 1.0 O3' A:ADP501 4.4 54.2 1.0 O1 A:PO4502 4.4 53.4 1.0 O5' A:ADP501 4.4 47.6 1.0 O2 A:PO4502 4.5 63.7 1.0 OD2 A:ASP225 4.5 89.0 1.0 O2B A:ADP501 4.5 50.8 1.0 C5' A:ADP501 4.6 51.3 1.0 O A:HOH608 4.8 52.9 1.0 CA A:ASP241 4.9 39.6 1.0 OD2 A:ASP221 5.0 44.4 1.0 C3' A:ADP501 5.0 59.6 1.0

Magnesium binding site 2 out of 2 in the Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Lexapeptide Dehydratase Complex Lxmky, Hydrolysed Atp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:40.4 occ:1.00 OD2 A:ASP241 1.8 40.0 1.0 OD1 A:ASP241 1.9 36.9 1.0 OE1 A:GLU243 2.0 49.4 1.0 O3B A:ADP501 2.0 44.0 1.0 O3 A:PO4502 2.0 45.0 1.0 CG A:ASP241 2.1 35.4 1.0 O A:HOH608 2.4 52.9 1.0 PB A:ADP501 3.1 47.5 1.0 CD A:GLU243 3.1 51.3 1.0 O1B A:ADP501 3.2 44.1 1.0 P A:PO4502 3.3 64.7 1.0 O4 A:PO4502 3.5 56.2 1.0 CB A:ASP241 3.6 37.2 1.0 MG A:MG503 3.6 48.0 1.0 CG A:GLU243 3.7 47.7 1.0 NZ A:LYS66 3.8 54.4 1.0 ND2 A:ASN50 3.9 57.7 1.0 NH1 A:ARG49 4.0 76.9 1.0 O3A A:ADP501 4.1 43.6 1.0 O1 A:PO4502 4.1 53.4 1.0 OE2 A:GLU243 4.1 57.8 1.0 O2B A:ADP501 4.2 50.8 1.0 CZ A:ARG49 4.2 106.2 1.0 O2A A:ADP501 4.3 52.4 1.0 OD2 A:ASP221 4.3 44.4 1.0 CB A:GLU243 4.3 43.9 1.0 NE A:ARG49 4.3 91.1 1.0 CA A:ASP241 4.5 39.6 1.0 O2 A:PO4502 4.5 63.7 1.0 PA A:ADP501 4.5 47.3 1.0 NE2 A:GLN226 4.6 38.3 1.0 O1A A:ADP501 4.7 41.3 1.0 NH2 A:ARG49 4.8 110.8 1.0 CE A:LYS66 4.8 53.6 1.0 O A:ASP241 4.8 48.1 1.0 OE1 A:GLN226 4.9 48.0 1.0 C A:ASP241 4.9 44.7 1.0 CG A:ARG49 4.9 89.8 1.0

G.T.Randall, E.S.Grant-Mackie, S.Chunkath, E.T.Williams, M.J.Middleditch, M.Tao, P.W.R.Harris, M.A.Brimble, G.Bashiri. A Stable Dehydratase Complex Catalyzes the Formation of Dehydrated Amino Acids in A Class V Lanthipeptide. Acs Chem.Biol. 2024.
ISSN: ESSN 1554-8937
PubMed: 39586055
DOI: 10.1021/ACSCHEMBIO.4C00637