Magnesium in PDB 3wqr: Crystal Structure of Pfdxr Complexed with Inhibitor-12

All present enzymatic activity of Crystal Structure of Pfdxr Complexed with Inhibitor-12:
1.1.1.267;

The structure of Crystal Structure of Pfdxr Complexed with Inhibitor-12, PDB code: 3wqr was solved by N.Tanaka, T.Umeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.081, 76.551, 104.095, 90.00, 90.68, 90.00
R / Rfree (%)	18 / 23

The structure of Crystal Structure of Pfdxr Complexed with Inhibitor-12 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Pfdxr Complexed with Inhibitor-12 (pdb code 3wqr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Pfdxr Complexed with Inhibitor-12, PDB code: 3wqr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Pfdxr Complexed with Inhibitor-12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pfdxr Complexed with Inhibitor-12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:10.4 occ:1.00 O18 A:LSX503 2.0 21.4 1.0 O15 A:LSX503 2.0 18.0 1.0 OE2 A:GLU315 2.0 17.9 1.0 OD1 A:ASP231 2.1 18.4 1.0 OE1 A:GLU233 2.1 19.6 1.0 OE2 A:GLU233 2.7 20.6 1.0 CD A:GLU233 2.8 19.1 1.0 C14 A:LSX503 2.8 19.3 1.0 N16 A:LSX503 2.8 19.9 1.0 CD A:GLU315 3.0 18.3 1.0 CG A:ASP231 3.1 19.7 1.0 OE1 A:GLU315 3.5 19.2 1.0 OD2 A:ASP231 3.5 21.4 1.0 NZ A:LYS205 3.6 18.5 1.0 OG A:SER232 3.9 18.7 1.0 N A:SER232 4.0 18.6 1.0 ND2 A:ASN311 4.1 16.8 1.0 C5N A:NDP501 4.2 21.4 1.0 C17 A:LSX503 4.2 18.8 1.0 C13 A:LSX503 4.2 19.4 1.0 CG A:GLU233 4.3 18.1 1.0 CG A:GLU315 4.3 16.3 1.0 CB A:ASP231 4.3 18.8 1.0 N A:GLU233 4.4 17.4 1.0 C A:ASP231 4.5 18.7 1.0 CA A:ASP231 4.6 19.2 1.0 NZ A:LYS312 4.6 13.9 1.0 C7 A:LSX503 4.7 19.6 1.0 C12 A:LSX503 4.7 20.6 1.0 CE A:LYS205 4.8 20.4 1.0 CB A:SER232 4.8 17.6 1.0 CA A:SER232 4.8 18.1 1.0 CB A:GLU233 4.9 17.6 1.0 C4N A:NDP501 5.0 20.5 1.0 C6N A:NDP501 5.0 21.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Pfdxr Complexed with Inhibitor-12


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Pfdxr Complexed with Inhibitor-12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:10.3 occ:1.00 O18 B:LSX505 2.0 18.0 1.0 O15 B:LSX505 2.0 16.5 1.0 OE1 B:GLU233 2.0 18.4 1.0 OE2 B:GLU315 2.1 14.8 1.0 OD1 B:ASP231 2.1 17.1 1.0 CD B:GLU233 2.7 18.1 1.0 C14 B:LSX505 2.7 15.2 1.0 OE2 B:GLU233 2.7 20.0 1.0 N16 B:LSX505 2.8 14.0 1.0 CD B:GLU315 3.1 16.0 1.0 CG B:ASP231 3.1 17.1 1.0 NZ B:LYS205 3.5 16.0 1.0 OE1 B:GLU315 3.6 18.0 1.0 OD2 B:ASP231 3.6 18.0 1.0 OG B:SER232 3.9 19.0 1.0 N B:SER232 4.0 17.3 1.0 ND2 B:ASN311 4.1 16.1 1.0 C5N B:NDP501 4.1 16.7 1.0 C17 B:LSX505 4.2 15.3 1.0 C13 B:LSX505 4.2 15.9 1.0 CG B:GLU233 4.2 16.4 1.0 CG B:GLU315 4.3 15.8 1.0 N B:GLU233 4.3 15.6 1.0 CB B:ASP231 4.4 17.1 1.0 C B:ASP231 4.5 17.0 1.0 C7 B:LSX505 4.6 17.3 1.0 CA B:ASP231 4.6 17.0 1.0 C12 B:LSX505 4.6 15.7 1.0 NZ B:LYS312 4.7 14.7 1.0 CB B:SER232 4.8 17.5 1.0 CB B:GLU233 4.8 15.6 1.0 CA B:SER232 4.8 17.1 1.0 CE B:LYS205 4.8 18.4 1.0 C4N B:NDP501 4.9 16.3 1.0 C6N B:NDP501 5.0 17.4 1.0 OD1 B:ASN311 5.0 16.6 1.0

S.Konzuch, T.Umeda, J.Held, S.Hahn, K.Brucher, C.Lienau, C.T.Behrendt, T.Grawert, A.Bacher, B.Illarionov, M.Fischer, B.Mordmuller, N.Tanaka, T.Kurz. Binding Modes of Reverse Fosmidomycin Analogs Toward the Antimalarial Target Ispc. J.Med.Chem. V. 57 8827 2014.
ISSN: ISSN 0022-2623
PubMed: 25254502
DOI: 10.1021/JM500850Y