Manganese in PDB 7x12: Crystal Structure of ME1 in Complex with Nadph

All present enzymatic activity of Crystal Structure of ME1 in Complex with Nadph:
1.1.1.40;

The structure of Crystal Structure of ME1 in Complex with Nadph, PDB code: 7x12 was solved by Y.Amano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.18 / 2.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	142.285, 181.594, 116.821, 90, 90, 90
R / Rfree (%)	21.6 / 25.8

The binding sites of Manganese atom in the Crystal Structure of ME1 in Complex with Nadph (pdb code 7x12). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of ME1 in Complex with Nadph, PDB code: 7x12:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of ME1 in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of ME1 in Complex with Nadph within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn601 b:36.6 occ:1.00 OD1 A:ASP279 2.0 28.1 1.0 OE2 A:GLU255 2.1 35.1 1.0 OD1 A:ASP256 2.2 33.7 1.0 O A:HOH748 2.2 31.9 1.0 O A:HOH727 2.2 34.5 1.0 O A:HOH716 2.4 34.4 1.0 CG A:ASP279 3.0 29.5 1.0 CD A:GLU255 3.1 33.7 1.0 CG A:ASP256 3.2 30.0 1.0 OD2 A:ASP279 3.4 30.3 1.0 OD2 A:ASP256 3.6 30.1 1.0 CG A:GLU255 3.6 30.0 1.0 O A:HOH708 4.0 32.2 1.0 OE1 A:GLU255 4.2 33.2 1.0 N A:ASP256 4.4 30.8 1.0 CB A:ASP279 4.4 30.2 1.0 CB A:ASP256 4.5 27.2 1.0 CD1 A:LEU167 4.5 37.9 1.0 OH A:TYR112 4.6 34.1 1.0 O A:HOH734 4.6 44.1 1.0 CA A:ASP256 4.7 27.0 1.0 O A:HOH751 4.8 44.9 1.0 CB A:GLU255 5.0 29.7 1.0 N A:LEU167 5.0 37.6 1.0 CA A:ASP279 5.0 32.3 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of ME1 in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of ME1 in Complex with Nadph within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn601 b:30.4 occ:1.00 OD1 B:ASP256 2.0 27.4 1.0 OD1 B:ASP279 2.1 26.7 1.0 OE2 B:GLU255 2.1 39.6 1.0 O B:HOH833 2.2 33.4 1.0 O B:HOH787 2.2 35.5 1.0 O B:HOH743 2.3 27.7 1.0 CG B:ASP279 3.0 29.0 1.0 CG B:ASP256 3.1 27.7 1.0 CD B:GLU255 3.1 38.5 1.0 OD2 B:ASP279 3.4 28.7 1.0 OD2 B:ASP256 3.5 26.8 1.0 CG B:GLU255 3.6 30.5 1.0 O B:HOH732 3.8 31.5 1.0 O B:HOH800 4.2 32.6 1.0 O B:HOH751 4.2 39.8 1.0 OE1 B:GLU255 4.2 39.7 1.0 N B:ASP256 4.3 29.6 1.0 OH B:TYR112 4.3 34.8 1.0 O B:HOH717 4.4 31.7 1.0 CB B:ASP256 4.4 27.3 1.0 CB B:ASP279 4.4 26.5 1.0 CA B:ASP256 4.5 27.9 1.0 CD1 B:LEU167 4.7 31.0 1.0 CB B:GLU255 4.9 30.8 1.0 N B:LEU167 4.9 33.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of ME1 in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of ME1 in Complex with Nadph within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn601 b:34.0 occ:1.00 O C:HOH795 2.0 30.9 1.0 OE2 C:GLU255 2.1 35.7 1.0 OD1 C:ASP279 2.1 34.5 1.0 OD1 C:ASP256 2.1 28.4 1.0 O C:HOH794 2.2 38.5 1.0 O C:HOH754 2.4 35.7 1.0 CG C:ASP256 3.1 28.0 1.0 CG C:ASP279 3.1 36.8 1.0 CD C:GLU255 3.1 32.9 1.0 OD2 C:ASP256 3.5 26.0 1.0 OD2 C:ASP279 3.5 33.4 1.0 CG C:GLU255 3.6 32.0 1.0 O C:HOH759 3.7 36.8 1.0 O C:HOH712 4.1 28.8 1.0 OE1 C:GLU255 4.2 31.9 1.0 O C:HOH737 4.3 40.8 1.0 N C:ASP256 4.4 28.5 1.0 CB C:ASP256 4.4 26.4 1.0 CB C:ASP279 4.4 30.8 1.0 CD1 C:LEU167 4.5 32.4 1.0 OH C:TYR112 4.5 36.9 1.0 CA C:ASP256 4.6 27.6 1.0 N C:LEU167 4.8 32.6 1.0 CB C:GLU255 4.9 30.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of ME1 in Complex with Nadph


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of ME1 in Complex with Nadph within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn601 b:34.1 occ:1.00 OD1 D:ASP256 2.1 30.8 1.0 OD1 D:ASP279 2.2 28.4 1.0 OE2 D:GLU255 2.2 31.2 1.0 O D:HOH729 2.3 28.5 1.0 O D:HOH839 2.3 36.5 1.0 O D:HOH808 2.3 34.0 1.0 CG D:ASP256 3.0 29.2 1.0 CG D:ASP279 3.2 31.2 1.0 CD D:GLU255 3.2 30.1 1.0 OD2 D:ASP256 3.3 26.5 1.0 OD2 D:ASP279 3.5 31.2 1.0 CG D:GLU255 3.6 27.0 1.0 O D:HOH728 3.7 35.9 1.0 O D:HOH809 4.1 43.9 1.0 OE1 D:GLU255 4.3 28.8 1.0 CB D:ASP256 4.3 26.2 1.0 N D:ASP256 4.4 26.1 1.0 CB D:ASP279 4.6 27.9 1.0 OH D:TYR112 4.6 32.3 1.0 CA D:ASP256 4.6 26.3 1.0 CD1 D:LEU167 4.7 28.6 1.0 CB D:GLU255 5.0 27.8 1.0

T.Yoshida, T.Kawabe, L.C.Cantley, C.A.Lyssiotis. Discovery and Characterization of A Novel Allosteric Small-Molecule Inhibitor of Nadp + -Dependent Malic Enzyme 1. Biochemistry V. 61 1548 2022.
ISSN: ISSN 0006-2960
PubMed: 35819845
DOI: 10.1021/ACS.BIOCHEM.2C00123