Manganese in PDB 8jnv: Pfdxr - MN2+ - MAMK89 Ternary Complex

All present enzymatic activity of Pfdxr - MN2+ - MAMK89 Ternary Complex:
1.1.1.267;

The structure of Pfdxr - MN2+ - MAMK89 Ternary Complex, PDB code: 8jnv was solved by S.Takada, Y.Sakamoto, N.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.31 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.637, 77.022, 111.275, 90, 92.67, 90
R / Rfree (%)	16.4 / 19.4

The structure of Pfdxr - MN2+ - MAMK89 Ternary Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Manganese atom in the Pfdxr - MN2+ - MAMK89 Ternary Complex (pdb code 8jnv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Pfdxr - MN2+ - MAMK89 Ternary Complex, PDB code: 8jnv:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Pfdxr - MN2+ - MAMK89 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pfdxr - MN2+ - MAMK89 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:11.8 occ:1.00 OE1 A:GLU233 2.0 11.0 1.0 OE2 A:GLU315 2.0 10.2 1.0 O2 A:UW0502 2.1 16.3 1.0 O1 A:UW0502 2.1 14.1 1.0 OD1 A:ASP231 2.2 12.6 1.0 CD A:GLU233 2.7 11.4 1.0 OE2 A:GLU233 2.7 13.2 1.0 C1 A:UW0502 2.9 12.7 1.0 N1 A:UW0502 2.9 12.1 1.0 CD A:GLU315 3.0 11.2 1.0 CG A:ASP231 3.2 11.8 1.0 OE1 A:GLU315 3.5 10.9 1.0 OD2 A:ASP231 3.6 11.3 1.0 NZ A:LYS205 3.6 15.2 1.0 O A:HOH748 3.9 21.1 1.0 O A:HOH668 3.9 16.1 1.0 OG A:SER232 4.0 11.6 1.0 N A:SER232 4.0 11.2 1.0 CG A:GLU233 4.2 10.9 1.0 ND2 A:ASN311 4.2 12.6 1.0 CG A:GLU315 4.2 11.5 1.0 C2 A:UW0502 4.3 13.8 1.0 C11 A:UW0502 4.3 13.5 1.0 CB A:ASP231 4.4 11.8 1.0 N A:GLU233 4.5 10.5 1.0 C A:ASP231 4.6 11.2 1.0 NZ A:LYS312 4.7 12.6 1.0 C13 A:UW0502 4.7 12.8 1.0 CA A:ASP231 4.7 11.4 1.0 C12 A:UW0502 4.8 12.9 1.0 CB A:SER232 4.8 11.1 1.0 CA A:SER232 4.9 11.3 1.0 CB A:GLU233 4.9 10.1 1.0 CE A:LYS205 4.9 17.2 1.0 CE1 A:HIS234 5.0 11.8 1.0

Manganese binding site 2 out of 2 in the Pfdxr - MN2+ - MAMK89 Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pfdxr - MN2+ - MAMK89 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:10.3 occ:1.00 OE1 B:GLU233 2.0 10.4 1.0 OE2 B:GLU315 2.1 9.3 1.0 OD1 B:ASP231 2.1 11.3 1.0 O2 B:UW0502 2.2 13.9 1.0 O1 B:UW0502 2.2 10.2 1.0 CD B:GLU233 2.8 10.0 1.0 OE2 B:GLU233 2.8 12.0 1.0 C1 B:UW0502 2.9 10.7 1.0 N1 B:UW0502 3.0 11.7 1.0 CD B:GLU315 3.0 10.0 1.0 CG B:ASP231 3.1 10.2 1.0 OE1 B:GLU315 3.5 11.4 1.0 OD2 B:ASP231 3.5 11.4 1.0 NZ B:LYS205 3.6 13.7 1.0 OG B:SER232 3.9 10.4 1.0 O B:HOH748 3.9 23.1 1.0 O B:HOH685 4.0 15.4 1.0 N B:SER232 4.0 9.4 1.0 ND2 B:ASN311 4.2 12.4 1.0 CG B:GLU233 4.2 9.7 1.0 CG B:GLU315 4.3 9.6 1.0 C2 B:UW0502 4.3 12.3 1.0 CB B:ASP231 4.3 9.2 1.0 C11 B:UW0502 4.4 10.2 1.0 N B:GLU233 4.4 8.7 1.0 C B:ASP231 4.6 9.7 1.0 CA B:ASP231 4.7 9.3 1.0 C13 B:UW0502 4.7 11.3 1.0 NZ B:LYS312 4.8 11.2 1.0 C12 B:UW0502 4.8 10.6 1.0 CB B:SER232 4.8 10.9 1.0 CE B:LYS205 4.8 13.8 1.0 CA B:SER232 4.8 9.6 1.0 CB B:GLU233 4.9 9.3 1.0 CE1 B:HIS234 4.9 13.0 1.0

M.A.Abdullaziz, S.Takada, B.Illarionov, L.Pessanha De Carvalho, Y.Sakamoto, S.Hofmann, T.Knak, A.L.Kiffe-Delf, F.Mazzone, K.Pfeffer, R.Kalscheuer, A.Bacher, J.Held, M.Fischer, N.Tanaka, T.Kurz. Reverse N -Substituted Hydroxamic Acid Derivatives of Fosmidomycin Target A Previously Unknown Subpocket of 1-Deoxy-D-Xylulose 5-Phosphate Reductoisomerase (Dxr). Acs Infect Dis. V. 10 1739 2024.
ISSN: ESSN 2373-8227
PubMed: 38647213
DOI: 10.1021/ACSINFECDIS.4C00100