Manganese in PDB 8jnw: Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex

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

The structure of Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex, PDB code: 8jnw 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)	63.93 / 1.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.518, 78.201, 111.144, 90, 92.64, 90
R / Rfree (%)	16.6 / 19

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

Calcium

(Ca)

3 atoms

The binding sites of Manganese atom in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex (pdb code 8jnw). 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+ - Nadph - MAMK89 Quaternary Complex, PDB code: 8jnw:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary 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+ - Nadph - MAMK89 Quaternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:12.6 occ:1.00 OE1 A:GLU233 2.0 12.8 1.0 OE2 A:GLU315 2.1 12.6 1.0 OD1 A:ASP231 2.1 12.1 1.0 O2 A:UW0503 2.1 14.1 1.0 O1 A:UW0503 2.1 13.6 1.0 CD A:GLU233 2.8 13.2 1.0 OE2 A:GLU233 2.8 15.1 1.0 C1 A:UW0503 2.8 11.5 1.0 N1 A:UW0503 2.9 13.5 1.0 CD A:GLU315 3.0 11.7 1.0 CG A:ASP231 3.1 13.4 1.0 OE1 A:GLU315 3.5 14.1 1.0 OD2 A:ASP231 3.6 12.8 1.0 NZ A:LYS205 3.6 14.2 1.0 N A:SER232 3.9 11.8 1.0 OG A:SER232 3.9 14.5 1.0 ND2 A:ASN311 4.2 12.2 1.0 CG A:GLU233 4.2 13.0 1.0 CG A:GLU315 4.3 11.3 1.0 C2 A:UW0503 4.3 14.1 1.0 C5N A:NDP501 4.3 16.4 1.0 C11 A:UW0503 4.3 12.9 1.0 CB A:ASP231 4.4 11.6 1.0 N A:GLU233 4.4 11.2 1.0 C A:ASP231 4.5 12.7 1.0 CA A:ASP231 4.6 12.3 1.0 C13 A:UW0503 4.7 14.7 1.0 CB A:SER232 4.7 13.1 1.0 CA A:SER232 4.7 11.6 1.0 C12 A:UW0503 4.7 14.1 1.0 NZ A:LYS312 4.7 13.2 1.0 CE A:LYS205 4.8 14.4 1.0 CB A:GLU233 4.9 12.3 1.0 C4N A:NDP501 4.9 17.7 1.0 CE1 A:HIS234 4.9 12.3 1.0

Manganese binding site 2 out of 2 in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary 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+ - Nadph - MAMK89 Quaternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn502 b:9.7 occ:1.00 OE2 B:GLU315 2.1 10.0 1.0 OE1 B:GLU233 2.1 12.2 1.0 O1 B:UW0503 2.1 11.0 1.0 O2 B:UW0503 2.1 11.2 1.0 OD1 B:ASP231 2.1 10.7 1.0 CD B:GLU233 2.8 10.9 1.0 C1 B:UW0503 2.8 10.1 1.0 OE2 B:GLU233 2.8 12.2 1.0 N1 B:UW0503 2.9 9.9 1.0 CD B:GLU315 3.1 10.2 1.0 CG B:ASP231 3.2 10.8 1.0 OE1 B:GLU315 3.5 11.9 1.0 NZ B:LYS205 3.5 12.8 1.0 OD2 B:ASP231 3.6 10.6 1.0 OG B:SER232 3.9 11.7 1.0 N B:SER232 3.9 9.1 1.0 C2 B:UW0503 4.2 12.4 1.0 ND2 B:ASN311 4.2 11.0 1.0 C11 B:UW0503 4.3 11.0 1.0 CG B:GLU233 4.3 10.3 1.0 CG B:GLU315 4.3 9.7 1.0 C5N B:NDP501 4.3 13.0 1.0 CB B:ASP231 4.4 10.3 1.0 N B:GLU233 4.4 9.0 1.0 C B:ASP231 4.5 9.4 1.0 CA B:ASP231 4.7 10.2 1.0 C13 B:UW0503 4.7 11.5 1.0 CB B:SER232 4.7 10.8 1.0 NZ B:LYS312 4.7 11.0 1.0 CA B:SER232 4.8 9.6 1.0 C12 B:UW0503 4.8 11.9 1.0 CE B:LYS205 4.8 12.4 1.0 CB B:GLU233 4.8 9.7 1.0 C4N B:NDP501 4.9 13.7 1.0 CE1 B:HIS234 4.9 11.1 1.0 ND1 B:HIS234 5.0 11.2 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