Manganese in PDB 9job: Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex

The structure of Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex, PDB code: 9job 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 / 1.39
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 (%)	16.5 / 18.9

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 9job). 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: 9job:
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:15.3 occ:1.00 OE1 A:GLU233 2.0 15.6 1.0 OE2 A:GLU315 2.1 14.7 1.0 OD1 A:ASP231 2.1 14.8 1.0 O2 A:UW0503 2.1 17.0 1.0 O1 A:UW0503 2.1 16.2 1.0 CD A:GLU233 2.8 16.7 1.0 OE2 A:GLU233 2.8 18.3 1.0 C1 A:UW0503 2.8 14.4 1.0 N1 A:UW0503 2.9 16.2 1.0 CD A:GLU315 3.0 13.6 1.0 CG A:ASP231 3.1 16.4 1.0 OE1 A:GLU315 3.5 16.8 1.0 OD2 A:ASP231 3.6 15.7 1.0 NZ A:LYS205 3.6 17.1 1.0 N A:SER232 3.8 14.8 1.0 OG A:SER232 3.9 17.0 1.0 ND2 A:ASN311 4.2 14.9 1.0 CG A:GLU233 4.2 16.3 1.0 CG A:GLU315 4.3 13.6 1.0 C2 A:UW0503 4.3 17.0 1.0 C5N A:NDP501 4.3 19.8 1.0 C11 A:UW0503 4.3 15.2 1.0 CB A:ASP231 4.4 14.1 1.0 N A:GLU233 4.4 13.8 1.0 C A:ASP231 4.5 15.7 1.0 CA A:ASP231 4.6 14.7 1.0 C13 A:UW0503 4.7 16.9 1.0 CB A:SER232 4.7 15.6 1.0 CA A:SER232 4.7 14.5 1.0 C12 A:UW0503 4.7 16.5 1.0 NZ A:LYS312 4.8 15.8 1.0 CE A:LYS205 4.8 17.2 1.0 CB A:GLU233 4.9 14.8 1.0 C4N A:NDP501 4.9 19.9 1.0 CE1 A:HIS234 4.9 14.6 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:12.4 occ:1.00 OE2 B:GLU315 2.1 12.7 1.0 OE1 B:GLU233 2.1 14.6 1.0 O2 B:UW0503 2.1 13.8 1.0 O1 B:UW0503 2.1 13.5 1.0 OD1 B:ASP231 2.1 13.3 1.0 CD B:GLU233 2.8 13.0 1.0 OE2 B:GLU233 2.8 14.7 1.0 C1 B:UW0503 2.8 12.7 1.0 N1 B:UW0503 2.9 13.2 1.0 CD B:GLU315 3.0 12.7 1.0 CG B:ASP231 3.1 13.3 1.0 OE1 B:GLU315 3.5 14.5 1.0 NZ B:LYS205 3.6 15.2 1.0 OD2 B:ASP231 3.6 13.4 1.0 OG B:SER232 3.9 14.0 1.0 N B:SER232 3.9 11.9 1.0 C2 B:UW0503 4.2 15.5 1.0 ND2 B:ASN311 4.2 13.2 1.0 CG B:GLU233 4.3 12.9 1.0 C11 B:UW0503 4.3 13.3 1.0 C5N B:NDP501 4.3 15.5 1.0 CG B:GLU315 4.3 12.6 1.0 CB B:ASP231 4.4 12.4 1.0 N B:GLU233 4.4 11.7 1.0 C B:ASP231 4.5 11.7 1.0 C13 B:UW0503 4.7 14.4 1.0 CA B:ASP231 4.7 12.9 1.0 CB B:SER232 4.7 13.0 1.0 CA B:SER232 4.7 12.2 1.0 NZ B:LYS312 4.8 13.4 1.0 C12 B:UW0503 4.8 14.4 1.0 CE B:LYS205 4.8 15.0 1.0 CB B:GLU233 4.8 12.3 1.0 C4N B:NDP501 4.9 16.3 1.0 CE1 B:HIS234 4.9 13.9 1.0 ND1 B:HIS234 5.0 14.0 1.0

M.A.Abdullaziz, S.Takada, B.Illarionov, L.Pessanha De Carvalho, Y.Sakamoto, S.Hoefmann, 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