Calcium 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:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex (pdb code 8jnw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex, PDB code: 8jnw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:12.2 occ:1.00 O B:GLN239 2.3 11.2 1.0 O B:LEU241 2.3 13.2 1.0 OD1 A:ASP242 2.4 12.6 1.0 O A:HOH747 2.4 13.5 1.0 O B:HOH815 2.4 19.0 1.0 O A:HOH699 2.5 14.1 1.0 O B:HOH740 2.5 12.4 1.0 CG A:ASP242 3.3 13.0 1.0 C B:GLN239 3.4 10.4 1.0 C B:LEU241 3.5 12.4 1.0 OD2 A:ASP242 3.5 13.6 1.0 C B:CYS240 4.1 11.9 1.0 N B:LEU241 4.1 12.9 1.0 CA B:GLN239 4.2 9.8 1.0 N B:CYS240 4.3 10.6 1.0 O B:CYS240 4.4 13.4 1.0 N B:ASP242 4.4 12.7 1.0 CA B:LEU241 4.5 12.7 1.0 CA B:ASP242 4.5 12.5 1.0 N B:ASN243 4.5 12.5 1.0 CA B:CYS240 4.5 10.9 1.0 O B:HOH804 4.5 16.4 1.0 O B:PHE238 4.5 10.2 1.0 CB A:ASP242 4.6 13.2 1.0 O A:CYS240 4.7 14.0 1.0 CG B:ASN243 4.7 12.4 1.0 ND2 B:ASN243 4.7 12.3 1.0 OD1 B:ASN243 4.7 12.6 1.0 OH B:TYR366 4.9 13.8 1.0 NH2 B:ARG373 4.9 14.4 1.0 C B:ASP242 4.9 12.4 1.0 CA A:ASP242 4.9 12.8 1.0 N A:ASP242 4.9 12.5 1.0

Calcium binding site 2 out of 3 in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:24.5 occ:1.00 O B:SER139 2.2 23.4 1.0 OE2 B:GLU143 2.4 28.9 1.0 OE1 B:GLU143 2.6 27.2 1.0 CD B:GLU143 2.8 30.8 1.0 C B:SER139 3.5 26.1 1.0 O B:HOH786 4.3 25.9 1.0 CG B:GLU143 4.3 28.4 1.0 CA B:VAL140 4.3 28.1 1.0 N B:VAL140 4.4 25.7 1.0 CA B:SER139 4.4 24.2 1.0 CB B:SER139 4.6 23.3 1.0 CG1 B:VAL140 4.7 29.2 1.0

Calcium binding site 3 out of 3 in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:22.6 occ:1.00 O B:HOH927 2.3 38.2 1.0 OD2 B:ASP329 2.4 16.9 1.0 O B:HOH801 2.4 37.1 1.0 O B:HOH911 2.4 27.3 1.0 O B:HOH735 2.4 24.1 1.0 O B:HOH769 2.5 22.4 1.0 O B:HOH716 2.5 24.1 1.0 O B:HOH714 2.5 25.2 1.0 CG B:ASP329 3.3 15.2 1.0 OD1 B:ASP329 3.6 19.4 1.0 O B:HOH656 4.0 16.0 1.0 OD2 B:ASP326 4.2 27.9 1.0 O B:ASN263 4.5 14.6 1.0 O B:HOH745 4.5 24.8 1.0 OD1 B:ASN263 4.6 19.8 1.0 OD1 B:ASN328 4.7 29.6 1.0 CB B:ASP329 4.7 13.0 1.0 ND2 B:ASN328 4.9 35.3 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