Calcium in PDB 9joa: Pfdxr - MN2+ - MAMK89 Ternary Complex

The structure of Pfdxr - MN2+ - MAMK89 Ternary Complex, PDB code: 9joa 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 / 1.50
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 (%)	17.1 / 20.1

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

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pfdxr - MN2+ - MAMK89 Ternary Complex (pdb code 9joa). 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+ - MAMK89 Ternary Complex, PDB code: 9joa:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Pfdxr - MN2+ - MAMK89 Ternary 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+ - MAMK89 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:13.6 occ:1.00 O B:LEU241 2.3 15.0 1.0 O B:GLN239 2.3 11.3 1.0 OD1 A:ASP242 2.4 13.4 1.0 O A:HOH739 2.4 13.0 1.0 O A:HOH658 2.5 13.4 1.0 O B:HOH819 2.5 24.1 1.0 O B:HOH686 2.7 15.6 1.0 CG A:ASP242 3.3 14.6 1.0 C B:GLN239 3.4 11.2 1.0 C B:LEU241 3.5 13.7 1.0 OD2 A:ASP242 3.6 15.2 1.0 N B:LEU241 4.0 13.3 1.0 C B:CYS240 4.1 13.7 1.0 CA B:GLN239 4.2 10.4 1.0 O B:CYS240 4.3 13.8 1.0 N B:CYS240 4.4 11.7 1.0 N B:ASP242 4.4 14.7 1.0 CA B:LEU241 4.4 15.6 1.0 CA B:ASP242 4.5 14.2 1.0 CA B:CYS240 4.5 12.2 1.0 N B:ASN243 4.5 12.0 1.0 O B:PHE238 4.5 11.5 1.0 O B:HOH756 4.6 15.3 1.0 CB A:ASP242 4.6 15.2 1.0 O A:CYS240 4.7 13.5 1.0 ND2 B:ASN243 4.7 14.8 1.0 CG B:ASN243 4.8 14.7 1.0 OD1 B:ASN243 4.8 15.1 1.0 CA A:ASP242 4.9 15.0 1.0 N A:ASP242 4.9 12.8 1.0 OH B:TYR366 4.9 13.9 1.0 NH2 B:ARG373 4.9 14.9 1.0 C B:ASP242 4.9 12.9 1.0

Calcium binding site 2 out of 3 in the Pfdxr - MN2+ - MAMK89 Ternary 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+ - MAMK89 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:25.3 occ:1.00 O B:HOH826 2.1 40.8 1.0 O B:SER139 2.3 23.5 1.0 OE2 B:GLU143 2.4 28.0 1.0 OE1 B:GLU143 2.5 27.3 1.0 CD B:GLU143 2.8 27.7 1.0 C B:SER139 3.6 25.8 1.0 O B:HOH666 4.1 30.2 1.0 CG B:GLU143 4.3 26.2 1.0 CA B:VAL140 4.4 25.7 1.0 N B:VAL140 4.4 24.0 1.0 CA B:SER139 4.5 24.2 1.0 O B:HOH657 4.6 38.9 1.0 CB B:SER139 4.7 25.1 1.0 CG1 B:VAL140 4.9 29.3 1.0

Calcium binding site 3 out of 3 in the Pfdxr - MN2+ - MAMK89 Ternary 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+ - MAMK89 Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:25.2 occ:1.00 O B:HOH763 2.3 29.9 1.0 O B:HOH774 2.3 24.1 1.0 OD2 B:ASP329 2.3 16.0 1.0 O B:HOH751 2.4 30.1 1.0 O B:HOH898 2.4 40.2 1.0 O B:HOH885 2.5 28.8 1.0 O B:HOH626 2.5 33.1 1.0 O B:HOH705 2.6 24.1 1.0 CG B:ASP329 3.2 15.8 1.0 OD1 B:ASP329 3.5 18.6 1.0 O B:HOH659 3.9 18.1 1.0 OD2 B:ASP326 4.3 26.5 1.0 O B:ASN263 4.5 13.9 1.0 O B:HOH703 4.5 31.8 1.0 CB B:ASP329 4.6 14.1 1.0 ND2 B:ASN328 4.6 37.5 1.0 OD1 B:ASN263 4.7 24.3 1.0 OD1 B:ASN328 4.7 35.1 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