Calcium 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:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pfdxr - MN2+ - MAMK89 Ternary Complex (pdb code 8jnv). 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: 8jnv:
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:13.4 occ:1.00 O B:LEU241 2.3 15.8 1.0 O B:GLN239 2.3 10.3 1.0 OD1 A:ASP242 2.4 13.4 1.0 O B:HOH761 2.4 20.8 1.0 O A:HOH741 2.4 12.6 1.0 O A:HOH651 2.5 13.0 1.0 O B:HOH658 2.7 14.6 1.0 CG A:ASP242 3.3 14.9 1.0 C B:GLN239 3.4 10.5 1.0 C B:LEU241 3.5 14.4 1.0 OD2 A:ASP242 3.6 14.8 1.0 N B:LEU241 4.0 12.3 1.0 C B:CYS240 4.0 12.4 1.0 CA B:GLN239 4.2 9.8 1.0 O B:CYS240 4.3 12.4 1.0 N B:CYS240 4.3 10.5 1.0 CA B:LEU241 4.4 14.9 1.0 N B:ASP242 4.4 14.1 1.0 CA B:ASP242 4.5 13.9 1.0 CA B:CYS240 4.5 11.6 1.0 N B:ASN243 4.5 11.3 1.0 O B:PHE238 4.5 10.1 1.0 O B:HOH744 4.6 14.3 1.0 CB A:ASP242 4.7 14.7 1.0 O A:CYS240 4.7 12.8 1.0 ND2 B:ASN243 4.7 13.2 1.0 CG B:ASN243 4.8 13.2 1.0 OD1 B:ASN243 4.8 13.3 1.0 N A:ASP242 4.9 12.2 1.0 CA A:ASP242 4.9 14.3 1.0 NH2 B:ARG373 4.9 14.3 1.0 OH B:TYR366 4.9 13.3 1.0 C B:ASP242 4.9 12.5 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:24.7 occ:1.00 O B:SER139 2.4 22.9 1.0 OE2 B:GLU143 2.4 26.6 1.0 O B:HOH830 2.4 43.8 1.0 OE1 B:GLU143 2.6 26.2 1.0 CD B:GLU143 2.8 26.9 1.0 C B:SER139 3.5 25.4 1.0 O B:HOH664 4.2 28.2 1.0 CG B:GLU143 4.3 24.6 1.0 CA B:VAL140 4.4 24.7 1.0 N B:VAL140 4.4 23.3 1.0 CA B:SER139 4.4 23.7 1.0 O B:HOH644 4.6 37.4 1.0 CB B:SER139 4.6 26.0 1.0 CG1 B:VAL140 4.9 27.7 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:25.8 occ:1.00 OD2 B:ASP329 2.3 16.6 1.0 O B:HOH759 2.4 22.7 1.0 O B:HOH769 2.4 28.8 1.0 O B:HOH722 2.4 28.7 1.0 O B:HOH866 2.4 36.5 1.0 O B:HOH859 2.5 28.3 1.0 O B:HOH679 2.5 24.7 1.0 O B:HOH608 2.6 30.9 1.0 CG B:ASP329 3.2 15.4 1.0 OD1 B:ASP329 3.5 18.9 1.0 O B:HOH670 3.9 16.4 1.0 OD2 B:ASP326 4.2 24.6 1.0 O B:HOH637 4.4 31.7 1.0 O B:ASN263 4.4 13.3 1.0 ND2 B:ASN328 4.5 37.5 1.0 CB B:ASP329 4.6 13.9 1.0 OD1 B:ASN263 4.6 22.7 1.0 OD1 B:ASN328 4.9 39.2 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