Calcium 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:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Pfdxr - MN2+ - Nadph - MAMK89 Quaternary Complex (pdb code 9job). 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: 9job:
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:14.7 occ:1.00 O B:GLN239 2.3 14.0 1.0 O B:LEU241 2.3 15.9 1.0 OD1 A:ASP242 2.3 15.2 1.0 O A:HOH764 2.4 16.4 1.0 O B:HOH823 2.4 21.0 1.0 O A:HOH689 2.5 16.5 1.0 O B:HOH752 2.5 15.5 1.0 CG A:ASP242 3.3 15.4 1.0 C B:GLN239 3.4 13.0 1.0 C B:LEU241 3.5 14.9 1.0 OD2 A:ASP242 3.5 15.9 1.0 C B:CYS240 4.1 14.9 1.0 N B:LEU241 4.1 15.3 1.0 CA B:GLN239 4.2 12.3 1.0 N B:CYS240 4.3 12.8 1.0 O B:CYS240 4.4 16.1 1.0 N B:ASP242 4.4 15.2 1.0 CA B:LEU241 4.5 15.0 1.0 CA B:ASP242 4.5 14.6 1.0 N B:ASN243 4.5 15.0 1.0 CA B:CYS240 4.5 13.2 1.0 O B:HOH817 4.5 18.8 1.0 O B:PHE238 4.5 13.0 1.0 CB A:ASP242 4.6 15.8 1.0 O A:CYS240 4.7 16.2 1.0 ND2 B:ASN243 4.7 14.9 1.0 CG B:ASN243 4.7 15.0 1.0 OD1 B:ASN243 4.7 15.3 1.0 OH B:TYR366 4.9 16.4 1.0 C B:ASP242 4.9 15.0 1.0 NH2 B:ARG373 4.9 17.4 1.0 CA A:ASP242 4.9 15.4 1.0 N A:ASP242 4.9 15.4 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:27.2 occ:1.00 O B:SER139 2.2 26.1 1.0 OE2 B:GLU143 2.4 32.0 1.0 OE1 B:GLU143 2.6 29.5 1.0 CD B:GLU143 2.9 33.3 1.0 C B:SER139 3.5 29.0 1.0 O B:HOH797 4.3 29.1 1.0 CA B:VAL140 4.3 32.1 1.0 N B:VAL140 4.4 28.6 1.0 CG B:GLU143 4.4 30.6 1.0 CA B:SER139 4.4 26.5 1.0 O B:HOH688 4.5 45.6 1.0 CB B:SER139 4.6 26.3 1.0 CG1 B:VAL140 4.7 33.1 1.0 OG B:SER139 5.0 32.6 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:25.1 occ:1.00 OD2 B:ASP329 2.4 19.1 1.0 O B:HOH929 2.4 31.3 1.0 O B:HOH709 2.4 27.3 1.0 O B:HOH946 2.4 40.9 1.0 O B:HOH763 2.5 26.3 1.0 O B:HOH762 2.5 24.3 1.0 O B:HOH742 2.5 28.0 1.0 O B:HOH770 2.6 38.2 1.0 CG B:ASP329 3.3 17.1 1.0 OD1 B:ASP329 3.6 22.5 1.0 O B:HOH666 4.0 18.3 1.0 OD2 B:ASP326 4.3 31.7 1.0 O B:ASN263 4.5 17.1 1.0 O B:HOH755 4.5 27.8 1.0 OD1 B:ASN328 4.6 32.1 1.0 OD1 B:ASN263 4.6 22.1 1.0 CB B:ASP329 4.7 15.3 1.0 ND2 B:ASN328 4.8 38.3 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