Magnesium in PDB 5jvj: C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer

All present enzymatic activity of C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer:
2.7.9.1;

The structure of C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer, PDB code: 5jvj was solved by A.Minges, A.Hoeppner, G.Groth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.42 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	208.736, 69.044, 166.763, 90.00, 112.84, 90.00
R / Rfree (%)	23.7 / 26.1

The binding sites of Magnesium atom in the C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer (pdb code 5jvj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer, PDB code: 5jvj:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:23.9 occ:1.00 O1P A:PEP901 2.1 23.7 1.0 OE1 A:GLU748 2.1 38.4 1.0 OD2 A:ASP772 2.6 23.5 1.0 O2 A:PEP901 2.7 19.6 1.0 O1 A:PEP901 2.8 14.5 1.0 CD A:GLU748 2.9 36.3 1.0 P A:PEP901 2.9 19.4 1.0 OE2 A:GLU748 3.0 37.0 1.0 NH1 A:ARG619 3.4 19.6 1.0 OD2 A:ASP622 3.5 33.5 1.0 C1 A:PEP901 3.5 16.2 1.0 C2 A:PEP901 3.5 17.7 1.0 O3P A:PEP901 3.7 19.6 1.0 CG A:ASP772 3.8 26.2 1.0 NH2 A:ARG619 3.9 15.6 1.0 CZ A:ARG619 3.9 18.1 1.0 NH1 A:ARG669 4.0 34.5 1.0 O2P A:PEP901 4.2 24.8 1.0 CG A:GLU748 4.3 33.6 1.0 CB A:ASP772 4.6 24.9 1.0 CE A:MET746 4.6 24.1 1.0 C3 A:PEP901 4.7 19.0 1.0 OD1 A:ASP772 4.7 28.6 1.0 CG A:ASP622 4.7 33.5 1.0 O2' A:PEP901 4.8 13.3 1.0 CB A:GLU748 4.9 31.3 1.0 CD1 A:LEU710 4.9 37.4 1.0

Magnesium binding site 2 out of 2 in the C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C4-Type Pyruvate Phosphate Dikinase: Different Conformational States of the Nucleotide Binding Domain in the Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:18.2 occ:1.00 OE1 B:GLU748 2.0 56.6 1.0 OD2 B:ASP772 2.1 53.7 1.0 O2' B:PEP901 2.3 44.5 1.0 O2 B:PEP901 2.5 39.6 1.0 O3P B:PEP901 2.6 41.1 1.0 CD B:GLU748 2.9 54.8 1.0 OE2 B:GLU748 3.0 55.5 1.0 C1 B:PEP901 3.1 43.9 1.0 P B:PEP901 3.1 41.3 1.0 C2 B:PEP901 3.2 41.2 1.0 CG B:ASP772 3.3 50.9 1.0 OD2 B:ASP622 3.8 94.6 1.0 NH1 B:ARG669 3.9 57.9 1.0 NH1 B:ARG619 3.9 53.0 1.0 CB B:ASP772 4.1 48.5 1.0 O1P B:PEP901 4.1 41.8 1.0 CG B:GLU748 4.3 52.6 1.0 O2P B:PEP901 4.3 42.7 1.0 OD1 B:ASP772 4.3 50.2 1.0 O1 B:PEP901 4.3 43.9 1.0 NH2 B:ARG619 4.4 54.0 1.0 C3 B:PEP901 4.4 41.6 1.0 CZ B:ARG619 4.5 53.7 1.0 CB B:GLU748 4.7 48.8 1.0 CE B:MET746 4.8 49.8 1.0 CD1 B:LEU710 4.9 81.6 1.0

A.Minges, D.Ciupka, C.Winkler, A.Hoppner, H.Gohlke, G.Groth. Structural Intermediates and Directionality of the Swiveling Motion of Pyruvate Phosphate Dikinase. Sci Rep V. 7 45389 2017.
ISSN: ESSN 2045-2322
PubMed: 28358005
DOI: 10.1038/SREP45389