Magnesium in PDB 1vbh: Pyruvate Phosphate Dikinase with Bound Mg-Pep From Maize

All present enzymatic activity of Pyruvate Phosphate Dikinase with Bound Mg-Pep From Maize:
2.7.9.1;

The structure of Pyruvate Phosphate Dikinase with Bound Mg-Pep From Maize, PDB code: 1vbh was solved by T.Nakanishi, T.Nakatsu, M.Matsuoka, K.Sakata, H.Kato, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.63 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.339, 100.510, 108.155, 90.00, 98.48, 90.00
R / Rfree (%)	23 / 25.9

The binding sites of Magnesium atom in the Pyruvate Phosphate Dikinase with Bound Mg-Pep From Maize (pdb code 1vbh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Pyruvate Phosphate Dikinase with Bound Mg-Pep From Maize, PDB code: 1vbh:

Magnesium binding site 1 out of 1 in the Pyruvate Phosphate Dikinase with Bound Mg-Pep From Maize


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pyruvate Phosphate Dikinase with Bound Mg-Pep From Maize within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2000 b:38.2 occ:1.00 OE1 A:GLU750 2.1 28.9 1.0 OD2 A:ASP774 2.2 29.7 1.0 O A:HOH3018 2.2 27.4 1.0 O3P A:PEP3000 2.5 47.2 1.0 O2' A:PEP3000 2.7 38.7 1.0 O2 A:PEP3000 2.8 44.7 1.0 CG A:ASP774 3.1 30.7 1.0 CD A:GLU750 3.2 24.1 1.0 P A:PEP3000 3.2 43.7 1.0 C1 A:PEP3000 3.3 40.6 1.0 C2 A:PEP3000 3.5 42.1 1.0 OE2 A:GLU750 3.6 19.6 1.0 CB A:ASP774 3.8 25.0 1.0 NH2 A:ARG671 3.9 15.2 0.5 OD2 A:ASP624 3.9 46.6 1.0 CE A:MET748 3.9 39.6 1.0 OD1 A:ASP774 4.0 35.7 1.0 NH1 A:ARG621 4.0 29.3 1.0 O2P A:PEP3000 4.2 44.0 1.0 O1P A:PEP3000 4.3 45.7 1.0 O1 A:PEP3000 4.5 40.2 1.0 CG A:GLU750 4.5 23.1 1.0 O A:HOH3019 4.6 45.1 1.0 CZ A:ARG621 4.7 27.3 1.0 CB A:GLU750 4.7 25.0 1.0 C3 A:PEP3000 4.8 39.1 1.0 CG A:ASP624 4.8 44.0 1.0 NH2 A:ARG621 4.9 29.3 1.0 CZ A:ARG671 5.0 16.9 0.5 N A:ASP774 5.0 22.5 1.0

T.Nakanishi, T.Nakatsu, M.Matsuoka, K.Sakata, H.Kato. Crystal Structures of Pyruvate Phosphate Dikinase From Maize Revealed An Alternative Conformation in the Swiveling-Domain Motion Biochemistry V. 44 1136 2005.
ISSN: ISSN 0006-2960
PubMed: 15667207
DOI: 10.1021/BI0484522