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Magnesium in PDB 2ddo: Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution

Enzymatic activity of Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution

All present enzymatic activity of Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution:
2.7.1.35;

Protein crystallography data

The structure of Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution, PDB code: 2ddo was solved by M.K.Safo, F.N.Musayev, M.L.Di Salvo, S.Hunt, J.B.Claude, V.Schirch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.94 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.128, 74.356, 107.210, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution (pdb code 2ddo). 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 Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution, PDB code: 2ddo:

Magnesium binding site 1 out of 1 in 2ddo

Go back to Magnesium Binding Sites List in 2ddo
Magnesium binding site 1 out of 1 in the Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene at 2.6 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg284

b:54.6
occ:0.80
 O3G A:ATP285 2.3 88.0 0.8
O1G A:ATP285 2.8 77.9 0.8
PG A:ATP285 3.0 87.5 0.8
O3B A:ATP285 3.3 85.5 0.8
OE2 A:GLU162 3.4 43.6 1.0
O1B A:ATP285 3.5 76.9 0.8
OH A:TYR136 3.6 61.9 1.0
OE1 A:GLU162 3.9 48.5 1.0
PB A:ATP285 4.0 80.5 0.8
CD A:GLU162 4.0 29.8 1.0
O3A A:ATP285 4.2 78.9 0.8
CG2 A:VAL127 4.2 43.2 1.0
CG1 A:VAL127 4.2 39.5 1.0
O2G A:ATP285 4.4 76.9 0.8
CA A:VAL127 4.5 46.9 1.0
CB A:VAL127 4.5 50.0 1.0
OD2 A:ASP125 4.6 41.1 1.0
OD1 A:ASP125 4.6 47.6 1.0
OD1 A:ASN159 4.7 19.7 1.0
CZ A:TYR136 4.9 56.1 1.0
CG A:ASP125 5.0 37.1 1.0

Reference:

M.K.Safo, F.N.Musayev, M.L.Di Salvo, S.Hunt, J.B.Claude, V.Schirch. Crystal Structure of Pyridoxal Kinase From the Escherichia Coli Pdxk Gene: Implications For the Classification of Pyridoxal Kinases. J.Bacteriol. V. 188 4542 2006.
ISSN: ISSN 0021-9193
PubMed: 16740960
DOI: 10.1128/JB.00122-06
Page generated: Sun Aug 10 10:26:10 2025

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