Magnesium in PDB 1dek: Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp

All present enzymatic activity of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp:
2.7.4.13;

The structure of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp, PDB code: 1dek was solved by A.Teplyakov, P.Sebastiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	155.200, 58.500, 75.700, 90.00, 108.10, 90.00
R / Rfree (%)	18.7 / n/a

The binding sites of Magnesium atom in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp (pdb code 1dek). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp, PDB code: 1dek:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg300 b:44.1 occ:1.00 OE1 A:GLU108 2.5 44.7 1.0 OH A:TYR42 2.6 35.8 1.0 OE1 A:GLN85 2.7 31.4 1.0 CD A:GLU108 3.4 48.7 1.0 CB A:GLU108 3.5 38.5 1.0 CZ A:TYR42 3.6 29.0 1.0 CB A:CYS88 3.6 26.4 1.0 CE2 A:TYR42 3.7 23.7 1.0 O A:HOH425 3.8 57.1 1.0 CG A:GLU108 3.9 40.4 1.0 CD A:GLN85 3.9 23.4 1.0 OE2 A:GLU108 4.5 60.0 1.0 O A:GLN85 4.5 16.2 1.0 SG A:CYS88 4.6 31.3 1.0 NE2 A:GLN85 4.6 26.6 1.0 CA A:GLU108 4.8 42.7 1.0 CE1 A:TYR42 4.8 25.0 1.0 CG A:GLN85 4.9 21.3 1.0 CA A:GLN85 4.9 21.0 1.0 N A:GLU108 4.9 53.5 1.0 CA A:CYS88 4.9 23.2 1.0 CB A:GLN85 5.0 21.2 1.0 N A:TYR89 5.0 19.9 1.0 C A:CYS88 5.0 21.1 1.0

Magnesium binding site 2 out of 2 in the Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Deoxynucleoside Monophosphate Kinase Complexed with Deoxy-Gmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg300 b:37.5 occ:0.50 OE2 B:GLU108 2.3 71.4 1.0 OH B:TYR42 2.3 41.0 1.0 OE1 B:GLN85 2.5 40.8 1.0 CE2 B:TYR42 2.9 33.8 1.0 CZ B:TYR42 3.0 38.6 1.0 CD B:GLU108 3.3 79.4 1.0 O B:HOH378 3.5 52.3 1.0 CG B:GLU108 3.5 73.7 1.0 CD B:GLN85 3.6 36.0 1.0 CB B:CYS88 3.7 33.0 1.0 O B:GLN85 3.8 32.5 1.0 CD2 B:TYR42 4.2 30.6 1.0 NE2 B:GLN85 4.3 37.1 1.0 CE1 B:TYR42 4.3 36.0 1.0 OE1 B:GLU108 4.4 79.0 1.0 CA B:GLN85 4.5 26.3 1.0 CB B:GLN85 4.6 28.1 1.0 C B:GLN85 4.6 27.3 1.0 CG B:GLN85 4.7 35.2 1.0 N B:TYR89 4.7 23.0 1.0 SG B:CYS88 4.7 36.6 1.0 C B:CYS88 4.9 29.4 1.0 CA B:CYS88 4.9 27.7 1.0

A.Teplyakov, P.Sebastiao, G.Obmolova, A.Perrakis, G.S.Brush, M.J.Bessman, K.S.Wilson. Crystal Structure of Bacteriophage T4 Deoxynucleotide Kinase with Its Substrates Dgmp and Atp. Embo J. V. 15 3487 1996.
ISSN: ISSN 0261-4189
PubMed: 8670851